Starting phenix.real_space_refine
on Fri Dec  8 07:00:10 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktu_23030/12_2023/7ktu_23030.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktu_23030/12_2023/7ktu_23030.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktu_23030/12_2023/7ktu_23030.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktu_23030/12_2023/7ktu_23030.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktu_23030/12_2023/7ktu_23030.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktu_23030/12_2023/7ktu_23030.pdb"
  }
  resolution = 4.15
  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=   0.031
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      43      5.16       5
     C    4671      2.51       5
     N    1373      2.21       5
     O    1490      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG  416": "NH1" <-> "NH2"
    Residue "A ARG  450": "NH1" <-> "NH2"
    Residue "A ARG  460": "NH1" <-> "NH2"
    Residue "A ARG  479": "NH1" <-> "NH2"
    Residue "A ARG  512": "NH1" <-> "NH2"
    Residue "A ARG  586": "NH1" <-> "NH2"
    Residue "A PHE  599": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  832": "NH1" <-> "NH2"
    Residue "A ARG  975": "NH1" <-> "NH2"
    Residue "A ARG 1055": "NH1" <-> "NH2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 7577
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 995, 7577
          Classifications: {'peptide': 995}
          Link IDs: {'PTRANS': 35, 'TRANS': 959}
          Chain breaks: 1
  Time building chain proxies: 4.61, per 1000 atoms: 0.61
  Number of scatterers: 7577
  At special positions: 0
  Unit cell: (82.5, 98.175, 127.875, 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      43     16.00
     O    1490      8.00
     N    1373      7.00
     C    4671      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: 3.11
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1886

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 0 sheets defined
      86.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 30
      Proline residue:  A  15  - end of helix
      removed outlier: 3.601A  pdb=" N   HIS A  22 " --> pdb=" O   GLN A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 64
      removed outlier: 3.603A  pdb=" N   ALA A  46 " --> pdb=" O   ALA A  42 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA A  50 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL A  51 " --> pdb=" O   VAL A  47 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU A  54 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   VAL A  57 " --> pdb=" O   ASN A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 98
      removed outlier: 4.084A  pdb=" N   ASP A  73 " --> pdb=" O   ILE A  69 " (cutoff:3.500A)
      Proline residue:  A  75  - end of helix
      removed outlier: 3.771A  pdb=" N   ILE A  79 " --> pdb=" O   PRO A  75 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LYS A  80 " --> pdb=" O   PRO A  76 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL A  81 " --> pdb=" O   ALA A  77 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLN A  90 " --> pdb=" O   THR A  86 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLN A  96 " --> pdb=" O   ALA A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 106
    Processing helix  chain 'A' and resid 108 through 151
      removed outlier: 3.610A  pdb=" N   ILE A 115 " --> pdb=" O   GLY A 111 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   LEU A 116 " --> pdb=" O   SER A 112 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ALA A 129 " --> pdb=" O   THR A 125 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   ILE A 134 " --> pdb=" O   GLU A 130 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ILE A 135 " --> pdb=" O   VAL A 131 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   ARG A 136 " --> pdb=" O   ARG A 132 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   VAL A 137 " --> pdb=" O   LYS A 133 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL A 151 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 182
      removed outlier: 3.855A  pdb=" N   LEU A 157 " --> pdb=" O   THR A 153 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   VAL A 158 " --> pdb=" O   MET A 154 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   THR A 159 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   GLY A 165 " --> pdb=" O   THR A 161 " (cutoff:3.500A)
      Proline residue:  A 166  - end of helix
      removed outlier: 3.759A  pdb=" N   LYS A 170 " --> pdb=" O   PRO A 166 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   GLU A 177 " --> pdb=" O   LYS A 173 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   GLN A 180 " --> pdb=" O   ASP A 176 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLU A 181 " --> pdb=" O   GLU A 177 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU A 182 " --> pdb=" O   ARG A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 201
      removed outlier: 3.847A  pdb=" N   MET A 190 " --> pdb=" O   GLU A 186 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   LEU A 191 " --> pdb=" O   HIS A 187 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   VAL A 192 " --> pdb=" O   ARG A 188 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   SER A 194 " --> pdb=" O   MET A 190 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   THR A 197 " --> pdb=" O   ASN A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 214
    Processing helix  chain 'A' and resid 215 through 217
      No H-bonds generated for 'chain 'A' and resid 215 through 217'
    Processing helix  chain 'A' and resid 224 through 250
      removed outlier: 4.290A  pdb=" N   LYS A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ASN A 229 " --> pdb=" O   GLU A 225 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   THR A 233 " --> pdb=" O   ASN A 229 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG A 246 " --> pdb=" O   ASN A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 259
    Processing helix  chain 'A' and resid 260 through 286
      removed outlier: 4.270A  pdb=" N   SER A 272 " --> pdb=" O   ARG A 268 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ASP A 274 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   SER A 275 " --> pdb=" O   ALA A 271 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ASN A 278 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   GLN A 279 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLY A 282 " --> pdb=" O   ASN A 278 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   TRP A 283 " --> pdb=" O   GLN A 279 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU A 284 " --> pdb=" O   ALA A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.867A  pdb=" N   GLN A 301 " --> pdb=" O   GLN A 297 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU A 303 " --> pdb=" O   ILE A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 342
      removed outlier: 3.785A  pdb=" N   ARG A 319 " --> pdb=" O   GLY A 315 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE A 321 " --> pdb=" O   GLU A 317 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   LEU A 322 " --> pdb=" O   ARG A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 358
    Processing helix  chain 'A' and resid 359 through 390
      removed outlier: 3.814A  pdb=" N   LEU A 363 " --> pdb=" O   GLY A 359 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLU A 368 " --> pdb=" O   THR A 364 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   MET A 377 " --> pdb=" O   LYS A 373 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LYS A 381 " --> pdb=" O   MET A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 396
      removed outlier: 4.128A  pdb=" N   TRP A 394 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU A 395 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 416
      removed outlier: 3.902A  pdb=" N   ARG A 409 " --> pdb=" O   GLU A 405 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ALA A 415 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 424
      removed outlier: 4.441A  pdb=" N   GLU A 420 " --> pdb=" O   ARG A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 433
      removed outlier: 3.673A  pdb=" N   ARG A 433 " --> pdb=" O   ASP A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 447
    Processing helix  chain 'A' and resid 448 through 453
    Processing helix  chain 'A' and resid 456 through 484
      removed outlier: 3.593A  pdb=" N   ARG A 460 " --> pdb=" O   SER A 456 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   THR A 475 " --> pdb=" O   GLN A 471 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   SER A 484 " --> pdb=" O   ALA A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 499
    Processing helix  chain 'A' and resid 500 through 506
    Processing helix  chain 'A' and resid 514 through 532
      removed outlier: 3.588A  pdb=" N   ILE A 519 " --> pdb=" O   GLY A 515 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ARG A 520 " --> pdb=" O   GLN A 516 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLY A 521 " --> pdb=" O   ALA A 517 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU A 522 " --> pdb=" O   ALA A 518 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   VAL A 532 " --> pdb=" O   ARG A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 556
      removed outlier: 3.926A  pdb=" N   GLN A 539 " --> pdb=" O   GLY A 535 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   ASP A 540 " --> pdb=" O   PRO A 536 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LYS A 544 " --> pdb=" O   ASP A 540 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL A 548 " --> pdb=" O   LYS A 544 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   LEU A 551 " --> pdb=" O   ARG A 547 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   ALA A 553 " --> pdb=" O   ASP A 549 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLN A 554 " --> pdb=" O   GLN A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 571
    Processing helix  chain 'A' and resid 573 through 596
      removed outlier: 4.105A  pdb=" N   GLN A 577 " --> pdb=" O   ALA A 573 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ASP A 578 " --> pdb=" O   SER A 574 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLU A 589 " --> pdb=" O   ALA A 585 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   THR A 592 " --> pdb=" O   GLN A 588 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   GLN A 593 " --> pdb=" O   GLU A 589 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLU A 594 " --> pdb=" O   ALA A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 615
      removed outlier: 3.674A  pdb=" N   LEU A 608 " --> pdb=" O   THR A 604 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA A 615 " --> pdb=" O   VAL A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 622 through 651
    Processing helix  chain 'A' and resid 654 through 683
      Proline residue:  A 673  - end of helix
      removed outlier: 3.518A  pdb=" N   VAL A 676 " --> pdb=" O   THR A 672 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   SER A 677 " --> pdb=" O   PRO A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 717
      removed outlier: 3.632A  pdb=" N   GLU A 693 " --> pdb=" O   GLN A 689 " (cutoff:3.500A)
      removed outlier: 5.219A  pdb=" N   HIS A 694 " --> pdb=" O   ALA A 690 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   PHE A 695 " --> pdb=" O   ALA A 691 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLU A 696 " --> pdb=" O   TYR A 692 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ASN A 700 " --> pdb=" O   GLU A 696 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ASP A 704 " --> pdb=" O   ASN A 700 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU A 712 " --> pdb=" O   LYS A 708 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 743
      removed outlier: 3.567A  pdb=" N   ALA A 725 " --> pdb=" O   SER A 721 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 774
      removed outlier: 3.638A  pdb=" N   GLY A 752 " --> pdb=" O   MET A 748 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ALA A 757 " --> pdb=" O   ALA A 753 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ASN A 761 " --> pdb=" O   ALA A 757 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ARG A 762 " --> pdb=" O   ARG A 758 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASN A 773 " --> pdb=" O   ARG A 769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 786
    Processing helix  chain 'A' and resid 786 through 807
      removed outlier: 3.666A  pdb=" N   LEU A 790 " --> pdb=" O   ALA A 786 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   THR A 793 " --> pdb=" O   GLU A 789 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   SER A 795 " --> pdb=" O   SER A 791 " (cutoff:3.500A)
      Proline residue:  A 796  - end of helix
    Processing helix  chain 'A' and resid 812 through 823
      removed outlier: 3.610A  pdb=" N   ARG A 823 " --> pdb=" O   ASP A 819 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 824 through 836
      removed outlier: 3.602A  pdb=" N   ALA A 829 " --> pdb=" O   LEU A 825 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   LYS A 830 " --> pdb=" O   GLY A 826 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 965 through 979
      removed outlier: 3.814A  pdb=" N   SER A 972 " --> pdb=" O   ALA A 968 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LEU A 973 " --> pdb=" O   ALA A 969 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   HIS A 974 " --> pdb=" O   ALA A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 985 through 1005
      removed outlier: 3.568A  pdb=" N   ALA A 990 " --> pdb=" O   ASP A 986 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1006 through 1007
      No H-bonds generated for 'chain 'A' and resid 1006 through 1007'
    Processing helix  chain 'A' and resid 1008 through 1010
      No H-bonds generated for 'chain 'A' and resid 1008 through 1010'
    Processing helix  chain 'A' and resid 1011 through 1038
      removed outlier: 3.594A  pdb=" N   ILE A1016 " --> pdb=" O   LYS A1012 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   VAL A1036 " --> pdb=" O   LEU A1032 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LYS A1038 " --> pdb=" O   LYS A1034 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1042 through 1053
      removed outlier: 3.611A  pdb=" N   ARG A1046 " --> pdb=" O   ASP A1042 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1054 through 1074
      removed outlier: 3.845A  pdb=" N   THR A1058 " --> pdb=" O   GLU A1054 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   SER A1060 " --> pdb=" O   ILE A1056 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   THR A1061 " --> pdb=" O   PRO A1057 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLN A1062 " --> pdb=" O   THR A1058 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   THR A1068 " --> pdb=" O   LYS A1064 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1080 through 1114
      removed outlier: 3.534A  pdb=" N   SER A1084 " --> pdb=" O   SER A1080 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   MET A1090 " --> pdb=" O   GLN A1086 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU A1091 " --> pdb=" O   ALA A1087 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ARG A1107 " --> pdb=" O   LYS A1103 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLU A1110 " --> pdb=" O   VAL A1106 " (cutoff:3.500A)

    535 hydrogen bonds defined for protein.
    1602 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.23

  Time building geometry restraints manager: 3.34 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1736
        1.33 -     1.45: 1313
        1.45 -     1.57: 4529
        1.57 -     1.69: 0
        1.69 -     1.81: 76
  Bond restraints: 7654
  Sorted by residual:
  bond pdb=" C   SER A 456 "
       pdb=" N   PRO A 457 "
    ideal  model  delta    sigma   weight residual
    1.336  1.387 -0.052 1.23e-02 6.61e+03 1.77e+01
  bond pdb=" C   ASP A 424 "
       pdb=" N   PRO A 425 "
    ideal  model  delta    sigma   weight residual
    1.337  1.382 -0.046 1.11e-02 8.12e+03 1.68e+01
  bond pdb=" CA  THR A 215 "
       pdb=" C   THR A 215 "
    ideal  model  delta    sigma   weight residual
    1.523  1.470  0.052 1.41e-02 5.03e+03 1.38e+01
  bond pdb=" C   THR A 215 "
       pdb=" O   THR A 215 "
    ideal  model  delta    sigma   weight residual
    1.236  1.207  0.028 1.35e-02 5.49e+03 4.40e+00
  bond pdb=" C   ASP A 505 "
       pdb=" N   ASN A 506 "
    ideal  model  delta    sigma   weight residual
    1.332  1.316  0.016 8.60e-03 1.35e+04 3.58e+00
  ... (remaining 7649 not shown)

  Histogram of bond angle deviations from ideal:
       98.84 -   105.90: 160
      105.90 -   112.95: 4206
      112.95 -   120.01: 2807
      120.01 -   127.06: 3094
      127.06 -   134.12: 58
  Bond angle restraints: 10325
  Sorted by residual:
  angle pdb=" C   LYS A 639 "
        pdb=" N   LEU A 640 "
        pdb=" CA  LEU A 640 "
      ideal   model   delta    sigma   weight residual
     120.54  127.14   -6.60 1.35e+00 5.49e-01 2.39e+01
  angle pdb=" N   VAL A 713 "
        pdb=" CA  VAL A 713 "
        pdb=" C   VAL A 713 "
      ideal   model   delta    sigma   weight residual
     110.72  106.66    4.06 1.01e+00 9.80e-01 1.62e+01
  angle pdb=" N   GLY A 401 "
        pdb=" CA  GLY A 401 "
        pdb=" C   GLY A 401 "
      ideal   model   delta    sigma   weight residual
     112.34  119.70   -7.36 2.04e+00 2.40e-01 1.30e+01
  angle pdb=" C   THR A 710 "
        pdb=" N   GLY A 711 "
        pdb=" CA  GLY A 711 "
      ideal   model   delta    sigma   weight residual
     120.13  124.50   -4.37 1.26e+00 6.30e-01 1.20e+01
  angle pdb=" N   GLN A 964 "
        pdb=" CA  GLN A 964 "
        pdb=" C   GLN A 964 "
      ideal   model   delta    sigma   weight residual
     109.81  117.43   -7.62 2.21e+00 2.05e-01 1.19e+01
  ... (remaining 10320 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.88: 4449
       15.88 -    31.75: 300
       31.75 -    47.63: 81
       47.63 -    63.50: 3
       63.50 -    79.38: 11
  Dihedral angle restraints: 4844
    sinusoidal: 1958
      harmonic: 2886
  Sorted by residual:
  dihedral pdb=" CA  ASN A1094 "
           pdb=" C   ASN A1094 "
           pdb=" N   ALA A1095 "
           pdb=" CA  ALA A1095 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.02   29.98     0      5.00e+00 4.00e-02 3.59e+01
  dihedral pdb=" CA  ALA A 615 "
           pdb=" C   ALA A 615 "
           pdb=" N   PRO A 616 "
           pdb=" CA  PRO A 616 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.28   26.72     0      5.00e+00 4.00e-02 2.86e+01
  dihedral pdb=" CA  ASP A 106 "
           pdb=" C   ASP A 106 "
           pdb=" N   TYR A 107 "
           pdb=" CA  TYR A 107 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.43   26.57     0      5.00e+00 4.00e-02 2.82e+01
  ... (remaining 4841 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 769
       0.043 -    0.085: 321
       0.085 -    0.128: 101
       0.128 -    0.171: 15
       0.171 -    0.213: 9
  Chirality restraints: 1215
  Sorted by residual:
  chirality pdb=" CB  ILE A 808 "
            pdb=" CA  ILE A 808 "
            pdb=" CG1 ILE A 808 "
            pdb=" CG2 ILE A 808 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CB  ILE A 519 "
            pdb=" CA  ILE A 519 "
            pdb=" CG1 ILE A 519 "
            pdb=" CG2 ILE A 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.86   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CB  ILE A 730 "
            pdb=" CA  ILE A 730 "
            pdb=" CG1 ILE A 730 "
            pdb=" CG2 ILE A 730 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.71e-01
  ... (remaining 1212 not shown)

  Planarity restraints: 1358
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  42 "    0.050 5.00e-02 4.00e+02   7.59e-02 9.22e+00
        pdb=" N   PRO A  43 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A  75 "   -0.044 5.00e-02 4.00e+02   6.55e-02 6.87e+00
        pdb=" N   PRO A  76 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A  76 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A  76 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 615 "    0.043 5.00e-02 4.00e+02   6.55e-02 6.85e+00
        pdb=" N   PRO A 616 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 616 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 616 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1355 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2010
        2.79 -     3.32: 8345
        3.32 -     3.84: 13479
        3.84 -     4.37: 16454
        4.37 -     4.90: 24124
  Nonbonded interactions: 64412
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 661 "
            pdb=" OG  SER A 664 "
     model   vdw
     2.259 2.440
  nonbonded pdb=" O   ILE A 211 "
            pdb=" OG1 THR A 214 "
     model   vdw
     2.259 2.440
  nonbonded pdb=" O   HIS A 694 "
            pdb=" OG1 THR A 697 "
     model   vdw
     2.263 2.440
  nonbonded pdb=" O   ILE A1065 "
            pdb=" OG1 THR A1068 "
     model   vdw
     2.269 2.440
  nonbonded pdb=" O   ALA A 440 "
            pdb=" OG  SER A 443 "
     model   vdw
     2.289 2.440
  ... (remaining 64407 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 group one per residue
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:                  0.010
  Normalize map: mean=0, sd=1:             0.790
  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:          3.810
  Check model and map are aligned:         0.110
  Set scattering table:                    0.080
  Process input model:                     25.010
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
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      :  0.006   0.058   7654  Z= 0.397
  Angle     :  1.047   9.532  10325  Z= 0.603
  Chirality :  0.052   0.213   1215
  Planarity :  0.007   0.076   1358
  Dihedral  : 12.608  79.380   2958
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  4.06 %
    Favored  : 95.57 %
  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: -5.35 (0.18), residues: 991
  helix: -3.49 (0.12), residues: 745
  sheet:  None (None), residues: 0
  loop : -2.82 (0.33), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.026   0.005   TRP A 980 
   HIS   0.008   0.003   HIS A 187 
   PHE   0.025   0.004   PHE A  78 
   TYR   0.021   0.003   TYR A 160 
   ARG   0.014   0.001   ARG A 780 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 206
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 0
  residues processed: 209
  average time/residue: 0.2387
  time to fit residues: 64.6000
Evaluate side-chains
  132 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.952 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1736
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 41 optimal weight:    8.9990
   chunk 25 optimal weight:    8.9990
   chunk 50 optimal weight:    0.2980
   chunk 40 optimal weight:    3.9990
   chunk 77 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 187 HIS
A 220 ASN
** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 527 HIS
A 550 GLN
** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 GLN
A1086 GLN
A1093 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7654  Z= 0.197
  Angle     :  0.691   8.088  10325  Z= 0.365
  Chirality :  0.039   0.150   1215
  Planarity :  0.005   0.052   1358
  Dihedral  :  6.080  24.713   1060
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 17.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  3.82 %
    Favored  : 95.81 %
  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: -3.37 (0.22), residues: 991
  helix: -1.80 (0.15), residues: 808
  sheet:  None (None), residues: 0
  loop : -3.27 (0.37), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.002   TRP A 258 
   HIS   0.005   0.001   HIS A 492 
   PHE   0.019   0.002   PHE A 232 
   TYR   0.015   0.001   TYR A 822 
   ARG   0.006   0.000   ARG A 669 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 206
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 0
  residues processed: 208
  average time/residue: 0.2266
  time to fit residues: 61.4238
Evaluate side-chains
  140 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.910 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1100
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    0.0270
   chunk 27 optimal weight:    5.9990
   chunk 74 optimal weight:    7.9990
   chunk 61 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9980
   chunk 97 optimal weight:    6.9990
   chunk 80 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.7440

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 358 GLN
** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 HIS
A 550 GLN
A 705 ASN
A 974 HIS
A1078 ASN
A1096 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.3979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7654  Z= 0.186
  Angle     :  0.665   8.147  10325  Z= 0.342
  Chirality :  0.040   0.136   1215
  Planarity :  0.004   0.047   1358
  Dihedral  :  5.539  25.756   1060
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 17.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.96 %
    Favored  : 96.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.24), residues: 991
  helix: -0.94 (0.17), residues: 809
  sheet:  None (None), residues: 0
  loop : -2.88 (0.40), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.032   0.002   TRP A 980 
   HIS   0.006   0.001   HIS A 492 
   PHE   0.020   0.002   PHE A 232 
   TYR   0.011   0.001   TYR A 822 
   ARG   0.004   0.000   ARG A 832 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 194
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 194
  average time/residue: 0.2193
  time to fit residues: 55.9848
Evaluate side-chains
  138 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.987 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2906
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 88 optimal weight:    8.9990
   chunk 67 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 42 optimal weight:   20.0000
   chunk 60 optimal weight:    0.8980
   chunk 90 optimal weight:    7.9990
   chunk 95 optimal weight:    9.9990
   chunk 47 optimal weight:   10.0000
   chunk 85 optimal weight:    3.9990
   chunk 25 optimal weight:    9.9990
   overall best weight:    3.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 HIS
A 701 GLN
A 705 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.4240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7654  Z= 0.266
  Angle     :  0.705   8.139  10325  Z= 0.370
  Chirality :  0.041   0.135   1215
  Planarity :  0.004   0.037   1358
  Dihedral  :  5.482  25.370   1060
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 23.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  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: -1.55 (0.25), residues: 991
  helix: -0.54 (0.17), residues: 812
  sheet:  None (None), residues: 0
  loop : -2.70 (0.43), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.034   0.003   TRP A 980 
   HIS   0.008   0.002   HIS A 187 
   PHE   0.019   0.002   PHE A 232 
   TYR   0.006   0.001   TYR A 537 
   ARG   0.005   0.001   ARG A 520 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.2346
  time to fit residues: 48.8479
Evaluate side-chains
  123 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.918 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0983
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 54 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 71 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 81 optimal weight:    8.9990
   chunk 66 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 48 optimal weight:    0.0470
   chunk 85 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.7480

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 HIS
A 550 GLN
A 705 ASN
A1051 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.4724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7654  Z= 0.172
  Angle     :  0.653   9.027  10325  Z= 0.331
  Chirality :  0.041   0.152   1215
  Planarity :  0.004   0.042   1358
  Dihedral  :  5.359  25.091   1060
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 17.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.34 %
    Favored  : 97.54 %
  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 (0.25), residues: 991
  helix: -0.18 (0.17), residues: 821
  sheet:  None (None), residues: 0
  loop : -2.71 (0.42), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.001   TRP A 980 
   HIS   0.006   0.001   HIS A 187 
   PHE   0.017   0.002   PHE A 599 
   TYR   0.015   0.002   TYR A 822 
   ARG   0.003   0.000   ARG A 178 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 168
  average time/residue: 0.2219
  time to fit residues: 49.0165
Evaluate side-chains
  133 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.837 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1388
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 86 optimal weight:   20.0000
   chunk 18 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 95 optimal weight:    8.9990
   chunk 79 optimal weight:    2.9990
   chunk 44 optimal weight:    9.9990
   chunk 7 optimal weight:    0.0970
   chunk 31 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 451 GLN
A 492 HIS
A 632 ASN
A 685 ASN
A 705 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.5024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7654  Z= 0.184
  Angle     :  0.663  10.167  10325  Z= 0.337
  Chirality :  0.041   0.149   1215
  Planarity :  0.004   0.048   1358
  Dihedral  :  5.250  25.582   1060
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 17.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  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: -0.72 (0.26), residues: 991
  helix:  0.04 (0.18), residues: 823
  sheet:  None (None), residues: 0
  loop : -2.56 (0.43), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.002   TRP A 980 
   HIS   0.007   0.001   HIS A 492 
   PHE   0.016   0.002   PHE A 232 
   TYR   0.008   0.001   TYR A 692 
   ARG   0.005   0.000   ARG A 409 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.2109
  time to fit residues: 46.1105
Evaluate side-chains
  121 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.873 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2213
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 95 optimal weight:   20.0000
   chunk 59 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 HIS
A 550 GLN
A 685 ASN
A 705 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.5140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7654  Z= 0.247
  Angle     :  0.720  11.436  10325  Z= 0.370
  Chirality :  0.042   0.165   1215
  Planarity :  0.004   0.038   1358
  Dihedral  :  5.322  25.163   1060
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 22.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  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: -0.56 (0.26), residues: 991
  helix:  0.17 (0.18), residues: 817
  sheet:  None (None), residues: 0
  loop : -2.54 (0.43), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP A 980 
   HIS   0.005   0.001   HIS A 492 
   PHE   0.018   0.003   PHE A 695 
   TYR   0.017   0.002   TYR A 692 
   ARG   0.009   0.001   ARG A 485 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.2078
  time to fit residues: 44.9794
Evaluate side-chains
  115 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.847 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1596
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 56 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 75 optimal weight:    3.9990
   chunk 86 optimal weight:   10.0000
   chunk 91 optimal weight:    5.9990
   chunk 83 optimal weight:    0.0970
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 HIS
** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 705 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.5420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7654  Z= 0.190
  Angle     :  0.684  11.680  10325  Z= 0.349
  Chirality :  0.041   0.179   1215
  Planarity :  0.004   0.039   1358
  Dihedral  :  5.239  25.503   1060
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 18.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  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: -0.31 (0.27), residues: 991
  helix:  0.35 (0.18), residues: 815
  sheet:  None (None), residues: 0
  loop : -2.46 (0.43), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.002   TRP A 258 
   HIS   0.006   0.001   HIS A 492 
   PHE   0.018   0.002   PHE A 232 
   TYR   0.018   0.001   TYR A 692 
   ARG   0.007   0.000   ARG A 669 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.2032
  time to fit residues: 45.0959
Evaluate side-chains
  129 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.886 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2382
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 88 optimal weight:    6.9990
   chunk 91 optimal weight:    0.4980
   chunk 53 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 80 optimal weight:    4.9990
   chunk 84 optimal weight:    9.9990
   chunk 58 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9980
   chunk 57 optimal weight:    5.9990
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 HIS
** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 705 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.5543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7654  Z= 0.206
  Angle     :  0.717  10.496  10325  Z= 0.368
  Chirality :  0.042   0.161   1215
  Planarity :  0.004   0.035   1358
  Dihedral  :  5.206  25.281   1060
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 20.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  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: -0.24 (0.27), residues: 991
  helix:  0.40 (0.18), residues: 815
  sheet:  None (None), residues: 0
  loop : -2.46 (0.43), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.002   TRP A 258 
   HIS   0.006   0.001   HIS A 492 
   PHE   0.016   0.002   PHE A 232 
   TYR   0.029   0.002   TYR A 692 
   ARG   0.006   0.001   ARG A 485 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.2027
  time to fit residues: 44.9021
Evaluate side-chains
  129 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.922 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2443
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   chunk 90 optimal weight:    6.9990
   chunk 78 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 83 optimal weight:    0.0070
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 HIS
** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 705 ASN
A1086 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.5912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7654  Z= 0.177
  Angle     :  0.704  10.822  10325  Z= 0.355
  Chirality :  0.041   0.177   1215
  Planarity :  0.004   0.038   1358
  Dihedral  :  5.107  25.556   1060
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 17.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  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: -0.05 (0.27), residues: 991
  helix:  0.53 (0.18), residues: 815
  sheet:  None (None), residues: 0
  loop : -2.42 (0.42), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.002   TRP A 258 
   HIS   0.007   0.001   HIS A 492 
   PHE   0.012   0.002   PHE A 232 
   TYR   0.033   0.002   TYR A 692 
   ARG   0.004   0.000   ARG A 485 

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.2371
  time to fit residues: 54.9186
Evaluate side-chains
  129 residues out of total 812 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.792 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1299
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 78 optimal weight:    8.9990
   chunk 32 optimal weight:    0.5980
   chunk 80 optimal weight:    3.9990
   chunk 9 optimal weight:    7.9990
   chunk 14 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 4 optimal weight:    8.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 HIS
** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 705 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.093206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.074734 restraints weight = 34991.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.076683 restraints weight = 25936.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.078161 restraints weight = 20514.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.6169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7654  Z= 0.193
  Angle     :  0.728   9.736  10325  Z= 0.369
  Chirality :  0.042   0.166   1215
  Planarity :  0.004   0.039   1358
  Dihedral  :  5.131  25.779   1060
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 18.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  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: -0.16 (0.27), residues: 991
  helix:  0.43 (0.18), residues: 814
  sheet:  None (None), residues: 0
  loop : -2.30 (0.44), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP A 283 
   HIS   0.007   0.002   HIS A 187 
   PHE   0.014   0.002   PHE A 232 
   TYR   0.028   0.002   TYR A 692 
   ARG   0.006   0.001   ARG A 485 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1773.83 seconds
wall clock time: 33 minutes 6.89 seconds (1986.89 seconds total)