Starting phenix.real_space_refine (version: 1.21rc1)
on Wed Oct  4 17:43:48 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n58_24182/10_2023/7n58_24182.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n58_24182/10_2023/7n58_24182.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n58_24182/10_2023/7n58_24182.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n58_24182/10_2023/7n58_24182.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n58_24182/10_2023/7n58_24182.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n58_24182/10_2023/7n58_24182.pdb"
  }
  resolution = 3.4
  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=   0.020
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      34      5.16       5
     C    5952      2.51       5
     N    1598      2.21       5
     O    1742      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ASP  120": "OD1" <-> "OD2"
    Residue "A PHE  195": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  205": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  217": "OE1" <-> "OE2"
    Residue "A PHE  427": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  459": "OE1" <-> "OE2"
    Residue "A TYR  488": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  651": "OE1" <-> "OE2"
    Residue "B ASP  120": "OD1" <-> "OD2"
    Residue "B PHE  195": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  205": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  217": "OE1" <-> "OE2"
    Residue "B PHE  427": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  459": "OE1" <-> "OE2"
    Residue "B TYR  488": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  651": "OE1" <-> "OE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib"
  Total number of atoms: 9326
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 600, 4663
          Classifications: {'peptide': 600}
          Link IDs: {'PTRANS': 13, 'TRANS': 586}
    Chain: "B"
      Number of atoms: 4663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 600, 4663
          Classifications: {'peptide': 600}
          Link IDs: {'PTRANS': 13, 'TRANS': 586}
  Time building chain proxies: 5.01, per 1000 atoms: 0.54
  Number of scatterers: 9326
  At special positions: 0
  Unit cell: (112.005, 98.325, 143.64, 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      34     16.00
     O    1742      8.00
     N    1598      7.00
     C    5952      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: 3.57
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2240

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 8 sheets defined
      66.9% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 117 through 132
      removed outlier: 3.646A  pdb=" N   MET A 121 " --> pdb=" O   ALA A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 169
      removed outlier: 4.281A  pdb=" N   ARG A 140 " --> pdb=" O   ASN A 136 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ALA A 153 " --> pdb=" O   PHE A 149 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LYS A 154 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   VAL A 158 " --> pdb=" O   LYS A 154 " (cutoff:3.500A)
      Proline residue:  A 161  - end of helix
      removed outlier: 3.518A  pdb=" N   VAL A 168 " --> pdb=" O   PHE A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 183
      removed outlier: 3.762A  pdb=" N   THR A 182 " --> pdb=" O   ALA A 179 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   THR A 183 " --> pdb=" O   SER A 180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 179 through 183'
    Processing helix  chain 'A' and resid 197 through 245
      removed outlier: 3.889A  pdb=" N   VAL A 201 " --> pdb=" O   THR A 197 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   THR A 220 " --> pdb=" O   ASN A 216 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ALA A 221 " --> pdb=" O   GLU A 217 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LYS A 225 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   VAL A 226 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ARG A 229 " --> pdb=" O   LYS A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 253
      removed outlier: 3.667A  pdb=" N   HIS A 250 " --> pdb=" O   ASP A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 279
      removed outlier: 3.584A  pdb=" N   LEU A 258 " --> pdb=" O   GLU A 254 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ASN A 259 " --> pdb=" O   THR A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 292
    Processing helix  chain 'A' and resid 293 through 296
    Processing helix  chain 'A' and resid 299 through 348
      removed outlier: 3.715A  pdb=" N   TRP A 304 " --> pdb=" O   ALA A 300 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ILE A 305 " --> pdb=" O   ALA A 301 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   THR A 306 " --> pdb=" O   PHE A 302 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   SER A 307 " --> pdb=" O   ALA A 303 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLN A 322 " --> pdb=" O   LEU A 318 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   TRP A 323 " --> pdb=" O   ALA A 319 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LYS A 326 " --> pdb=" O   GLN A 322 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   PHE A 327 " --> pdb=" O   TRP A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 355
      removed outlier: 3.744A  pdb=" N   VAL A 352 " --> pdb=" O   ASN A 348 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   PHE A 355 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 411
      removed outlier: 3.602A  pdb=" N   LYS A 364 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   THR A 379 " --> pdb=" O   ALA A 375 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLN A 380 " --> pdb=" O   ALA A 376 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ARG A 381 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   SER A 391 " --> pdb=" O   ASN A 387 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   PHE A 394 " --> pdb=" O   GLN A 390 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ALA A 397 " --> pdb=" O   ILE A 393 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU A 398 " --> pdb=" O   PHE A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 431
      removed outlier: 4.014A  pdb=" N   VAL A 422 " --> pdb=" O   ASP A 418 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ASN A 423 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   GLY A 424 " --> pdb=" O   VAL A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 438
      removed outlier: 4.310A  pdb=" N   LEU A 436 " --> pdb=" O   PRO A 432 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   GLY A 437 " --> pdb=" O   LEU A 433 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   SER A 438 " --> pdb=" O   ASN A 434 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 432 through 438'
    Processing helix  chain 'A' and resid 438 through 457
      removed outlier: 4.732A  pdb=" N   GLU A 442 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 526
      removed outlier: 3.956A  pdb=" N   ARG A 523 " --> pdb=" O   SER A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 555
    Processing helix  chain 'A' and resid 569 through 575
    Processing helix  chain 'A' and resid 581 through 593
    Processing helix  chain 'A' and resid 594 through 599
      removed outlier: 3.507A  pdb=" N   SER A 599 " --> pdb=" O   HIS A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 617 through 633
      removed outlier: 4.596A  pdb=" N   LEU A 631 " --> pdb=" O   ALA A 627 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   LYS A 632 " --> pdb=" O   ARG A 628 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   SER A 633 " --> pdb=" O   THR A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 662
      removed outlier: 3.596A  pdb=" N   GLU A 653 " --> pdb=" O   THR A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 696 through 702
      removed outlier: 3.545A  pdb=" N   LEU A 700 " --> pdb=" O   PRO A 696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 716
    Processing helix  chain 'B' and resid 118 through 132
    Processing helix  chain 'B' and resid 136 through 169
      removed outlier: 4.281A  pdb=" N   ARG B 140 " --> pdb=" O   ASN B 136 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ALA B 153 " --> pdb=" O   PHE B 149 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LYS B 154 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   VAL B 158 " --> pdb=" O   LYS B 154 " (cutoff:3.500A)
      Proline residue:  B 161  - end of helix
      removed outlier: 3.519A  pdb=" N   VAL B 168 " --> pdb=" O   PHE B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 183
      removed outlier: 3.761A  pdb=" N   THR B 182 " --> pdb=" O   ALA B 179 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   THR B 183 " --> pdb=" O   SER B 180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 179 through 183'
    Processing helix  chain 'B' and resid 197 through 245
      removed outlier: 3.888A  pdb=" N   VAL B 201 " --> pdb=" O   THR B 197 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   THR B 220 " --> pdb=" O   ASN B 216 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ALA B 221 " --> pdb=" O   GLU B 217 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LYS B 225 " --> pdb=" O   ALA B 221 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   VAL B 226 " --> pdb=" O   VAL B 222 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ARG B 229 " --> pdb=" O   LYS B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 253
      removed outlier: 3.667A  pdb=" N   HIS B 250 " --> pdb=" O   ASP B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 279
      removed outlier: 3.584A  pdb=" N   LEU B 258 " --> pdb=" O   GLU B 254 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ASN B 259 " --> pdb=" O   THR B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 292
    Processing helix  chain 'B' and resid 293 through 296
    Processing helix  chain 'B' and resid 299 through 348
      removed outlier: 3.715A  pdb=" N   TRP B 304 " --> pdb=" O   ALA B 300 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ILE B 305 " --> pdb=" O   ALA B 301 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   THR B 306 " --> pdb=" O   PHE B 302 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   SER B 307 " --> pdb=" O   ALA B 303 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLN B 322 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   TRP B 323 " --> pdb=" O   ALA B 319 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LYS B 326 " --> pdb=" O   GLN B 322 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   PHE B 327 " --> pdb=" O   TRP B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 355
      removed outlier: 3.744A  pdb=" N   VAL B 352 " --> pdb=" O   ASN B 348 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   PHE B 355 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 411
      removed outlier: 3.601A  pdb=" N   LYS B 364 " --> pdb=" O   TYR B 360 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   THR B 379 " --> pdb=" O   ALA B 375 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLN B 380 " --> pdb=" O   ALA B 376 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ARG B 381 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU B 386 " --> pdb=" O   SER B 382 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   SER B 391 " --> pdb=" O   ASN B 387 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   PHE B 394 " --> pdb=" O   GLN B 390 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   ALA B 397 " --> pdb=" O   ILE B 393 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU B 398 " --> pdb=" O   PHE B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 431
      removed outlier: 4.014A  pdb=" N   VAL B 422 " --> pdb=" O   ASP B 418 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ASN B 423 " --> pdb=" O   LEU B 419 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLY B 424 " --> pdb=" O   VAL B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 438
      removed outlier: 4.311A  pdb=" N   LEU B 436 " --> pdb=" O   PRO B 432 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   GLY B 437 " --> pdb=" O   LEU B 433 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   SER B 438 " --> pdb=" O   ASN B 434 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 432 through 438'
    Processing helix  chain 'B' and resid 438 through 457
      removed outlier: 4.732A  pdb=" N   GLU B 442 " --> pdb=" O   SER B 438 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 519 through 526
      removed outlier: 3.955A  pdb=" N   ARG B 523 " --> pdb=" O   SER B 519 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 547 through 555
    Processing helix  chain 'B' and resid 569 through 575
    Processing helix  chain 'B' and resid 581 through 593
    Processing helix  chain 'B' and resid 594 through 599
      removed outlier: 3.507A  pdb=" N   SER B 599 " --> pdb=" O   HIS B 595 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 617 through 633
      removed outlier: 4.597A  pdb=" N   LEU B 631 " --> pdb=" O   ALA B 627 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   LYS B 632 " --> pdb=" O   ARG B 628 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   SER B 633 " --> pdb=" O   THR B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 647 through 662
      removed outlier: 3.595A  pdb=" N   GLU B 653 " --> pdb=" O   THR B 649 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 702
      removed outlier: 3.544A  pdb=" N   LEU B 700 " --> pdb=" O   PRO B 696 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 716
    Processing sheet with id=AA1, first strand: chain 'A' and resid 501 through 502
      removed outlier: 3.737A  pdb=" N   ILE A 479 " --> pdb=" O   VAL A 502 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLU A 482 " --> pdb=" O   ASN A 535 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ASN A 535 " --> pdb=" O   GLU A 482 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 484 through 486
      removed outlier: 4.819A  pdb=" N   VAL A 484 " --> pdb=" O   GLY A 497 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   PHE A 486 " --> pdb=" O   LEU A 495 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU A 495 " --> pdb=" O   PHE A 486 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 556 through 557
      removed outlier: 6.907A  pdb=" N   GLY A 556 " --> pdb=" O   LEU A 638 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ILE A 670 " --> pdb=" O   CYS A 639 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   GLY A 512 " --> pdb=" O   ALA A 671 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   SER A 507 " --> pdb=" O   GLU A 682 " (cutoff:3.500A)
      removed outlier: 8.374A  pdb=" N   VAL A 684 " --> pdb=" O   SER A 507 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   ALA A 509 " --> pdb=" O   VAL A 684 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   LEU A 686 " --> pdb=" O   ALA A 509 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   VAL A 511 " --> pdb=" O   LEU A 686 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   ILE A 683 " --> pdb=" O   GLN A 694 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   GLN A 694 " --> pdb=" O   ILE A 683 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   VAL A 685 " --> pdb=" O   VAL A 692 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 567 through 568
    Processing sheet with id=AA5, first strand: chain 'B' and resid 501 through 502
      removed outlier: 3.737A  pdb=" N   ILE B 479 " --> pdb=" O   VAL B 502 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLU B 482 " --> pdb=" O   ASN B 535 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ASN B 535 " --> pdb=" O   GLU B 482 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 484 through 486
      removed outlier: 4.819A  pdb=" N   VAL B 484 " --> pdb=" O   GLY B 497 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   PHE B 486 " --> pdb=" O   LEU B 495 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU B 495 " --> pdb=" O   PHE B 486 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 556 through 557
      removed outlier: 6.908A  pdb=" N   GLY B 556 " --> pdb=" O   LEU B 638 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ILE B 670 " --> pdb=" O   CYS B 639 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   GLY B 512 " --> pdb=" O   ALA B 671 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   SER B 507 " --> pdb=" O   GLU B 682 " (cutoff:3.500A)
      removed outlier: 8.374A  pdb=" N   VAL B 684 " --> pdb=" O   SER B 507 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   ALA B 509 " --> pdb=" O   VAL B 684 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   LEU B 686 " --> pdb=" O   ALA B 509 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   VAL B 511 " --> pdb=" O   LEU B 686 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   ILE B 683 " --> pdb=" O   GLN B 694 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   GLN B 694 " --> pdb=" O   ILE B 683 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   VAL B 685 " --> pdb=" O   VAL B 692 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 567 through 568

    548 hydrogen bonds defined for protein.
    1626 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: 2.78

  Time building geometry restraints manager: 3.90 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: 3028
        1.34 -     1.46: 1371
        1.46 -     1.57: 5029
        1.57 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 9490
  Sorted by residual:
  bond pdb=" CB  GLU B 651 "
       pdb=" CG  GLU B 651 "
    ideal  model  delta    sigma   weight residual
    1.520  1.471  0.049 3.00e-02 1.11e+03 2.70e+00
  bond pdb=" CB  GLU A 651 "
       pdb=" CG  GLU A 651 "
    ideal  model  delta    sigma   weight residual
    1.520  1.471  0.049 3.00e-02 1.11e+03 2.67e+00
  bond pdb=" CB  LYS A 632 "
       pdb=" CG  LYS A 632 "
    ideal  model  delta    sigma   weight residual
    1.520  1.485  0.035 3.00e-02 1.11e+03 1.39e+00
  bond pdb=" CB  LYS B 632 "
       pdb=" CG  LYS B 632 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.32e+00
  bond pdb=" CD  LYS A 632 "
       pdb=" CE  LYS A 632 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.28e+00
  ... (remaining 9485 not shown)

  Histogram of bond angle deviations from ideal:
       98.66 -   105.73: 114
      105.73 -   112.79: 5116
      112.79 -   119.86: 3243
      119.86 -   126.92: 4301
      126.92 -   133.98: 68
  Bond angle restraints: 12842
  Sorted by residual:
  angle pdb=" N   VAL A 158 "
        pdb=" CA  VAL A 158 "
        pdb=" C   VAL A 158 "
      ideal   model   delta    sigma   weight residual
     113.39  107.51    5.88 1.47e+00 4.63e-01 1.60e+01
  angle pdb=" N   VAL B 158 "
        pdb=" CA  VAL B 158 "
        pdb=" C   VAL B 158 "
      ideal   model   delta    sigma   weight residual
     113.39  107.54    5.85 1.47e+00 4.63e-01 1.58e+01
  angle pdb=" CA  ARG A 232 "
        pdb=" CB  ARG A 232 "
        pdb=" CG  ARG A 232 "
      ideal   model   delta    sigma   weight residual
     114.10  107.07    7.03 2.00e+00 2.50e-01 1.23e+01
  angle pdb=" CA  ARG B 232 "
        pdb=" CB  ARG B 232 "
        pdb=" CG  ARG B 232 "
      ideal   model   delta    sigma   weight residual
     114.10  107.10    7.00 2.00e+00 2.50e-01 1.22e+01
  angle pdb=" CB  LYS B 632 "
        pdb=" CG  LYS B 632 "
        pdb=" CD  LYS B 632 "
      ideal   model   delta    sigma   weight residual
     111.30  103.96    7.34 2.30e+00 1.89e-01 1.02e+01
  ... (remaining 12837 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.39: 5006
       14.39 -    28.78: 491
       28.78 -    43.17: 141
       43.17 -    57.56: 26
       57.56 -    71.95: 12
  Dihedral angle restraints: 5676
    sinusoidal: 2206
      harmonic: 3470
  Sorted by residual:
  dihedral pdb=" CA  PRO B 696 "
           pdb=" C   PRO B 696 "
           pdb=" N   HIS B 697 "
           pdb=" CA  HIS B 697 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.30  -16.70     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  PRO A 696 "
           pdb=" C   PRO A 696 "
           pdb=" N   HIS A 697 "
           pdb=" CA  HIS A 697 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.30  -16.70     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  GLU B 373 "
           pdb=" CB  GLU B 373 "
           pdb=" CG  GLU B 373 "
           pdb=" CD  GLU B 373 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -104.54   44.54     3      1.50e+01 4.44e-03 8.01e+00
  ... (remaining 5673 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 986
       0.036 -    0.073: 366
       0.073 -    0.109: 101
       0.109 -    0.145: 41
       0.145 -    0.182: 12
  Chirality restraints: 1506
  Sorted by residual:
  chirality pdb=" CA  GLU B 458 "
            pdb=" N   GLU B 458 "
            pdb=" C   GLU B 458 "
            pdb=" CB  GLU B 458 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.25e-01
  chirality pdb=" CA  GLU A 458 "
            pdb=" N   GLU A 458 "
            pdb=" C   GLU A 458 "
            pdb=" CB  GLU A 458 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.17e-01
  chirality pdb=" CA  ILE A 293 "
            pdb=" N   ILE A 293 "
            pdb=" C   ILE A 293 "
            pdb=" CB  ILE A 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.70e-01
  ... (remaining 1503 not shown)

  Planarity restraints: 1630
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 188 "   -0.068 5.00e-02 4.00e+02   1.04e-01 1.71e+01
        pdb=" N   PRO A 189 "    0.179 5.00e-02 4.00e+02
        pdb=" CA  PRO A 189 "   -0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO A 189 "   -0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 188 "   -0.067 5.00e-02 4.00e+02   1.03e-01 1.71e+01
        pdb=" N   PRO B 189 "    0.179 5.00e-02 4.00e+02
        pdb=" CA  PRO B 189 "   -0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO B 189 "   -0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 213 "   -0.018 2.00e-02 2.50e+03   3.58e-02 1.28e+01
        pdb=" C   SER B 213 "    0.062 2.00e-02 2.50e+03
        pdb=" O   SER B 213 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   ALA B 214 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 1627 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 212
        2.70 -     3.25: 10201
        3.25 -     3.80: 13940
        3.80 -     4.35: 18003
        4.35 -     4.90: 28592
  Nonbonded interactions: 70948
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 449 "
            pdb=" OG  SER A 452 "
     model   vdw
     2.146 2.440
  nonbonded pdb=" O   ASP B 449 "
            pdb=" OG  SER B 452 "
     model   vdw
     2.147 2.440
  nonbonded pdb=" O   GLY B 176 "
            pdb=" OG1 THR B 177 "
     model   vdw
     2.223 2.440
  nonbonded pdb=" O   GLY A 176 "
            pdb=" OG1 THR A 177 "
     model   vdw
     2.224 2.440
  nonbonded pdb=" NE2 GLN A 445 "
            pdb=" OD2 ASP A 449 "
     model   vdw
     2.259 2.520
  ... (remaining 70943 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.160
  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:          6.020
  Check model and map are aligned:         0.140
  Set scattering table:                    0.080
  Process input model:                     26.490
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6378
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      :  0.004   0.049   9490  Z= 0.224
  Angle     :  0.841  10.328  12842  Z= 0.468
  Chirality :  0.045   0.182   1506
  Planarity :  0.007   0.104   1630
  Dihedral  : 13.091  71.950   3436
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  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: -0.83 (0.23), residues: 1196
  helix:  0.34 (0.19), residues: 734
  sheet: -0.40 (0.52), residues: 70
  loop : -2.25 (0.27), residues: 392

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.2243
  time to fit residues: 38.9770
Evaluate side-chains
  98 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 1.013 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4652
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 61 optimal weight:    0.3980
   chunk 48 optimal weight:    0.6980
   chunk 94 optimal weight:    0.0870
   chunk 36 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 108 optimal weight:    0.2980
   overall best weight:    0.4958

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6401
moved from start:          0.1176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9490  Z= 0.184
  Angle     :  0.638  10.136  12842  Z= 0.333
  Chirality :  0.039   0.150   1506
  Planarity :  0.005   0.061   1630
  Dihedral  :  4.007  14.781   1298
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  8.33 %
    Favored  : 90.87 %
  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:  0.39 (0.24), residues: 1196
  helix:  1.33 (0.19), residues: 730
  sheet:  0.19 (0.56), residues: 70
  loop : -1.81 (0.29), residues: 396

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 7
  residues processed: 107
  average time/residue: 0.2234
  time to fit residues: 33.8438
Evaluate side-chains
  103 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 1.007 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0919
  time to fit residues: 2.5929
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 60 optimal weight:    8.9990
   chunk 33 optimal weight:    0.7980
   chunk 90 optimal weight:    0.7980
   chunk 74 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 109 optimal weight:    3.9990
   chunk 117 optimal weight:    0.0570
   chunk 97 optimal weight:    0.8980
   chunk 108 optimal weight:    0.0770
   chunk 37 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.5256

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

Flipped N/Q/H residues before XYZ refinement:
B 566 ASN
B 679 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6441
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9490  Z= 0.159
  Angle     :  0.565   8.009  12842  Z= 0.295
  Chirality :  0.039   0.155   1506
  Planarity :  0.004   0.051   1630
  Dihedral  :  3.876  14.799   1298
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 12.30 %
    Favored  : 87.20 %
  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:  0.85 (0.24), residues: 1196
  helix:  1.77 (0.19), residues: 724
  sheet:  0.63 (0.68), residues: 44
  loop : -1.65 (0.28), residues: 428

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 1.120 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 112
  average time/residue: 0.2147
  time to fit residues: 34.0845
Evaluate side-chains
  97 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 1.015 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0873
  time to fit residues: 1.8852
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 82 optimal weight:    6.9990
   chunk 56 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 52 optimal weight:   10.0000
   chunk 73 optimal weight:    2.9990
   chunk 109 optimal weight:    9.9990
   chunk 115 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 31 optimal weight:    0.4980
   overall best weight:    1.6988

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

Flipped N/Q/H residues before XYZ refinement:
** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 572 ASN
A 679 GLN
B 250 HIS
** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 413 GLN
** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6682
moved from start:          0.2564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   9490  Z= 0.297
  Angle     :  0.659   9.076  12842  Z= 0.352
  Chirality :  0.043   0.142   1506
  Planarity :  0.005   0.046   1630
  Dihedral  :  4.304  17.853   1298
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.29 %
    Favored  : 83.73 %
  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:  0.39 (0.24), residues: 1196
  helix:  1.50 (0.19), residues: 734
  sheet:  0.71 (0.55), residues: 68
  loop : -2.34 (0.28), residues: 394

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 1.029 
Fit side-chains
  outliers start: 20
  outliers final: 10
  residues processed: 129
  average time/residue: 0.2299
  time to fit residues: 41.1903
Evaluate side-chains
  110 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 1.001 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0867
  time to fit residues: 3.0456
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9990
   chunk 80 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 104 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 367 GLN
** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6633
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9490  Z= 0.180
  Angle     :  0.554   7.746  12842  Z= 0.293
  Chirality :  0.039   0.139   1506
  Planarity :  0.004   0.048   1630
  Dihedral  :  4.103  16.043   1298
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 16.27 %
    Favored  : 82.44 %
  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:  0.64 (0.24), residues: 1196
  helix:  1.78 (0.19), residues: 726
  sheet:  0.81 (0.57), residues: 68
  loop : -2.33 (0.27), residues: 402

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 1.018 
Fit side-chains
  outliers start: 13
  outliers final: 6
  residues processed: 115
  average time/residue: 0.2215
  time to fit residues: 35.7117
Evaluate side-chains
  106 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.972 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0860
  time to fit residues: 2.3420
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 104 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 116 optimal weight:    8.9990
   chunk 96 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 60 optimal weight:    8.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 250 HIS
** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6629
moved from start:          0.3098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9490  Z= 0.164
  Angle     :  0.528   6.870  12842  Z= 0.280
  Chirality :  0.038   0.138   1506
  Planarity :  0.004   0.049   1630
  Dihedral  :  3.968  15.718   1298
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 18.65 %
    Favored  : 80.36 %
  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:  0.81 (0.25), residues: 1196
  helix:  1.91 (0.19), residues: 732
  sheet:  0.66 (0.59), residues: 68
  loop : -2.29 (0.28), residues: 396

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.999 
Fit side-chains
  outliers start: 10
  outliers final: 5
  residues processed: 110
  average time/residue: 0.2203
  time to fit residues: 34.0902
Evaluate side-chains
  102 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 1.007 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0834
  time to fit residues: 2.2329
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 111 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0040
   chunk 84 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0470
   chunk 64 optimal weight:    0.0040
   chunk 115 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    1.0106

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

Flipped N/Q/H residues before XYZ refinement:
A 243 HIS
** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 243 HIS
B 250 HIS
B 367 GLN
B 595 HIS
** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6670
moved from start:          0.3385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9490  Z= 0.192
  Angle     :  0.554   7.091  12842  Z= 0.294
  Chirality :  0.039   0.138   1506
  Planarity :  0.004   0.049   1630
  Dihedral  :  4.001  15.320   1298
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 20.34 %
    Favored  : 78.77 %
  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:  0.73 (0.25), residues: 1196
  helix:  1.89 (0.19), residues: 732
  sheet:  0.44 (0.58), residues: 70
  loop : -2.38 (0.28), residues: 394

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.983 
Fit side-chains
  outliers start: 9
  outliers final: 2
  residues processed: 108
  average time/residue: 0.2461
  time to fit residues: 37.7396
Evaluate side-chains
  97 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 1.056 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1042
  time to fit residues: 1.8869
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 46 optimal weight:    4.9990
   chunk 69 optimal weight:    0.6980
   chunk 34 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 90 optimal weight:    0.7980
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6649
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9490  Z= 0.163
  Angle     :  0.531   7.053  12842  Z= 0.280
  Chirality :  0.038   0.138   1506
  Planarity :  0.004   0.049   1630
  Dihedral  :  3.920  15.332   1298
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 20.83 %
    Favored  : 78.08 %
  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:  0.81 (0.25), residues: 1196
  helix:  1.97 (0.19), residues: 734
  sheet:  0.52 (0.59), residues: 68
  loop : -2.40 (0.28), residues: 394

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
  outliers start: 11
  outliers final: 5
  residues processed: 100
  average time/residue: 0.2456
  time to fit residues: 34.0771
Evaluate side-chains
  93 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 88
  time to evaluate  : 0.915 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0875
  time to fit residues: 2.2414
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 110 optimal weight:    0.9980
   chunk 101 optimal weight:    4.9990
   chunk 107 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 84 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 97 optimal weight:    0.0570
   chunk 70 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 243 HIS
** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6642
moved from start:          0.3635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9490  Z= 0.161
  Angle     :  0.529   7.067  12842  Z= 0.278
  Chirality :  0.038   0.138   1506
  Planarity :  0.004   0.048   1630
  Dihedral  :  3.854  15.312   1298
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 21.33 %
    Favored  : 78.17 %
  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:  0.86 (0.25), residues: 1196
  helix:  2.01 (0.19), residues: 734
  sheet:  0.58 (0.60), residues: 68
  loop : -2.37 (0.28), residues: 394

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.979 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 100
  average time/residue: 0.2528
  time to fit residues: 34.4461
Evaluate side-chains
  97 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 93
  time to evaluate  : 0.896 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0933
  time to fit residues: 2.0406
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 119 optimal weight:    4.9990
   chunk 110 optimal weight:    7.9990
   chunk 95 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0000
   chunk 75 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 243 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6644
moved from start:          0.3758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9490  Z= 0.164
  Angle     :  0.541   7.411  12842  Z= 0.283
  Chirality :  0.038   0.165   1506
  Planarity :  0.004   0.048   1630
  Dihedral  :  3.856  15.618   1298
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 21.83 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.25), residues: 1196
  helix:  2.00 (0.19), residues: 734
  sheet:  0.60 (0.60), residues: 68
  loop : -2.40 (0.27), residues: 394

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 1.076 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 99
  average time/residue: 0.2429
  time to fit residues: 33.0871
Evaluate side-chains
  95 residues out of total 1008 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 1.056 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0812
  time to fit residues: 1.4437
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 95 optimal weight:    0.4980
   chunk 39 optimal weight:    8.9990
   chunk 97 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 17 optimal weight:    0.3980
   chunk 83 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 411 ASN
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 572 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.197285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.166992 restraints weight = 14150.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.4074 rms_B_bonded: 2.49
r_work: 0.3994 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6883
moved from start:          0.3870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9490  Z= 0.162
  Angle     :  0.540   7.494  12842  Z= 0.283
  Chirality :  0.038   0.138   1506
  Planarity :  0.004   0.048   1630
  Dihedral  :  3.828  15.450   1298
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 22.22 %
    Favored  : 77.38 %
  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:  0.87 (0.25), residues: 1196
  helix:  2.03 (0.19), residues: 734
  sheet:  0.62 (0.60), residues: 68
  loop : -2.40 (0.27), residues: 394
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1990.19 seconds
wall clock time: 36 minutes 49.99 seconds (2209.99 seconds total)