Starting phenix.real_space_refine (version: dev)
on Sat Feb 18 06:45:01 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktt_23029/02_2023/7ktt_23029.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktt_23029/02_2023/7ktt_23029.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktt_23029/02_2023/7ktt_23029.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktt_23029/02_2023/7ktt_23029.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktt_23029/02_2023/7ktt_23029.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktt_23029/02_2023/7ktt_23029.pdb"
  }
  resolution = 4.17
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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
-------------------------------------------------------------------------------
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=   0.030
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
Process input model

  Symmetric amino acids flipped
    Residue "A PHE   78": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  126": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  268": "NH1" <-> "NH2"
    Residue "A ARG  409": "NH1" <-> "NH2"
    Residue "A ARG  450": "NH1" <-> "NH2"
    Residue "A ARG  460": "NH1" <-> "NH2"
    Residue "A ARG  479": "NH1" <-> "NH2"
    Residue "A ARG  586": "NH1" <-> "NH2"
    Residue "A ARG  975": "NH1" <-> "NH2"
    Residue "A ARG 1055": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib"
  Total number of atoms: 7568
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 994, 7568
          Classifications: {'peptide': 994}
          Link IDs: {'PTRANS': 35, 'TRANS': 958}
          Chain breaks: 1
  Time building chain proxies: 4.81, per 1000 atoms: 0.64
  Number of scatterers: 7568
  At special positions: 0
  Unit cell: (84.15, 96.525, 128.7, 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    1487      8.00
     N    1372      7.00
     C    4666      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: 3.51
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1884

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 0 sheets defined
      83.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 25
      Proline residue:  A  15  - end of helix
      removed outlier: 4.726A  pdb=" N   GLN A  19 " --> pdb=" O   PRO A  15 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ILE A  20 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   HIS A  22 " --> pdb=" O   GLN A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 64
      removed outlier: 3.538A  pdb=" N   ALA A  45 " --> pdb=" O   THR A  41 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ASN A  53 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
      removed outlier: 5.042A  pdb=" N   LEU A  54 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   GLU A  60 " --> pdb=" O   ARG A  56 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLN A  63 " --> pdb=" O   LYS A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 98
      removed outlier: 3.879A  pdb=" N   LYS A  71 " --> pdb=" O   ASP A  67 " (cutoff:3.500A)
      Proline residue:  A  75  - end of helix
      removed outlier: 3.920A  pdb=" N   ILE A  79 " --> pdb=" O   PRO A  75 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LYS A  80 " --> pdb=" O   PRO A  76 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LYS A  87 " --> pdb=" O   ASN A  83 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLN A  90 " --> pdb=" O   THR A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 126
      removed outlier: 3.639A  pdb=" N   ASP A 106 " --> pdb=" O   VAL A 102 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   ARG A 113 " --> pdb=" O   ILE A 109 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   GLY A 114 " --> pdb=" O   ASP A 110 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   LEU A 116 " --> pdb=" O   SER A 112 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   PHE A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 151
      removed outlier: 4.308A  pdb=" N   ILE A 134 " --> pdb=" O   GLU A 130 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ARG A 136 " --> pdb=" O   ARG A 132 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLU A 149 " --> pdb=" O   LEU A 145 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   VAL A 150 " --> pdb=" O   THR A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 155
      No H-bonds generated for 'chain 'A' and resid 153 through 155'
    Processing helix  chain 'A' and resid 156 through 164
    Processing helix  chain 'A' and resid 164 through 182
      removed outlier: 4.292A  pdb=" N   LYS A 170 " --> pdb=" O   PRO A 166 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LYS A 173 " --> pdb=" O   THR A 169 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   MET A 174 " --> pdb=" O   LYS A 170 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLN A 180 " --> pdb=" O   ASP A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 218
      removed outlier: 4.274A  pdb=" N   MET A 190 " --> pdb=" O   GLU A 186 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   VAL A 192 " --> pdb=" O   ARG A 188 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   SER A 194 " --> pdb=" O   MET A 190 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   THR A 197 " --> pdb=" O   ASN A 193 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   VAL A 198 " --> pdb=" O   SER A 194 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LYS A 199 " --> pdb=" O   MET A 195 " (cutoff:3.500A)
      Proline residue:  A 203  - end of helix
      removed outlier: 3.571A  pdb=" N   VAL A 213 " --> pdb=" O   MET A 209 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   THR A 214 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 249
      removed outlier: 4.010A  pdb=" N   LEU A 227 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ILE A 241 " --> pdb=" O   MET A 237 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ASN A 242 " --> pdb=" O   SER A 238 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ILE A 244 " --> pdb=" O   GLU A 240 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ARG A 246 " --> pdb=" O   ASN A 242 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LEU A 248 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLN A 249 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 261
    Processing helix  chain 'A' and resid 262 through 276
      removed outlier: 3.796A  pdb=" N   MET A 266 " --> pdb=" O   ASP A 262 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LYS A 267 " --> pdb=" O   THR A 263 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ALA A 271 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 286
      removed outlier: 3.734A  pdb=" N   ALA A 280 " --> pdb=" O   LYS A 276 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   TRP A 283 " --> pdb=" O   GLN A 279 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A 284 " --> pdb=" O   ALA A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 310
      removed outlier: 3.746A  pdb=" N   ALA A 298 " --> pdb=" O   ALA A 294 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LYS A 308 " --> pdb=" O   ASP A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 321
      removed outlier: 3.519A  pdb=" N   ILE A 321 " --> pdb=" O   GLU A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 342
      removed outlier: 3.587A  pdb=" N   MET A 327 " --> pdb=" O   GLY A 323 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLN A 330 " --> pdb=" O   LYS A 326 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   MET A 331 " --> pdb=" O   MET A 327 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ARG A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 350
    Processing helix  chain 'A' and resid 351 through 379
      removed outlier: 3.648A  pdb=" N   GLN A 355 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   VAL A 356 " --> pdb=" O   LYS A 352 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   SER A 357 " --> pdb=" O   ALA A 353 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU A 360 " --> pdb=" O   VAL A 356 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   VAL A 362 " --> pdb=" O   GLN A 358 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   LEU A 363 " --> pdb=" O   GLY A 359 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ALA A 370 " --> pdb=" O   LYS A 366 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ARG A 372 " --> pdb=" O   GLU A 368 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LYS A 373 " --> pdb=" O   ASN A 369 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LEU A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   THR A 378 " --> pdb=" O   LEU A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 395
      removed outlier: 3.660A  pdb=" N   ILE A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   ASP A 389 " --> pdb=" O   ALA A 385 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   TRP A 394 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU A 395 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 422
      removed outlier: 3.631A  pdb=" N   LEU A 412 " --> pdb=" O   ILE A 408 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ALA A 413 " --> pdb=" O   ARG A 409 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   GLU A 414 " --> pdb=" O   GLY A 410 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE A 418 " --> pdb=" O   GLU A 414 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   ALA A 419 " --> pdb=" O   ALA A 415 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   GLU A 420 " --> pdb=" O   ARG A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 446
      removed outlier: 3.912A  pdb=" N   SER A 439 " --> pdb=" O   LEU A 435 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ALA A 440 " --> pdb=" O   GLY A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 450
    Processing helix  chain 'A' and resid 455 through 478
      removed outlier: 4.358A  pdb=" N   ALA A 461 " --> pdb=" O   PRO A 457 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ALA A 467 " --> pdb=" O   ALA A 463 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   THR A 468 " --> pdb=" O   LYS A 464 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   THR A 475 " --> pdb=" O   GLN A 471 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   LYS A 476 " --> pdb=" O   ASN A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 483
    Processing helix  chain 'A' and resid 492 through 502
      removed outlier: 3.569A  pdb=" N   LYS A 496 " --> pdb=" O   HIS A 492 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA A 500 " --> pdb=" O   LYS A 496 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   ARG A 502 " --> pdb=" O   GLU A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 523
      removed outlier: 3.812A  pdb=" N   ALA A 517 " --> pdb=" O   GLY A 513 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ARG A 520 " --> pdb=" O   GLN A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 530
    Processing helix  chain 'A' and resid 535 through 551
      removed outlier: 4.095A  pdb=" N   GLN A 539 " --> pdb=" O   GLY A 535 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ASP A 540 " --> pdb=" O   PRO A 536 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   LEU A 541 " --> pdb=" O   TYR A 537 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LYS A 544 " --> pdb=" O   ASP A 540 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   VAL A 548 " --> pdb=" O   LYS A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 582
      removed outlier: 3.670A  pdb=" N   LYS A 581 " --> pdb=" O   GLN A 577 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ASP A 582 " --> pdb=" O   ASP A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 599
      removed outlier: 3.809A  pdb=" N   GLU A 594 " --> pdb=" O   ALA A 590 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   SER A 596 " --> pdb=" O   THR A 592 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ASP A 597 " --> pdb=" O   GLN A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 615
    Processing helix  chain 'A' and resid 623 through 651
    Processing helix  chain 'A' and resid 654 through 685
      Proline residue:  A 673  - end of helix
      removed outlier: 3.546A  pdb=" N   ILE A 681 " --> pdb=" O   SER A 677 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU A 682 " --> pdb=" O   ALA A 678 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU A 683 " --> pdb=" O   ALA A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 717
      removed outlier: 3.833A  pdb=" N   TYR A 692 " --> pdb=" O   ASN A 688 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   GLU A 693 " --> pdb=" O   GLN A 689 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   HIS A 694 " --> pdb=" O   ALA A 690 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLY A 711 " --> pdb=" O   GLU A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 743
      removed outlier: 3.537A  pdb=" N   LEU A 723 " --> pdb=" O   THR A 719 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ALA A 729 " --> pdb=" O   ALA A 725 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASN A 743 " --> pdb=" O   VAL A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 774
      removed outlier: 3.515A  pdb=" N   LEU A 749 " --> pdb=" O   GLN A 745 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ARG A 759 " --> pdb=" O   SER A 755 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ASN A 761 " --> pdb=" O   ALA A 757 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ARG A 762 " --> pdb=" O   ARG A 758 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU A 764 " --> pdb=" O   ALA A 760 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASN A 773 " --> pdb=" O   ARG A 769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 806
      removed outlier: 3.674A  pdb=" N   SER A 787 " --> pdb=" O   VAL A 783 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   SER A 795 " --> pdb=" O   SER A 791 " (cutoff:3.500A)
      Proline residue:  A 796  - end of helix
      removed outlier: 3.548A  pdb=" N   GLY A 806 " --> pdb=" O   LYS A 802 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 812 through 835
      removed outlier: 3.864A  pdb=" N   ILE A 824 " --> pdb=" O   SER A 820 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   LEU A 825 " --> pdb=" O   GLY A 821 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   GLY A 826 " --> pdb=" O   TYR A 822 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   ALA A 827 " --> pdb=" O   ARG A 823 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   VAL A 831 " --> pdb=" O   ALA A 827 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   ARG A 832 " --> pdb=" O   VAL A 828 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   PHE A 835 " --> pdb=" O   VAL A 831 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 963 through 978
      removed outlier: 4.054A  pdb=" N   LEU A 967 " --> pdb=" O   ASN A 963 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   GLN A 971 " --> pdb=" O   LEU A 967 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   GLU A 976 " --> pdb=" O   SER A 972 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 986 through 997
    Processing helix  chain 'A' and resid 1011 through 1039
      removed outlier: 3.998A  pdb=" N   LEU A1015 " --> pdb=" O   THR A1011 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ILE A1022 " --> pdb=" O   CYS A1018 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ALA A1023 " --> pdb=" O   ALA A1019 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   THR A1030 " --> pdb=" O   SER A1026 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1042 through 1054
      removed outlier: 3.715A  pdb=" N   VAL A1052 " --> pdb=" O   ASN A1048 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLU A1054 " --> pdb=" O   LEU A1050 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1054 through 1073
      removed outlier: 3.903A  pdb=" N   THR A1058 " --> pdb=" O   GLU A1054 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ILE A1059 " --> pdb=" O   ARG A1055 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   SER A1060 " --> pdb=" O   ILE A1056 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   THR A1068 " --> pdb=" O   LYS A1064 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   THR A1072 " --> pdb=" O   THR A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1082 through 1114
      removed outlier: 3.608A  pdb=" N   SER A1101 " --> pdb=" O   ASN A1097 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLU A1110 " --> pdb=" O   VAL A1106 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ILE A1114 " --> pdb=" O   GLU A1110 " (cutoff:3.500A)

    505 hydrogen bonds defined for protein.
    1509 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: 2.24

  Time building geometry restraints manager: 3.75 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: 2547
        1.34 -     1.46: 917
        1.46 -     1.57: 4105
        1.57 -     1.69: 0
        1.69 -     1.81: 76
  Bond restraints: 7645
  Sorted by residual:
  bond pdb=" C   ILE A1056 "
       pdb=" N   PRO A1057 "
    ideal  model  delta    sigma   weight residual
    1.334  1.384 -0.050 2.34e-02 1.83e+03 4.56e+00
  bond pdb=" CG  LEU A 529 "
       pdb=" CD1 LEU A 529 "
    ideal  model  delta    sigma   weight residual
    1.521  1.454  0.067 3.30e-02 9.18e+02 4.12e+00
  bond pdb=" C   SER A 346 "
       pdb=" N   PRO A 347 "
    ideal  model  delta    sigma   weight residual
    1.334  1.376 -0.042 2.34e-02 1.83e+03 3.17e+00
  bond pdb=" CA  PRO A   2 "
       pdb=" C   PRO A   2 "
    ideal  model  delta    sigma   weight residual
    1.527  1.510  0.017 1.07e-02 8.73e+03 2.44e+00
  bond pdb=" C   SER A 795 "
       pdb=" N   PRO A 796 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.25e-02 6.40e+03 2.10e+00
  ... (remaining 7640 not shown)

  Histogram of bond angle deviations from ideal:
       98.29 -   105.80: 167
      105.80 -   113.32: 4323
      113.32 -   120.83: 3800
      120.83 -   128.34: 1981
      128.34 -   135.86: 43
  Bond angle restraints: 10314
  Sorted by residual:
  angle pdb=" C   VAL A1005 "
        pdb=" N   ARG A1006 "
        pdb=" CA  ARG A1006 "
      ideal   model   delta    sigma   weight residual
     121.54  129.46   -7.92 1.91e+00 2.74e-01 1.72e+01
  angle pdb=" C   THR A   6 "
        pdb=" N   ARG A   7 "
        pdb=" CA  ARG A   7 "
      ideal   model   delta    sigma   weight residual
     121.54  127.82   -6.28 1.91e+00 2.74e-01 1.08e+01
  angle pdb=" N   SER A 795 "
        pdb=" CA  SER A 795 "
        pdb=" C   SER A 795 "
      ideal   model   delta    sigma   weight residual
     109.81  116.92   -7.11 2.21e+00 2.05e-01 1.04e+01
  angle pdb=" N   VAL A 102 "
        pdb=" CA  VAL A 102 "
        pdb=" C   VAL A 102 "
      ideal   model   delta    sigma   weight residual
     108.88  115.69   -6.81 2.16e+00 2.14e-01 9.95e+00
  angle pdb=" C   ARG A1076 "
        pdb=" N   THR A1077 "
        pdb=" CA  THR A1077 "
      ideal   model   delta    sigma   weight residual
     125.02  130.49   -5.47 1.76e+00 3.23e-01 9.65e+00
  ... (remaining 10309 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.86: 4389
       15.86 -    31.71: 332
       31.71 -    47.57: 99
       47.57 -    63.42: 5
       63.42 -    79.28: 13
  Dihedral angle restraints: 4838
    sinusoidal: 1955
      harmonic: 2883
  Sorted by residual:
  dihedral pdb=" CA  GLU A 707 "
           pdb=" C   GLU A 707 "
           pdb=" N   LYS A 708 "
           pdb=" CA  LYS A 708 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.94   28.06     0      5.00e+00 4.00e-02 3.15e+01
  dihedral pdb=" CA  ASN A 700 "
           pdb=" C   ASN A 700 "
           pdb=" N   GLN A 701 "
           pdb=" CA  GLN A 701 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.25   25.75     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  ILE A 824 "
           pdb=" C   ILE A 824 "
           pdb=" N   LEU A 825 "
           pdb=" CA  LEU A 825 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.88  -25.12     0      5.00e+00 4.00e-02 2.52e+01
  ... (remaining 4835 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 727
       0.044 -    0.089: 351
       0.089 -    0.133: 110
       0.133 -    0.177: 21
       0.177 -    0.222: 5
  Chirality restraints: 1214
  Sorted by residual:
  chirality pdb=" CG  LEU A 640 "
            pdb=" CB  LEU A 640 "
            pdb=" CD1 LEU A 640 "
            pdb=" CD2 LEU A 640 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  THR A 604 "
            pdb=" N   THR A 604 "
            pdb=" C   THR A 604 "
            pdb=" CB  THR A 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.33    0.20 2.00e-01 2.50e+01 9.53e-01
  chirality pdb=" CB  THR A1011 "
            pdb=" CA  THR A1011 "
            pdb=" OG1 THR A1011 "
            pdb=" CG2 THR A1011 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 9.12e-01
  ... (remaining 1211 not shown)

  Planarity restraints: 1357
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A  75 "   -0.053 5.00e-02 4.00e+02   7.96e-02 1.01e+01
        pdb=" N   PRO A  76 "    0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO A  76 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A  76 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A  14 "    0.046 5.00e-02 4.00e+02   6.87e-02 7.56e+00
        pdb=" N   PRO A  15 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A  15 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A  15 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 672 "   -0.042 5.00e-02 4.00e+02   6.21e-02 6.18e+00
        pdb=" N   PRO A 673 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A 673 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 673 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 1354 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1724
        2.77 -     3.30: 8308
        3.30 -     3.84: 13628
        3.84 -     4.37: 16336
        4.37 -     4.90: 24266
  Nonbonded interactions: 64262
  Sorted by model distance:
  nonbonded pdb=" O   VAL A  57 "
            pdb=" OG1 THR A  61 "
     model   vdw
     2.239 2.440
  nonbonded pdb=" O   PHE A 599 "
            pdb=" OG1 THR A 602 "
     model   vdw
     2.259 2.440
  nonbonded pdb=" O   ILE A 211 "
            pdb=" OG1 THR A 214 "
     model   vdw
     2.262 2.440
  nonbonded pdb=" O   HIS A 974 "
            pdb=" OG1 THR A 978 "
     model   vdw
     2.281 2.440
  nonbonded pdb=" OD2 ASP A 733 "
            pdb=" NH2 ARG A 759 "
     model   vdw
     2.295 2.520
  ... (remaining 64257 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
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      43      5.16       5
     C    4666      2.51       5
     N    1372      2.21       5
     O    1487      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
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:                  0.000
  Normalize map: mean=0, sd=1:             0.660
  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:          4.180
  Check model and map are aligned:         0.100
  Process input model:                     23.750
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Set scattering table:                    0.070
  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:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.007   0.067   7645  Z= 0.452
  Angle     :  1.037  10.857  10314  Z= 0.557
  Chirality :  0.056   0.222   1214
  Planarity :  0.008   0.080   1357
  Dihedral  : 13.234  79.278   2954
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer Outliers :  0.25 %
  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: -5.41 (0.18), residues: 990
  helix: -3.53 (0.12), residues: 738
  sheet:  None (None), residues: 0
  loop : -2.89 (0.31), residues: 252

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 811 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 173
  time to evaluate  : 0.968 
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: 2
  outliers final: 0
  residues processed: 175
  average time/residue: 0.2106
  time to fit residues: 49.2210
Evaluate side-chains
  117 residues out of total 811 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.968 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3298
-------------------------------------------------------------------------------
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:    4.9990
   chunk 75 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9990
   chunk 77 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0030
   chunk 47 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    1.1998

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

Flipped N/Q/H residues before XYZ refinement:
A  27 HIS
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  63 GLN
** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 HIS
A 516 GLN
A 554 GLN
** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 745 GLN
A 974 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.2582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7645  Z= 0.186
  Angle     :  0.659   8.486  10314  Z= 0.349
  Chirality :  0.041   0.153   1214
  Planarity :  0.006   0.058   1357
  Dihedral  :  6.135  20.962   1059
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 17.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer Outliers :  0.12 %
  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: -2.96 (0.23), residues: 990
  helix: -1.67 (0.16), residues: 815
  sheet:  None (None), residues: 0
  loop : -2.35 (0.42), residues: 175

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 811 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.963 
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: 1
  outliers final: 0
  residues processed: 168
  average time/residue: 0.2017
  time to fit residues: 45.8196
Evaluate side-chains
  114 residues out of total 811 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.948 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3448
-------------------------------------------------------------------------------
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:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   chunk 61 optimal weight:    9.9990
   chunk 24 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 80 optimal weight:    0.4980
   chunk 89 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 550 GLN
A 554 GLN
A 761 ASN
A 974 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.3159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7645  Z= 0.177
  Angle     :  0.620   6.840  10314  Z= 0.325
  Chirality :  0.041   0.149   1214
  Planarity :  0.005   0.052   1357
  Dihedral  :  5.645  19.832   1059
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 17.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer Outliers :  0.12 %
  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: -1.61 (0.25), residues: 990
  helix: -0.68 (0.17), residues: 811
  sheet:  None (None), residues: 0
  loop : -2.12 (0.44), residues: 179

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 811 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 1.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 158
  average time/residue: 0.1860
  time to fit residues: 41.1373
Evaluate side-chains
  106 residues out of total 811 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.879 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1954
-------------------------------------------------------------------------------
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:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0050
   chunk 42 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 95 optimal weight:    7.9990
   chunk 47 optimal weight:    0.6980
   chunk 85 optimal weight:    7.9990
   chunk 25 optimal weight:    0.5980
   overall best weight:    1.4598

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 ASN
** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 761 ASN
A 974 HIS
A1017 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.3670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7645  Z= 0.174
  Angle     :  0.595   7.346  10314  Z= 0.309
  Chirality :  0.041   0.143   1214
  Planarity :  0.004   0.051   1357
  Dihedral  :  5.327  18.608   1059
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 16.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer Outliers :  0.25 %
  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: 990
  helix: -0.10 (0.18), residues: 821
  sheet:  None (None), residues: 0
  loop : -1.71 (0.46), residues: 169

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 811 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 166
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 167
  average time/residue: 0.1925
  time to fit residues: 44.0756
Evaluate side-chains
  119 residues out of total 811 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 117
  time to evaluate  : 1.090 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1109
  time to fit residues: 1.5143
-------------------------------------------------------------------------------
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:    6.9990
   chunk 54 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 39 optimal weight:    8.9990
   chunk 81 optimal weight:    6.9990
   chunk 66 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 48 optimal weight:    6.9990
   chunk 85 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 ASN
** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 369 ASN
** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 761 ASN
A 974 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.3754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7645  Z= 0.240
  Angle     :  0.660   7.605  10314  Z= 0.344
  Chirality :  0.042   0.175   1214
  Planarity :  0.005   0.049   1357
  Dihedral  :  5.387  24.796   1059
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 20.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer Outliers :  0.00 %
  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: -0.54 (0.26), residues: 990
  helix:  0.06 (0.18), residues: 812
  sheet:  None (None), residues: 0
  loop : -1.76 (0.43), residues: 178

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 811 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1776
  time to fit residues: 38.4924
Evaluate side-chains
  114 residues out of total 811 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.828 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1293
-------------------------------------------------------------------------------
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:   10.0000
   chunk 86 optimal weight:    0.0980
   chunk 18 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 23 optimal weight:    9.9990
   chunk 95 optimal weight:    3.9990
   chunk 79 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 ASN
** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.4101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7645  Z= 0.182
  Angle     :  0.617   6.940  10314  Z= 0.319
  Chirality :  0.042   0.140   1214
  Planarity :  0.004   0.051   1357
  Dihedral  :  5.261  22.843   1059
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 17.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer Outliers :  0.00 %
  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: -0.32 (0.27), residues: 990
  helix:  0.23 (0.18), residues: 819
  sheet:  None (None), residues: 0
  loop : -1.89 (0.43), residues: 171

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 811 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.1879
  time to fit residues: 39.9884
Evaluate side-chains
  115 residues out of total 811 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.979 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1569
-------------------------------------------------------------------------------
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:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 95 optimal weight:    9.9990
   chunk 59 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 44 optimal weight:    0.2980
   chunk 38 optimal weight:    0.9980
   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  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 ASN
A 187 HIS
** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.4396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7645  Z= 0.169
  Angle     :  0.624   7.151  10314  Z= 0.322
  Chirality :  0.042   0.186   1214
  Planarity :  0.004   0.051   1357
  Dihedral  :  5.191  23.328   1059
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 17.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer Outliers :  0.00 %
  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: -0.08 (0.27), residues: 990
  helix:  0.42 (0.18), residues: 818
  sheet:  None (None), residues: 0
  loop : -1.95 (0.44), residues: 172

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 811 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.1878
  time to fit residues: 40.2524
Evaluate side-chains
  116 residues out of total 811 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 1.026 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3981
-------------------------------------------------------------------------------
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:    7.9990
   chunk 28 optimal weight:   10.0000
   chunk 18 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9990
   chunk 8 optimal weight:    7.9990
   chunk 75 optimal weight:    5.9990
   chunk 86 optimal weight:    0.0020
   chunk 91 optimal weight:    8.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    2.3996

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 ASN
A 369 ASN
A 492 HIS
** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 GLN
A 960 GLN
A 974 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.4446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7645  Z= 0.221
  Angle     :  0.664   7.029  10314  Z= 0.344
  Chirality :  0.043   0.167   1214
  Planarity :  0.005   0.052   1357
  Dihedral  :  5.232  22.140   1059
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 21.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer Outliers :  0.12 %
  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: -0.12 (0.27), residues: 990
  helix:  0.34 (0.18), residues: 823
  sheet:  None (None), residues: 0
  loop : -1.70 (0.46), residues: 167

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 811 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 154
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 155
  average time/residue: 0.2064
  time to fit residues: 43.8048
Evaluate side-chains
  114 residues out of total 811 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 1.049 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3290
-------------------------------------------------------------------------------
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:    9.9990
   chunk 91 optimal weight:   10.0000
   chunk 53 optimal weight:    6.9990
   chunk 38 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 80 optimal weight:    0.5980
   chunk 84 optimal weight:    6.9990
   chunk 58 optimal weight:    0.1980
   chunk 94 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A   5 HIS
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 ASN
A 369 ASN
A 492 HIS
** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 GLN
A 960 GLN
A 974 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.4698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7645  Z= 0.181
  Angle     :  0.645   6.923  10314  Z= 0.331
  Chirality :  0.042   0.157   1214
  Planarity :  0.004   0.054   1357
  Dihedral  :  5.177  23.160   1059
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 18.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer Outliers :  0.25 %
  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:  0.10 (0.27), residues: 990
  helix:  0.54 (0.19), residues: 817
  sheet:  None (None), residues: 0
  loop : -1.83 (0.45), residues: 173

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 811 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 158
  time to evaluate  : 0.964 
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: 2
  outliers final: 0
  residues processed: 159
  average time/residue: 0.2059
  time to fit residues: 45.2682
Evaluate side-chains
  122 residues out of total 811 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.947 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4480
-------------------------------------------------------------------------------
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:    5.9990
   chunk 65 optimal weight:    6.9990
   chunk 98 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   chunk 60 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 62 optimal weight:   10.0000
   chunk 83 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 ASN
A 369 ASN
** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 974 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.4653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7645  Z= 0.240
  Angle     :  0.692   9.298  10314  Z= 0.360
  Chirality :  0.043   0.172   1214
  Planarity :  0.005   0.051   1357
  Dihedral  :  5.249  24.515   1059
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 22.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer Outliers :  0.00 %
  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: -0.09 (0.27), residues: 990
  helix:  0.37 (0.18), residues: 818
  sheet:  None (None), residues: 0
  loop : -1.70 (0.46), residues: 172

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 811 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.988 
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: 155
  average time/residue: 0.2004
  time to fit residues: 42.7877
Evaluate side-chains
  119 residues out of total 811 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.958 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3160
-------------------------------------------------------------------------------
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:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 78 optimal weight:    4.9990
   chunk 32 optimal weight:   10.0000
   chunk 80 optimal weight:    3.9990
   chunk 9 optimal weight:   10.0000
   chunk 14 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 369 ASN
** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 974 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.087024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.071693 restraints weight = 37694.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.073139 restraints weight = 28738.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.074166 restraints weight = 23380.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.4777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7645  Z= 0.208
  Angle     :  0.666   7.739  10314  Z= 0.345
  Chirality :  0.043   0.160   1214
  Planarity :  0.004   0.052   1357
  Dihedral  :  5.192  23.638   1059
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 20.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer Outliers :  0.00 %
  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: -0.00 (0.27), residues: 990
  helix:  0.44 (0.18), residues: 821
  sheet:  None (None), residues: 0
  loop : -1.74 (0.46), residues: 169

===============================================================================
Job complete
usr+sys time: 1653.23 seconds
wall clock time: 31 minutes 13.28 seconds (1873.28 seconds total)