Starting phenix.real_space_refine
on Wed Feb 14 02:33:56 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i39_35146/02_2024/8i39_35146_trim_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i39_35146/02_2024/8i39_35146.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i39_35146/02_2024/8i39_35146.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i39_35146/02_2024/8i39_35146.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i39_35146/02_2024/8i39_35146_trim_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i39_35146/02_2024/8i39_35146_trim_updated.pdb"
  }
  resolution = 2.85
  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=   0.000 sd=   0.184
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      50      5.16       5
     C    5495      2.51       5
     N    1398      2.21       5
     O    1470      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE   42": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A TYR   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   96": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  144": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  195": "OE1" <-> "OE2"
    Residue "A PHE  272": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  288": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  298": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  315": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  412": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  441": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  442": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  446": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  453": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  466": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  475": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  480": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  481": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  492": "OE1" <-> "OE2"
    Residue "A PHE  499": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  516": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  526": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  564": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  583": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  586": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  598": "OE1" <-> "OE2"
    Residue "A GLU  627": "OE1" <-> "OE2"
    Residue "A GLU  628": "OE1" <-> "OE2"
    Residue "A ASP  632": "OD1" <-> "OD2"
    Residue "A TYR  654": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  659": "NH1" <-> "NH2"
    Residue "B PHE   42": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP   44": "OD1" <-> "OD2"
    Residue "B TYR   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   96": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  144": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  195": "OE1" <-> "OE2"
    Residue "B PHE  272": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  288": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  298": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  315": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  412": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  441": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  442": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  446": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  453": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  466": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  475": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  480": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  481": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  492": "OE1" <-> "OE2"
    Residue "B PHE  499": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  516": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  526": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  564": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  583": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  586": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  598": "OE1" <-> "OE2"
    Residue "B GLU  627": "OE1" <-> "OE2"
    Residue "B GLU  628": "OE1" <-> "OE2"
    Residue "B ASP  632": "OD1" <-> "OD2"
    Residue "B TYR  654": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  659": "NH1" <-> "NH2"
  Time to flip residues: 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 8413
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 538, 4197
          Classifications: {'peptide': 538}
          Link IDs: {'PTRANS': 17, 'TRANS': 520}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 4197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 538, 4197
          Classifications: {'peptide': 538}
          Link IDs: {'PTRANS': 17, 'TRANS': 520}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 19
          Unusual residues: {'A8S': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.02, per 1000 atoms: 0.60
  Number of scatterers: 8413
  At special positions: 0
  Unit cell: (77.35, 103.53, 119, 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      50     16.00
     O    1470      8.00
     N    1398      7.00
     C    5495      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: 3.06
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1980

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      50 helices and 2 sheets defined
      42.2% alpha, 4.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 107 through 114
      removed outlier: 4.118A  pdb=" N   ALA A 113 " --> pdb=" O   THR A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 168
      removed outlier: 3.595A  pdb=" N   LEU A 161 " --> pdb=" O   VAL A 157 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL A 164 " --> pdb=" O   THR A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 188
    Processing helix  chain 'A' and resid 192 through 194
      No H-bonds generated for 'chain 'A' and resid 192 through 194'
    Processing helix  chain 'A' and resid 211 through 218
      removed outlier: 3.618A  pdb=" N   SER A 216 " --> pdb=" O   ARG A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 254
      removed outlier: 3.809A  pdb=" N   VAL A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU A 249 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ALA A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 273
      removed outlier: 3.543A  pdb=" N   GLN A 273 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 269 through 273'
    Processing helix  chain 'A' and resid 293 through 301
      removed outlier: 4.280A  pdb=" N   ALA A 297 " --> pdb=" O   ARG A 293 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   GLU A 300 " --> pdb=" O   MET A 296 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   SER A 301 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 321
    Processing helix  chain 'A' and resid 338 through 343
      removed outlier: 3.634A  pdb=" N   THR A 343 " --> pdb=" O   GLN A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 398
      removed outlier: 3.961A  pdb=" N   PHE A 387 " --> pdb=" O   ILE A 383 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   CYS A 391 " --> pdb=" O   PHE A 387 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU A 397 " --> pdb=" O   LEU A 393 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LEU A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 402
      No H-bonds generated for 'chain 'A' and resid 400 through 402'
    Processing helix  chain 'A' and resid 412 through 415
      No H-bonds generated for 'chain 'A' and resid 412 through 415'
    Processing helix  chain 'A' and resid 417 through 420
      No H-bonds generated for 'chain 'A' and resid 417 through 420'
    Processing helix  chain 'A' and resid 433 through 436
      No H-bonds generated for 'chain 'A' and resid 433 through 436'
    Processing helix  chain 'A' and resid 439 through 454
      removed outlier: 3.914A  pdb=" N   GLY A 448 " --> pdb=" O   SER A 444 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
    Processing helix  chain 'A' and resid 460 through 471
      removed outlier: 5.289A  pdb=" N   ALA A 464 " --> pdb=" O   GLN A 461 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE A 465 " --> pdb=" O   GLU A 462 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   PHE A 466 " --> pdb=" O   ARG A 463 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   THR A 467 " --> pdb=" O   ALA A 464 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ARG A 468 " --> pdb=" O   ILE A 465 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ARG A 470 " --> pdb=" O   THR A 467 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ALA A 471 " --> pdb=" O   ARG A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 491
      removed outlier: 4.031A  pdb=" N   SER A 490 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   MET A 491 " --> pdb=" O   GLY A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 500
      removed outlier: 3.524A  pdb=" N   SER A 498 " --> pdb=" O   VAL A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 540
      removed outlier: 3.874A  pdb=" N   LEU A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 550
      No H-bonds generated for 'chain 'A' and resid 547 through 550'
    Processing helix  chain 'A' and resid 554 through 562
      removed outlier: 3.614A  pdb=" N   THR A 561 " --> pdb=" O   ALA A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 577
      No H-bonds generated for 'chain 'A' and resid 575 through 577'
    Processing helix  chain 'A' and resid 582 through 593
      removed outlier: 3.510A  pdb=" N   GLN A 593 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 657
      removed outlier: 3.576A  pdb=" N   ALA A 653 " --> pdb=" O   TYR A 649 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 114
      removed outlier: 4.118A  pdb=" N   ALA B 113 " --> pdb=" O   THR B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 168
      removed outlier: 3.595A  pdb=" N   LEU B 161 " --> pdb=" O   VAL B 157 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL B 164 " --> pdb=" O   THR B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 188
    Processing helix  chain 'B' and resid 192 through 194
      No H-bonds generated for 'chain 'B' and resid 192 through 194'
    Processing helix  chain 'B' and resid 211 through 218
      removed outlier: 3.618A  pdb=" N   SER B 216 " --> pdb=" O   ARG B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 254
      removed outlier: 3.809A  pdb=" N   VAL B 246 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU B 249 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ALA B 253 " --> pdb=" O   LEU B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 273
      removed outlier: 3.542A  pdb=" N   GLN B 273 " --> pdb=" O   SER B 269 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 269 through 273'
    Processing helix  chain 'B' and resid 293 through 301
      removed outlier: 4.279A  pdb=" N   ALA B 297 " --> pdb=" O   ARG B 293 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   GLU B 300 " --> pdb=" O   MET B 296 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   SER B 301 " --> pdb=" O   ALA B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 321
    Processing helix  chain 'B' and resid 338 through 343
      removed outlier: 3.634A  pdb=" N   THR B 343 " --> pdb=" O   GLN B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 398
      removed outlier: 3.961A  pdb=" N   PHE B 387 " --> pdb=" O   ILE B 383 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   CYS B 391 " --> pdb=" O   PHE B 387 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU B 397 " --> pdb=" O   LEU B 393 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LEU B 398 " --> pdb=" O   LEU B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 402
      No H-bonds generated for 'chain 'B' and resid 400 through 402'
    Processing helix  chain 'B' and resid 412 through 415
      No H-bonds generated for 'chain 'B' and resid 412 through 415'
    Processing helix  chain 'B' and resid 417 through 420
      No H-bonds generated for 'chain 'B' and resid 417 through 420'
    Processing helix  chain 'B' and resid 433 through 436
      No H-bonds generated for 'chain 'B' and resid 433 through 436'
    Processing helix  chain 'B' and resid 439 through 454
      removed outlier: 3.914A  pdb=" N   GLY B 448 " --> pdb=" O   SER B 444 " (cutoff:3.500A)
      Proline residue:  B 451  - end of helix
    Processing helix  chain 'B' and resid 460 through 471
      removed outlier: 5.289A  pdb=" N   ALA B 464 " --> pdb=" O   GLN B 461 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE B 465 " --> pdb=" O   GLU B 462 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   PHE B 466 " --> pdb=" O   ARG B 463 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   THR B 467 " --> pdb=" O   ALA B 464 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ARG B 468 " --> pdb=" O   ILE B 465 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ARG B 470 " --> pdb=" O   THR B 467 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ALA B 471 " --> pdb=" O   ARG B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 478 through 491
      removed outlier: 4.031A  pdb=" N   SER B 490 " --> pdb=" O   LEU B 486 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   MET B 491 " --> pdb=" O   GLY B 487 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 494 through 500
      removed outlier: 3.524A  pdb=" N   SER B 498 " --> pdb=" O   VAL B 494 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 540
      removed outlier: 3.875A  pdb=" N   LEU B 533 " --> pdb=" O   ALA B 529 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 547 through 550
      No H-bonds generated for 'chain 'B' and resid 547 through 550'
    Processing helix  chain 'B' and resid 554 through 562
      removed outlier: 3.614A  pdb=" N   THR B 561 " --> pdb=" O   ALA B 557 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 575 through 577
      No H-bonds generated for 'chain 'B' and resid 575 through 577'
    Processing helix  chain 'B' and resid 582 through 593
      removed outlier: 3.510A  pdb=" N   GLN B 593 " --> pdb=" O   LEU B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 657
      removed outlier: 3.576A  pdb=" N   ALA B 653 " --> pdb=" O   TYR B 649 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 288 through 291
      removed outlier: 6.263A  pdb=" N   VAL A 260 " --> pdb=" O   MET A  97 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   VAL A  99 " --> pdb=" O   VAL A 260 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   THR A 262 " --> pdb=" O   VAL A  99 " (cutoff:3.500A)
      removed outlier: 8.492A  pdb=" N   GLY A 101 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   SER A 263 " --> pdb=" O   LEU A 230 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 288 through 291
      removed outlier: 6.262A  pdb=" N   VAL B 260 " --> pdb=" O   MET B  97 " (cutoff:3.500A)
      removed outlier: 7.587A  pdb=" N   VAL B  99 " --> pdb=" O   VAL B 260 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   THR B 262 " --> pdb=" O   VAL B  99 " (cutoff:3.500A)
      removed outlier: 8.491A  pdb=" N   GLY B 101 " --> pdb=" O   THR B 262 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   SER B 263 " --> pdb=" O   LEU B 230 " (cutoff:3.500A)

    226 hydrogen bonds defined for protein.
    654 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: 2.14

  Time building geometry restraints manager: 3.34 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1279
        1.30 -     1.42: 2251
        1.42 -     1.55: 4961
        1.55 -     1.68: 12
        1.68 -     1.81: 84
  Bond restraints: 8587
  Sorted by residual:
  bond pdb=" C1  A8S B 701 "
       pdb=" O11 A8S B 701 "
    ideal  model  delta    sigma   weight residual
    1.250  1.167  0.083 2.00e-02 2.50e+03 1.70e+01
  bond pdb=" C3  A8S B 701 "
       pdb=" C4  A8S B 701 "
    ideal  model  delta    sigma   weight residual
    1.463  1.381  0.082 2.00e-02 2.50e+03 1.68e+01
  bond pdb=" C1  A8S B 701 "
       pdb=" O12 A8S B 701 "
    ideal  model  delta    sigma   weight residual
    1.249  1.173  0.076 2.00e-02 2.50e+03 1.45e+01
  bond pdb=" C1  A8S B 701 "
       pdb=" C2  A8S B 701 "
    ideal  model  delta    sigma   weight residual
    1.512  1.457  0.055 2.00e-02 2.50e+03 7.63e+00
  bond pdb=" CB  GLU A 183 "
       pdb=" CG  GLU A 183 "
    ideal  model  delta    sigma   weight residual
    1.520  1.595 -0.075 3.00e-02 1.11e+03 6.29e+00
  ... (remaining 8582 not shown)

  Histogram of bond angle deviations from ideal:
       99.57 -   106.48: 195
      106.48 -   113.39: 4819
      113.39 -   120.29: 3356
      120.29 -   127.20: 3187
      127.20 -   134.11: 84
  Bond angle restraints: 11641
  Sorted by residual:
  angle pdb=" CA  GLU B 183 "
        pdb=" CB  GLU B 183 "
        pdb=" CG  GLU B 183 "
      ideal   model   delta    sigma   weight residual
     114.10  128.78  -14.68 2.00e+00 2.50e-01 5.39e+01
  angle pdb=" CA  GLU A 183 "
        pdb=" CB  GLU A 183 "
        pdb=" CG  GLU A 183 "
      ideal   model   delta    sigma   weight residual
     114.10  128.74  -14.64 2.00e+00 2.50e-01 5.36e+01
  angle pdb=" CA  GLU A 188 "
        pdb=" CB  GLU A 188 "
        pdb=" CG  GLU A 188 "
      ideal   model   delta    sigma   weight residual
     114.10  127.95  -13.85 2.00e+00 2.50e-01 4.79e+01
  angle pdb=" CA  GLU B 188 "
        pdb=" CB  GLU B 188 "
        pdb=" CG  GLU B 188 "
      ideal   model   delta    sigma   weight residual
     114.10  127.94  -13.84 2.00e+00 2.50e-01 4.79e+01
  angle pdb=" N   HIS A 403 "
        pdb=" CA  HIS A 403 "
        pdb=" C   HIS A 403 "
      ideal   model   delta    sigma   weight residual
     114.04  105.48    8.56 1.24e+00 6.50e-01 4.77e+01
  ... (remaining 11636 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.95: 4722
       19.95 -    39.91: 275
       39.91 -    59.86: 40
       59.86 -    79.81: 9
       79.81 -    99.76: 12
  Dihedral angle restraints: 5058
    sinusoidal: 1976
      harmonic: 3082
  Sorted by residual:
  dihedral pdb=" CA  MET B 310 "
           pdb=" C   MET B 310 "
           pdb=" N   ASN B 311 "
           pdb=" CA  ASN B 311 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.46   23.54     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  MET A 310 "
           pdb=" C   MET A 310 "
           pdb=" N   ASN A 311 "
           pdb=" CA  ASN A 311 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.49   23.51     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CA  LYS A 133 "
           pdb=" C   LYS A 133 "
           pdb=" N   ILE A 134 "
           pdb=" CA  ILE A 134 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.72  -22.28     0      5.00e+00 4.00e-02 1.99e+01
  ... (remaining 5055 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1222
       0.073 -    0.146: 156
       0.146 -    0.219: 8
       0.219 -    0.292: 0
       0.292 -    0.364: 1
  Chirality restraints: 1387
  Sorted by residual:
  chirality pdb=" C7  A8S B 701 "
            pdb=" C12 A8S B 701 "
            pdb=" C8  A8S B 701 "
            pdb=" O7  A8S B 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.32   -0.36 2.00e-01 2.50e+01 3.32e+00
  chirality pdb=" CA  GLU A 188 "
            pdb=" N   GLU A 188 "
            pdb=" C   GLU A 188 "
            pdb=" CB  GLU A 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.83e-01
  chirality pdb=" CA  GLU B 188 "
            pdb=" N   GLU B 188 "
            pdb=" C   GLU B 188 "
            pdb=" CB  GLU B 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.81e-01
  ... (remaining 1384 not shown)

  Planarity restraints: 1424
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3  A8S B 701 "   -0.244 2.00e-02 2.50e+03   2.51e-01 6.31e+02
        pdb=" C4  A8S B 701 "    0.202 2.00e-02 2.50e+03
        pdb=" C5  A8S B 701 "    0.296 2.00e-02 2.50e+03
        pdb=" C7  A8S B 701 "   -0.254 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1  A8S B 701 "   -0.128 2.00e-02 2.50e+03   1.07e-01 1.42e+02
        pdb=" C2  A8S B 701 "    0.175 2.00e-02 2.50e+03
        pdb=" C3  A8S B 701 "    0.030 2.00e-02 2.50e+03
        pdb=" C4  A8S B 701 "    0.016 2.00e-02 2.50e+03
        pdb=" C6  A8S B 701 "   -0.094 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 450 "    0.045 5.00e-02 4.00e+02   6.74e-02 7.26e+00
        pdb=" N   PRO B 451 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO B 451 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 451 "    0.037 5.00e-02 4.00e+02
  ... (remaining 1421 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 144
        2.67 -     3.23: 8284
        3.23 -     3.79: 12012
        3.79 -     4.34: 19209
        4.34 -     4.90: 29650
  Nonbonded interactions: 69299
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 298 "
            pdb=" OG  SER B 301 "
     model   vdw
     2.116 2.440
  nonbonded pdb=" O   TYR A 298 "
            pdb=" OG  SER A 301 "
     model   vdw
     2.117 2.440
  nonbonded pdb=" O   PRO A 102 "
            pdb=" OG  SER A 105 "
     model   vdw
     2.136 2.440
  nonbonded pdb=" O   PRO B 102 "
            pdb=" OG  SER B 105 "
     model   vdw
     2.137 2.440
  nonbonded pdb=" OE2 GLU B 300 "
            pdb=" OG  SER B 305 "
     model   vdw
     2.209 2.440
  ... (remaining 69294 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' and resid 36 through 660)
}

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:             1.170
  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:          2.680
  Check model and map are aligned:         0.130
  Set scattering table:                    0.080
  Process input model:                     25.910
  Find NCS groups from input model:        0.460
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.083   8587  Z= 0.555
  Angle     :  0.901  14.682  11641  Z= 0.504
  Chirality :  0.050   0.364   1387
  Planarity :  0.009   0.251   1424
  Dihedral  : 14.167  99.764   3078
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 22.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  4.81 %
    Favored  : 94.97 %
  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: -5.71 (0.19), residues: 1056
  helix: -4.67 (0.10), residues: 572
  sheet: -2.41 (0.57), residues: 56
  loop : -2.36 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP A 426 
 HIS   0.011   0.003   HIS B 427 
 PHE   0.028   0.002   PHE B 499 
 TYR   0.027   0.003   TYR A 475 
 ARG   0.008   0.001   ARG B  48 

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 914 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 146
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 MET cc_start: 0.7579 (ttm) cc_final: 0.7282 (ttm)
REVERT: A  148 ASP cc_start: 0.7773 (m-30) cc_final: 0.7547 (m-30)
REVERT: A  180 ARG cc_start: 0.7258 (mtp180) cc_final: 0.6950 (mtm180)
REVERT: A  224 ASN cc_start: 0.7914 (t0) cc_final: 0.7490 (t0)
REVERT: A  227 LEU cc_start: 0.8199 (tp) cc_final: 0.7943 (tp)
REVERT: A  424 MET cc_start: 0.7713 (mmm) cc_final: 0.7447 (mmm)
REVERT: A  430 TYR cc_start: 0.7900 (p90) cc_final: 0.7597 (p90)
REVERT: A  469 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7494 (mt-10)
REVERT: A  474 MET cc_start: 0.8257 (ttt) cc_final: 0.7957 (ttt)
REVERT: A  475 TYR cc_start: 0.8743 (p90) cc_final: 0.8529 (p90)
REVERT: A  555 MET cc_start: 0.8615 (mmm) cc_final: 0.8270 (mmm)
REVERT: A  568 LYS cc_start: 0.7958 (mmtm) cc_final: 0.7568 (mmmt)
REVERT: B   97 MET cc_start: 0.7163 (ttm) cc_final: 0.6756 (ttm)
REVERT: B  139 LEU cc_start: 0.8547 (mt) cc_final: 0.8343 (tp)
REVERT: B  180 ARG cc_start: 0.7293 (mtp180) cc_final: 0.7017 (mtm180)
REVERT: B  270 ARG cc_start: 0.6542 (mtt180) cc_final: 0.6310 (mtt180)
REVERT: B  291 LYS cc_start: 0.7537 (mmmt) cc_final: 0.7067 (tptp)
REVERT: B  430 TYR cc_start: 0.7819 (p90) cc_final: 0.7342 (p90)
REVERT: B  474 MET cc_start: 0.8242 (ttt) cc_final: 0.7924 (ttt)
REVERT: B  506 MET cc_start: 0.7258 (mtp) cc_final: 0.7027 (mtp)
REVERT: B  545 LYS cc_start: 0.7742 (mptt) cc_final: 0.7504 (pttm)
REVERT: B  555 MET cc_start: 0.8237 (mmm) cc_final: 0.7888 (mmm)
REVERT: B  568 LYS cc_start: 0.8183 (mmtm) cc_final: 0.7812 (mmmt)
  outliers start: 2
  outliers final: 0
  residues processed: 148
  average time/residue: 1.3620
  time to fit residues: 213.3610
Evaluate side-chains
  114 residues out of total 914 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0060
   chunk 54 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 83 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 50 optimal weight:   10.0000
   chunk 61 optimal weight:    2.9990
   chunk 96 optimal weight:    0.0050
   overall best weight:    0.5210

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

Flipped N/Q/H residues before XYZ refinement:
A 130 ASN
A 219 HIS
A 321 ASN
A 454 ASN
B 130 ASN
B 219 HIS
B 321 ASN
B 325 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.1979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8587  Z= 0.158
  Angle     :  0.586   5.286  11641  Z= 0.302
  Chirality :  0.040   0.131   1387
  Planarity :  0.005   0.036   1424
  Dihedral  :  6.628  43.355   1188
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  :  9.19 %
    Favored  : 88.84 %
  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: -4.62 (0.22), residues: 1056
  helix: -3.38 (0.15), residues: 616
  sheet: -2.25 (0.54), residues: 80
  loop : -2.20 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 447 
 HIS   0.005   0.001   HIS B 395 
 PHE   0.022   0.001   PHE A 144 
 TYR   0.018   0.001   TYR B 475 
 ARG   0.006   0.000   ARG B 293 

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 914 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 145
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 MET cc_start: 0.7473 (ttm) cc_final: 0.7253 (ttm)
REVERT: A  232 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7205 (mt-10)
REVERT: A  291 LYS cc_start: 0.7294 (mmmt) cc_final: 0.6099 (ttpp)
REVERT: A  469 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7320 (mt-10)
REVERT: A  474 MET cc_start: 0.7990 (ttt) cc_final: 0.7679 (ttt)
REVERT: A  555 MET cc_start: 0.8386 (mmm) cc_final: 0.8025 (mmm)
REVERT: B  139 LEU cc_start: 0.8748 (mt) cc_final: 0.8440 (tp)
REVERT: B  158 ARG cc_start: 0.7411 (ttp80) cc_final: 0.7172 (ttp80)
REVERT: B  291 LYS cc_start: 0.7541 (mmmt) cc_final: 0.7109 (tptp)
REVERT: B  395 HIS cc_start: 0.7555 (t-170) cc_final: 0.6879 (m90)
REVERT: B  474 MET cc_start: 0.7877 (ttt) cc_final: 0.7602 (ttp)
REVERT: B  505 TRP cc_start: 0.7997 (m100) cc_final: 0.7641 (m100)
REVERT: B  555 MET cc_start: 0.8026 (mmm) cc_final: 0.7730 (mmm)
REVERT: B  658 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7188 (mtm180)
  outliers start: 18
  outliers final: 6
  residues processed: 155
  average time/residue: 1.2151
  time to fit residues: 200.4214
Evaluate side-chains
  136 residues out of total 914 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 128
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  388 SER
Chi-restraints excluded: chain A residue  571 SER
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  658 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 80 optimal weight:   20.0000
   chunk 65 optimal weight:    0.0870
   chunk 26 optimal weight:   10.0000
   chunk 96 optimal weight:    0.7980
   chunk 104 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0270
   chunk 95 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   chunk 77 optimal weight:    0.0020
   overall best weight:    0.3024

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

Flipped N/Q/H residues before XYZ refinement:
B 454 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   8587  Z= 0.115
  Angle     :  0.506   5.658  11641  Z= 0.259
  Chirality :  0.038   0.147   1387
  Planarity :  0.004   0.031   1424
  Dihedral  :  4.862  24.056   1188
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 11.82 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.61 (0.23), residues: 1056
  helix: -2.34 (0.18), residues: 610
  sheet: -1.73 (0.55), residues: 80
  loop : -2.29 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 447 
 HIS   0.002   0.001   HIS A 427 
 PHE   0.021   0.001   PHE A 144 
 TYR   0.017   0.001   TYR A 475 
 ARG   0.007   0.000   ARG B 293 

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 914 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 136
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 GLU cc_start: 0.6180 (tt0) cc_final: 0.5942 (tt0)
REVERT: A  188 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7712 (pp20)
REVERT: A  280 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6759 (mm)
REVERT: A  291 LYS cc_start: 0.7066 (mmmt) cc_final: 0.5930 (ttpp)
REVERT: A  469 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7310 (mt-10)
REVERT: A  505 TRP cc_start: 0.7910 (m100) cc_final: 0.7662 (m100)
REVERT: A  555 MET cc_start: 0.8305 (mmm) cc_final: 0.8041 (mmp)
REVERT: B  232 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6853 (mp0)
REVERT: B  291 LYS cc_start: 0.7307 (mmmt) cc_final: 0.6921 (tptp)
REVERT: B  395 HIS cc_start: 0.7487 (t-170) cc_final: 0.6774 (m90)
REVERT: B  505 TRP cc_start: 0.7968 (m100) cc_final: 0.7726 (m100)
  outliers start: 24
  outliers final: 7
  residues processed: 151
  average time/residue: 1.1890
  time to fit residues: 191.4723
Evaluate side-chains
  130 residues out of total 914 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 GLU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  388 SER
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  569 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 96 optimal weight:    0.7980
   chunk 102 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 27 optimal weight:   20.0000
   chunk 85 optimal weight:    1.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8587  Z= 0.249
  Angle     :  0.568   7.629  11641  Z= 0.287
  Chirality :  0.042   0.149   1387
  Planarity :  0.004   0.032   1424
  Dihedral  :  5.047  29.071   1188
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 14.11 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.11 (0.24), residues: 1056
  helix: -1.98 (0.19), residues: 606
  sheet: -1.44 (0.54), residues: 80
  loop : -2.01 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 426 
 HIS   0.005   0.001   HIS A 427 
 PHE   0.024   0.002   PHE A 144 
 TYR   0.025   0.002   TYR B 475 
 ARG   0.005   0.000   ARG B 158 

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 914 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 123
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 ASP cc_start: 0.7657 (t0) cc_final: 0.6495 (p0)
REVERT: A  232 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7124 (mt-10)
REVERT: A  280 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6823 (mm)
REVERT: A  291 LYS cc_start: 0.7423 (mmmt) cc_final: 0.7109 (tptp)
REVERT: A  469 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7166 (mt-10)
REVERT: A  555 MET cc_start: 0.8274 (mmm) cc_final: 0.8041 (mmm)
REVERT: A  654 TYR cc_start: 0.8165 (t80) cc_final: 0.7922 (t80)
REVERT: B  136 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7566 (mmmm)
REVERT: B  158 ARG cc_start: 0.7469 (ttp80) cc_final: 0.7231 (ttp80)
REVERT: B  232 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7087 (mp0)
REVERT: B  291 LYS cc_start: 0.7477 (mmmt) cc_final: 0.7151 (tptp)
REVERT: B  387 PHE cc_start: 0.7789 (m-80) cc_final: 0.7460 (m-80)
REVERT: B  395 HIS cc_start: 0.7530 (t-170) cc_final: 0.6842 (m90)
REVERT: B  505 TRP cc_start: 0.8077 (m100) cc_final: 0.7728 (m100)
  outliers start: 30
  outliers final: 15
  residues processed: 143
  average time/residue: 1.2098
  time to fit residues: 184.2731
Evaluate side-chains
  135 residues out of total 914 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  388 SER
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain B residue  136 LYS
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  188 GLU
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  569 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 58 optimal weight:    8.9990
   chunk 1 optimal weight:    8.9990
   chunk 76 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   chunk 87 optimal weight:    0.6980
   chunk 70 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    0.6980
   chunk 91 optimal weight:    3.9990
   chunk 25 optimal weight:    9.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.2961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8587  Z= 0.316
  Angle     :  0.605   6.850  11641  Z= 0.304
  Chirality :  0.044   0.144   1387
  Planarity :  0.004   0.033   1424
  Dihedral  :  5.157  33.302   1188
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 13.57 %
    Favored  : 81.40 %
  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: -2.95 (0.24), residues: 1056
  helix: -1.95 (0.19), residues: 610
  sheet: -1.42 (0.53), residues: 80
  loop : -1.74 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 426 
 HIS   0.005   0.002   HIS A 403 
 PHE   0.027   0.002   PHE A 144 
 TYR   0.038   0.002   TYR A 475 
 ARG   0.006   0.000   ARG B 293 

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 914 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 119
  time to evaluate  : 0.852 
Fit side-chains
REVERT: A   95 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6316 (tt0)
REVERT: A  148 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7284 (m-30)
REVERT: A  183 GLU cc_start: 0.7244 (pp20) cc_final: 0.6922 (pt0)
REVERT: A  280 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6856 (mm)
REVERT: A  287 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7247 (mp)
REVERT: A  291 LYS cc_start: 0.7532 (mmmt) cc_final: 0.7227 (tptp)
REVERT: A  555 MET cc_start: 0.8297 (mmm) cc_final: 0.8046 (mmp)
REVERT: A  654 TYR cc_start: 0.8235 (t80) cc_final: 0.7986 (t80)
REVERT: B   90 MET cc_start: 0.8301 (tmm) cc_final: 0.7820 (tmt)
REVERT: B  287 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6593 (mp)
REVERT: B  291 LYS cc_start: 0.7547 (mmmt) cc_final: 0.7117 (tptp)
REVERT: B  395 HIS cc_start: 0.7603 (t-170) cc_final: 0.6881 (m90)
  outliers start: 46
  outliers final: 20
  residues processed: 152
  average time/residue: 1.0760
  time to fit residues: 175.1768
Evaluate side-chains
  142 residues out of total 914 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  148 ASP
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  388 SER
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  188 GLU
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  569 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 20 optimal weight:    0.4980
   chunk 60 optimal weight:   10.0000
   chunk 25 optimal weight:   10.0000
   chunk 102 optimal weight:    0.5980
   chunk 85 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   chunk 98 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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: 0.7384
moved from start:          0.3322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8587  Z= 0.163
  Angle     :  0.542   6.988  11641  Z= 0.273
  Chirality :  0.040   0.145   1387
  Planarity :  0.004   0.058   1424
  Dihedral  :  4.527  23.784   1188
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 15.32 %
    Favored  : 80.85 %
  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: -2.44 (0.25), residues: 1056
  helix: -1.48 (0.20), residues: 602
  sheet: -1.19 (0.53), residues: 80
  loop : -1.66 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 447 
 HIS   0.003   0.001   HIS B 434 
 PHE   0.020   0.001   PHE B  42 
 TYR   0.032   0.001   TYR A 475 
 ARG   0.016   0.000   ARG A 244 

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 914 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 120
  time to evaluate  : 0.942 
Fit side-chains
REVERT: A  280 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6843 (mm)
REVERT: A  287 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7151 (mp)
REVERT: A  291 LYS cc_start: 0.7445 (mmmt) cc_final: 0.7156 (tptp)
REVERT: A  348 LEU cc_start: 0.4717 (OUTLIER) cc_final: 0.4360 (tp)
REVERT: A  395 HIS cc_start: 0.7634 (t70) cc_final: 0.6879 (m90)
REVERT: A  430 TYR cc_start: 0.7765 (p90) cc_final: 0.7529 (p90)
REVERT: A  505 TRP cc_start: 0.8066 (m100) cc_final: 0.7747 (m100)
REVERT: B  232 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6718 (mt-10)
REVERT: B  287 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6565 (mp)
REVERT: B  291 LYS cc_start: 0.7429 (mmmt) cc_final: 0.7024 (tptp)
REVERT: B  395 HIS cc_start: 0.7546 (t-170) cc_final: 0.6875 (m90)
REVERT: B  469 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7030 (mt-10)
REVERT: B  474 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6999 (ttm)
REVERT: B  505 TRP cc_start: 0.8070 (m100) cc_final: 0.7763 (m100)
REVERT: B  635 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7785 (ttt)
  outliers start: 35
  outliers final: 14
  residues processed: 140
  average time/residue: 1.1779
  time to fit residues: 176.1539
Evaluate side-chains
  137 residues out of total 914 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  388 SER
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain B residue   92 SER
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  474 MET
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  569 VAL
Chi-restraints excluded: chain B residue  635 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 58 optimal weight:    9.9990
   chunk 74 optimal weight:    9.9990
   chunk 86 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 102 optimal weight:    6.9990
   chunk 63 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0670
   overall best weight:    1.5324

-------------------------------------------------------------------------------
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: 0.7430
moved from start:          0.3308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8587  Z= 0.277
  Angle     :  0.601   7.536  11641  Z= 0.300
  Chirality :  0.043   0.144   1387
  Planarity :  0.005   0.070   1424
  Dihedral  :  4.712  30.200   1188
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 16.41 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.40 (0.25), residues: 1056
  helix: -1.46 (0.20), residues: 604
  sheet: -1.07 (0.52), residues: 80
  loop : -1.64 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 426 
 HIS   0.004   0.001   HIS B 434 
 PHE   0.023   0.002   PHE B  42 
 TYR   0.041   0.002   TYR A 475 
 ARG   0.016   0.001   ARG B 244 

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 914 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 111
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
REVERT: A  237 LEU cc_start: 0.8625 (mt) cc_final: 0.8289 (tp)
REVERT: A  280 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6830 (mm)
REVERT: A  287 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7138 (mp)
REVERT: A  291 LYS cc_start: 0.7513 (mmmt) cc_final: 0.7241 (tptp)
REVERT: A  348 LEU cc_start: 0.4495 (OUTLIER) cc_final: 0.4154 (tp)
REVERT: A  505 TRP cc_start: 0.8063 (m100) cc_final: 0.7716 (m100)
REVERT: A  654 TYR cc_start: 0.8218 (t80) cc_final: 0.7999 (t80)
REVERT: B  287 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6655 (mp)
REVERT: B  291 LYS cc_start: 0.7499 (mmmt) cc_final: 0.7037 (tptp)
REVERT: B  395 HIS cc_start: 0.7570 (t-170) cc_final: 0.6868 (m90)
REVERT: B  505 TRP cc_start: 0.8048 (m100) cc_final: 0.7701 (m100)
  outliers start: 37
  outliers final: 21
  residues processed: 139
  average time/residue: 1.1293
  time to fit residues: 167.7568
Evaluate side-chains
  138 residues out of total 914 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  388 SER
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain A residue  571 SER
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain B residue   92 SER
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  569 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 20 optimal weight:    0.2980
   chunk 19 optimal weight:    7.9990
   chunk 64 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 50 optimal weight:    8.9990
   chunk 9 optimal weight:    3.9990
   chunk 80 optimal weight:    0.4980
   chunk 92 optimal weight:    0.7980
   chunk 97 optimal weight:    0.3980
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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: 0.7366
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8587  Z= 0.143
  Angle     :  0.525   7.836  11641  Z= 0.263
  Chirality :  0.039   0.143   1387
  Planarity :  0.004   0.049   1424
  Dihedral  :  4.263  25.176   1188
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 16.41 %
    Favored  : 79.87 %
  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: -1.82 (0.26), residues: 1056
  helix: -0.99 (0.21), residues: 600
  sheet: -0.87 (0.54), residues: 80
  loop : -1.39 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 447 
 HIS   0.003   0.001   HIS B 434 
 PHE   0.016   0.001   PHE A 275 
 TYR   0.033   0.001   TYR A 475 
 ARG   0.012   0.000   ARG B 293 

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 914 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 120
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8274 (tmm) cc_final: 0.7801 (tmt)
REVERT: A  232 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7006 (mt-10)
REVERT: A  237 LEU cc_start: 0.8638 (mt) cc_final: 0.8249 (tp)
REVERT: A  280 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6857 (mm)
REVERT: A  287 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7000 (mp)
REVERT: A  291 LYS cc_start: 0.7193 (mmmt) cc_final: 0.6918 (tptp)
REVERT: A  395 HIS cc_start: 0.7623 (t70) cc_final: 0.6879 (m90)
REVERT: A  469 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6998 (mt-10)
REVERT: A  505 TRP cc_start: 0.8045 (m100) cc_final: 0.7735 (m100)
REVERT: B  287 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6606 (mp)
REVERT: B  291 LYS cc_start: 0.7419 (mmmt) cc_final: 0.7069 (tptp)
REVERT: B  395 HIS cc_start: 0.7545 (t-170) cc_final: 0.6866 (m90)
REVERT: B  469 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6977 (mt-10)
REVERT: B  474 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6890 (ttm)
REVERT: B  505 TRP cc_start: 0.8035 (m100) cc_final: 0.7728 (m100)
REVERT: B  542 MET cc_start: 0.7908 (mmt) cc_final: 0.7569 (mmm)
  outliers start: 34
  outliers final: 16
  residues processed: 142
  average time/residue: 1.1017
  time to fit residues: 167.9131
Evaluate side-chains
  138 residues out of total 914 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  388 SER
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  474 MET
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  569 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:    0.5980
   chunk 97 optimal weight:    3.9990
   chunk 57 optimal weight:    6.9990
   chunk 41 optimal weight:    0.7980
   chunk 74 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 94 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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: 0.7405
moved from start:          0.3517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8587  Z= 0.235
  Angle     :  0.568   8.879  11641  Z= 0.283
  Chirality :  0.042   0.145   1387
  Planarity :  0.004   0.054   1424
  Dihedral  :  4.452  31.858   1188
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 16.85 %
    Favored  : 79.87 %
  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: -1.82 (0.26), residues: 1056
  helix: -0.98 (0.21), residues: 602
  sheet: -0.86 (0.54), residues: 80
  loop : -1.38 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 447 
 HIS   0.004   0.001   HIS B 434 
 PHE   0.021   0.002   PHE B  42 
 TYR   0.039   0.002   TYR A 475 
 ARG   0.013   0.001   ARG B 293 

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 914 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 113
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8248 (tmm) cc_final: 0.7756 (tmt)
REVERT: A  232 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7094 (mt-10)
REVERT: A  237 LEU cc_start: 0.8655 (mt) cc_final: 0.8254 (tp)
REVERT: A  280 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6858 (mm)
REVERT: A  287 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7077 (mp)
REVERT: A  291 LYS cc_start: 0.7450 (mmmt) cc_final: 0.7175 (tptp)
REVERT: A  395 HIS cc_start: 0.7659 (t70) cc_final: 0.6888 (m90)
REVERT: A  505 TRP cc_start: 0.8060 (m100) cc_final: 0.7735 (m100)
REVERT: A  542 MET cc_start: 0.7925 (mmt) cc_final: 0.7588 (mmt)
REVERT: A  654 TYR cc_start: 0.8214 (t80) cc_final: 0.8006 (t80)
REVERT: B  183 GLU cc_start: 0.7154 (pp20) cc_final: 0.6917 (pp20)
REVERT: B  287 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6690 (mp)
REVERT: B  291 LYS cc_start: 0.7457 (mmmt) cc_final: 0.7092 (tptp)
REVERT: B  395 HIS cc_start: 0.7591 (t-170) cc_final: 0.6866 (m90)
REVERT: B  430 TYR cc_start: 0.7773 (p90) cc_final: 0.7527 (p90)
REVERT: B  505 TRP cc_start: 0.8044 (m100) cc_final: 0.7724 (m100)
REVERT: B  542 MET cc_start: 0.8033 (mmt) cc_final: 0.7595 (mmt)
  outliers start: 30
  outliers final: 19
  residues processed: 135
  average time/residue: 1.1247
  time to fit residues: 162.3542
Evaluate side-chains
  134 residues out of total 914 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  388 SER
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  432 ASP
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  569 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 105 optimal weight:    0.0970
   chunk 97 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 66 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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: 0.7382
moved from start:          0.3625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8587  Z= 0.188
  Angle     :  0.550   9.351  11641  Z= 0.273
  Chirality :  0.041   0.141   1387
  Planarity :  0.004   0.052   1424
  Dihedral  :  4.302  29.156   1188
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 17.51 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.26), residues: 1056
  helix: -0.81 (0.21), residues: 604
  sheet: -0.87 (0.54), residues: 80
  loop : -1.45 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 505 
 HIS   0.003   0.001   HIS B 434 
 PHE   0.026   0.001   PHE A 275 
 TYR   0.037   0.002   TYR A 475 
 ARG   0.012   0.000   ARG B 293 

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 914 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7054 (mt-10)
REVERT: A  237 LEU cc_start: 0.8656 (mt) cc_final: 0.8240 (tp)
REVERT: A  280 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6851 (mm)
REVERT: A  287 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7059 (mp)
REVERT: A  291 LYS cc_start: 0.7307 (mmmt) cc_final: 0.7057 (tptp)
REVERT: A  395 HIS cc_start: 0.7641 (t70) cc_final: 0.6879 (m90)
REVERT: A  542 MET cc_start: 0.7982 (mmt) cc_final: 0.7595 (mmt)
REVERT: A  654 TYR cc_start: 0.8159 (t80) cc_final: 0.7876 (t80)
REVERT: B  183 GLU cc_start: 0.7217 (pp20) cc_final: 0.6963 (tt0)
REVERT: B  287 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6679 (mp)
REVERT: B  291 LYS cc_start: 0.7413 (mmmt) cc_final: 0.7051 (tptp)
REVERT: B  395 HIS cc_start: 0.7576 (t-170) cc_final: 0.6865 (m90)
REVERT: B  430 TYR cc_start: 0.7758 (p90) cc_final: 0.7456 (p90)
  outliers start: 26
  outliers final: 20
  residues processed: 138
  average time/residue: 1.1140
  time to fit residues: 164.5147
Evaluate side-chains
  137 residues out of total 914 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  388 SER
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain A residue  639 VAL
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  569 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 23 optimal weight:    7.9990
   chunk 84 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0670
   chunk 15 optimal weight:    0.9990
   chunk 73 optimal weight:    0.2980
   chunk 4 optimal weight:    7.9990
   overall best weight:    0.6720

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.182334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.118746 restraints weight = 8218.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.93
r_work: 0.3312 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.3713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8587  Z= 0.149
  Angle     :  0.515   7.131  11641  Z= 0.258
  Chirality :  0.039   0.140   1387
  Planarity :  0.004   0.050   1424
  Dihedral  :  4.062  22.630   1188
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.83 %
    Favored  : 79.21 %
  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: -1.38 (0.26), residues: 1056
  helix: -0.51 (0.22), residues: 602
  sheet: -0.83 (0.55), residues: 80
  loop : -1.40 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 434 
 PHE   0.026   0.001   PHE A 275 
 TYR   0.036   0.001   TYR A 475 
 ARG   0.012   0.000   ARG B 293 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3394.18 seconds
wall clock time: 60 minutes 57.77 seconds (3657.77 seconds total)