Starting phenix.real_space_refine
on Thu Feb 13 22:47:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vr1_32096/02_2025/7vr1_32096.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vr1_32096/02_2025/7vr1_32096.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/cci-nas-00/data/ceres_data/7vr1_32096/02_2025/7vr1_32096.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vr1_32096/02_2025/7vr1_32096.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vr1_32096/02_2025/7vr1_32096.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vr1_32096/02_2025/7vr1_32096.cif"
  }
  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=   0.004
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      42      5.16       5
     C    6110      2.51       5
     N    1668      2.21       5
     O    1702      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9522
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 4761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 598, 4761
          Classifications: {'peptide': 598}
          Link IDs: {'PTRANS': 21, 'TRANS': 576}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 4761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 598, 4761
          Classifications: {'peptide': 598}
          Link IDs: {'PTRANS': 21, 'TRANS': 576}
          Chain breaks: 2
  Time building chain proxies: 5.61, per 1000 atoms: 0.59
  Number of scatterers: 9522
  At special positions: 0
  Unit cell: (114.182, 73.5593, 146.021, 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      42     16.00
     O    1702      8.00
     N    1668      7.00
     C    6110      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  - 3.00
        Amino acid           : True  - 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: 2.25
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2244

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 5 sheets defined
      67.2% alpha, 2.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'B' and resid 70 through 83
      removed outlier: 3.784A  pdb=" N   LEU B  81 " --> pdb=" O   TRP B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 100
      removed outlier: 3.516A  pdb=" N   HIS B  97 " --> pdb=" O   LEU B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 123
      removed outlier: 3.641A  pdb=" N   PHE B 106 " --> pdb=" O   VAL B 102 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LEU B 107 " --> pdb=" O   SER B 103 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TYR B 110 " --> pdb=" O   PHE B 106 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ARG B 117 " --> pdb=" O   ARG B 113 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 140
    Processing helix  chain 'B' and resid 140 through 175
      removed outlier: 3.546A  pdb=" N   SER B 149 " --> pdb=" O   THR B 145 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ARG B 152 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ALA B 168 " --> pdb=" O   SER B 164 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ARG B 172 " --> pdb=" O   ALA B 168 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   LEU B 173 " --> pdb=" O   HIS B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 186
      removed outlier: 3.887A  pdb=" N   SER B 184 " --> pdb=" O   TYR B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 216
      removed outlier: 3.632A  pdb=" N   SER B 196 " --> pdb=" O   ASN B 192 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ASP B 200 " --> pdb=" O   SER B 196 " (cutoff:3.500A)
      removed outlier: 4.965A  pdb=" N   VAL B 201 " --> pdb=" O   LEU B 197 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   VAL B 202 " --> pdb=" O   THR B 198 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ALA B 203 " --> pdb=" O   GLU B 199 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ALA B 209 " --> pdb=" O   ALA B 205 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   HIS B 210 " --> pdb=" O   ALA B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 235
      removed outlier: 3.782A  pdb=" N   LEU B 230 " --> pdb=" O   SER B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 261
      removed outlier: 3.859A  pdb=" N   ALA B 245 " --> pdb=" O   ALA B 241 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ILE B 246 " --> pdb=" O   TRP B 242 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU B 258 " --> pdb=" O   THR B 254 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   PHE B 261 " --> pdb=" O   VAL B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 289
      removed outlier: 3.505A  pdb=" N   PHE B 265 " --> pdb=" O   PHE B 261 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   VAL B 286 " --> pdb=" O   MET B 282 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   VAL B 287 " --> pdb=" O   HIS B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 297
    Processing helix  chain 'B' and resid 298 through 337
      removed outlier: 3.561A  pdb=" N   SER B 309 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LEU B 313 " --> pdb=" O   SER B 309 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU B 319 " --> pdb=" O   SER B 315 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   TRP B 326 " --> pdb=" O   LEU B 322 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   TYR B 327 " --> pdb=" O   GLU B 323 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   MET B 329 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU B 334 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 353
      removed outlier: 3.654A  pdb=" N   MET B 346 " --> pdb=" O   SER B 342 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   VAL B 347 " --> pdb=" O   GLY B 343 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   VAL B 349 " --> pdb=" O   LEU B 345 " (cutoff:3.500A)
      Proline residue:  B 350  - end of helix
    Processing helix  chain 'B' and resid 361 through 371
      removed outlier: 3.719A  pdb=" N   LYS B 367 " --> pdb=" O   GLU B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 407
      removed outlier: 3.623A  pdb=" N   THR B 382 " --> pdb=" O   VAL B 378 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLU B 383 " --> pdb=" O   SER B 379 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   THR B 386 " --> pdb=" O   THR B 382 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ALA B 388 " --> pdb=" O   ALA B 384 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LEU B 392 " --> pdb=" O   ALA B 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 431
      removed outlier: 3.781A  pdb=" N   GLY B 414 " --> pdb=" O   THR B 410 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   MET B 422 " --> pdb=" O   ARG B 418 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLU B 427 " --> pdb=" O   PHE B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 535 through 539
    Processing helix  chain 'B' and resid 553 through 558
    Processing helix  chain 'B' and resid 575 through 584
      removed outlier: 3.747A  pdb=" N   ILE B 579 " --> pdb=" O   ASP B 575 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 592
      removed outlier: 3.922A  pdb=" N   LEU B 589 " --> pdb=" O   LEU B 585 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLN B 590 " --> pdb=" O   HIS B 586 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ARG B 591 " --> pdb=" O   HIS B 587 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 600 through 605
      removed outlier: 3.710A  pdb=" N   VAL B 604 " --> pdb=" O   ASP B 600 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU B 605 " --> pdb=" O   TRP B 601 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 600 through 605'
    Processing helix  chain 'B' and resid 606 through 622
      removed outlier: 3.577A  pdb=" N   GLN B 611 " --> pdb=" O   GLY B 607 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   MET B 618 " --> pdb=" O   GLY B 614 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE B 619 " --> pdb=" O   MET B 615 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   TYR B 620 " --> pdb=" O   ALA B 616 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   HIS B 621 " --> pdb=" O   ARG B 617 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG B 622 " --> pdb=" O   MET B 618 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 636 through 651
      removed outlier: 3.739A  pdb=" N   LYS B 642 " --> pdb=" O   ASP B 638 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 666
      removed outlier: 3.787A  pdb=" N   LYS B 665 " --> pdb=" O   SER B 662 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 685 through 688
      removed outlier: 4.328A  pdb=" N   ALA B 688 " --> pdb=" O   ASP B 685 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 685 through 688'
    Processing helix  chain 'B' and resid 689 through 695
      removed outlier: 3.572A  pdb=" N   THR B 693 " --> pdb=" O   ARG B 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 83
      removed outlier: 3.514A  pdb=" N   LEU A  81 " --> pdb=" O   TRP A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 123
      removed outlier: 3.622A  pdb=" N   GLY A  92 " --> pdb=" O   CYS A  88 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL A 123 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 175
      removed outlier: 3.612A  pdb=" N   GLN A 136 " --> pdb=" O   TRP A 132 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU A 142 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
      Proline residue:  A 143  - end of helix
      removed outlier: 3.523A  pdb=" N   ARG A 152 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ARG A 172 " --> pdb=" O   ALA A 168 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   LEU A 173 " --> pdb=" O   HIS A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 186
      removed outlier: 3.815A  pdb=" N   SER A 184 " --> pdb=" O   TYR A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 199
      removed outlier: 3.603A  pdb=" N   SER A 196 " --> pdb=" O   ASN A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 235
      removed outlier: 3.605A  pdb=" N   ALA A 209 " --> pdb=" O   ALA A 205 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   HIS A 210 " --> pdb=" O   ALA A 206 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   LYS A 217 " --> pdb=" O   SER A 213 " (cutoff:3.500A)
      Proline residue:  A 218  - end of helix
    Processing helix  chain 'A' and resid 241 through 260
      removed outlier: 4.195A  pdb=" N   ALA A 245 " --> pdb=" O   ALA A 241 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ILE A 246 " --> pdb=" O   TRP A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 289
      removed outlier: 3.705A  pdb=" N   PHE A 265 " --> pdb=" O   PHE A 261 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   VAL A 286 " --> pdb=" O   MET A 282 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   VAL A 287 " --> pdb=" O   HIS A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 297
    Processing helix  chain 'A' and resid 298 through 337
      removed outlier: 3.551A  pdb=" N   GLU A 302 " --> pdb=" O   GLY A 298 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   TRP A 326 " --> pdb=" O   LEU A 322 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   TYR A 327 " --> pdb=" O   GLU A 323 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   MET A 329 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 353
      removed outlier: 3.784A  pdb=" N   VAL A 347 " --> pdb=" O   GLY A 343 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL A 349 " --> pdb=" O   LEU A 345 " (cutoff:3.500A)
      Proline residue:  A 350  - end of helix
    Processing helix  chain 'A' and resid 363 through 372
      removed outlier: 3.809A  pdb=" N   LYS A 367 " --> pdb=" O   GLU A 363 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LEU A 370 " --> pdb=" O   LYS A 366 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   LYS A 372 " --> pdb=" O   ALA A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 406
      removed outlier: 3.576A  pdb=" N   ARG A 381 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   THR A 382 " --> pdb=" O   VAL A 378 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   GLU A 383 " --> pdb=" O   SER A 379 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   THR A 386 " --> pdb=" O   THR A 382 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ALA A 388 " --> pdb=" O   ALA A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 431
      removed outlier: 3.522A  pdb=" N   ARG A 431 " --> pdb=" O   GLU A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 537
      No H-bonds generated for 'chain 'A' and resid 535 through 537'
    Processing helix  chain 'A' and resid 553 through 558
    Processing helix  chain 'A' and resid 575 through 584
      removed outlier: 3.874A  pdb=" N   ILE A 579 " --> pdb=" O   ASP A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 622
      removed outlier: 3.581A  pdb=" N   GLN A 611 " --> pdb=" O   GLY A 607 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   MET A 615 " --> pdb=" O   GLN A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 650
      removed outlier: 3.898A  pdb=" N   LYS A 642 " --> pdb=" O   ASP A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 664
    Processing sheet with id=AA1, first strand: chain 'B' and resid 474 through 475
    Processing sheet with id=AA2, first strand: chain 'B' and resid 504 through 505
      removed outlier: 6.331A  pdb=" N   ALA B 626 " --> pdb=" O   LEU B 655 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   ILE B 657 " --> pdb=" O   ALA B 626 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   LEU B 628 " --> pdb=" O   ILE B 657 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 672 through 673
    Processing sheet with id=AA4, first strand: chain 'A' and resid 474 through 475
    Processing sheet with id=AA5, first strand: chain 'A' and resid 539 through 542
      removed outlier: 6.262A  pdb=" N   PHE A 540 " --> pdb=" O   LEU A 627 " (cutoff:3.500A)

    524 hydrogen bonds defined for protein.
    1542 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: 2.60

  Time building geometry restraints manager: 2.64 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: 3110
        1.34 -     1.46: 1706
        1.46 -     1.58: 4840
        1.58 -     1.70: 0
        1.70 -     1.81: 70
  Bond restraints: 9726
  Sorted by residual:
  bond pdb=" C   ARG B 622 "
       pdb=" O   ARG B 622 "
    ideal  model  delta    sigma   weight residual
    1.235  1.240 -0.005 4.70e-03 4.53e+04 1.04e+00
  bond pdb=" CA  ILE A 558 "
       pdb=" CB  ILE A 558 "
    ideal  model  delta    sigma   weight residual
    1.540  1.527  0.013 1.36e-02 5.41e+03 9.55e-01
  bond pdb=" C   GLN B 472 "
       pdb=" N   GLY B 473 "
    ideal  model  delta    sigma   weight residual
    1.322  1.333 -0.011 1.20e-02 6.94e+03 8.51e-01
  bond pdb=" CG  GLU B 471 "
       pdb=" CD  GLU B 471 "
    ideal  model  delta    sigma   weight residual
    1.516  1.496  0.020 2.50e-02 1.60e+03 6.15e-01
  bond pdb=" CB  MET A 548 "
       pdb=" CG  MET A 548 "
    ideal  model  delta    sigma   weight residual
    1.520  1.542 -0.022 3.00e-02 1.11e+03 5.49e-01
  ... (remaining 9721 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 12921
        1.56 -     3.13: 189
        3.13 -     4.69: 37
        4.69 -     6.25: 19
        6.25 -     7.81: 8
  Bond angle restraints: 13174
  Sorted by residual:
  angle pdb=" C   GLN B 177 "
        pdb=" CA  GLN B 177 "
        pdb=" CB  GLN B 177 "
      ideal   model   delta    sigma   weight residual
     110.42  116.01   -5.59 1.99e+00 2.53e-01 7.89e+00
  angle pdb=" CB  MET A 548 "
        pdb=" CG  MET A 548 "
        pdb=" SD  MET A 548 "
      ideal   model   delta    sigma   weight residual
     112.70  120.51   -7.81 3.00e+00 1.11e-01 6.78e+00
  angle pdb=" CB  MET B 548 "
        pdb=" CG  MET B 548 "
        pdb=" SD  MET B 548 "
      ideal   model   delta    sigma   weight residual
     112.70  119.83   -7.13 3.00e+00 1.11e-01 5.66e+00
  angle pdb=" N   GLU B 291 "
        pdb=" CA  GLU B 291 "
        pdb=" C   GLU B 291 "
      ideal   model   delta    sigma   weight residual
     113.72  110.23    3.49 1.52e+00 4.33e-01 5.28e+00
  angle pdb=" N   GLY A 500 "
        pdb=" CA  GLY A 500 "
        pdb=" C   GLY A 500 "
      ideal   model   delta    sigma   weight residual
     113.18  118.54   -5.36 2.37e+00 1.78e-01 5.12e+00
  ... (remaining 13169 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.27: 5139
       16.27 -    32.55: 526
       32.55 -    48.82: 136
       48.82 -    65.09: 10
       65.09 -    81.36: 9
  Dihedral angle restraints: 5820
    sinusoidal: 2338
      harmonic: 3482
  Sorted by residual:
  dihedral pdb=" CA  GLU B 471 "
           pdb=" C   GLU B 471 "
           pdb=" N   GLN B 472 "
           pdb=" CA  GLN B 472 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.21   29.79     0      5.00e+00 4.00e-02 3.55e+01
  dihedral pdb=" CA  TRP A 679 "
           pdb=" C   TRP A 679 "
           pdb=" N   LYS A 680 "
           pdb=" CA  LYS A 680 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.20   17.80     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  GLU A 499 "
           pdb=" C   GLU A 499 "
           pdb=" N   GLY A 500 "
           pdb=" CA  GLY A 500 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.27  -17.73     0      5.00e+00 4.00e-02 1.26e+01
  ... (remaining 5817 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1279
       0.057 -    0.113: 191
       0.113 -    0.170: 11
       0.170 -    0.226: 0
       0.226 -    0.283: 1
  Chirality restraints: 1482
  Sorted by residual:
  chirality pdb=" CB  ILE B 558 "
            pdb=" CA  ILE B 558 "
            pdb=" CG1 ILE B 558 "
            pdb=" CG2 ILE B 558 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" CA  ILE B 657 "
            pdb=" N   ILE B 657 "
            pdb=" C   ILE B 657 "
            pdb=" CB  ILE B 657 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.23e-01
  chirality pdb=" CA  PHE A 517 "
            pdb=" N   PHE A 517 "
            pdb=" C   PHE A 517 "
            pdb=" CB  PHE A 517 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.98e-01
  ... (remaining 1479 not shown)

  Planarity restraints: 1670
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 523 "   -0.006 2.00e-02 2.50e+03   1.23e-02 1.51e+00
        pdb=" C   LEU B 523 "    0.021 2.00e-02 2.50e+03
        pdb=" O   LEU B 523 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   TRP B 524 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 333 "    0.006 2.00e-02 2.50e+03   1.20e-02 1.45e+00
        pdb=" C   PHE A 333 "   -0.021 2.00e-02 2.50e+03
        pdb=" O   PHE A 333 "    0.008 2.00e-02 2.50e+03
        pdb=" N   LEU A 334 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 533 "   -0.020 5.00e-02 4.00e+02   2.96e-02 1.40e+00
        pdb=" N   PRO B 534 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO B 534 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 534 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 1667 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2114
        2.78 -     3.31: 9280
        3.31 -     3.84: 15127
        3.84 -     4.37: 17111
        4.37 -     4.90: 30172
  Nonbonded interactions: 73804
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B  90 "
            pdb=" OG  SER B 161 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OD1 ASP B 200 "
            pdb=" NH1 ARG B 418 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" NH2 ARG B 285 "
            pdb=" O   MET A 548 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" O   THR A 632 "
            pdb=" NH1 ARG A 660 "
     model   vdw
     2.307 3.120
  nonbonded pdb=" OE2 GLU A  90 "
            pdb=" OG  SER A 161 "
     model   vdw
     2.311 3.040
  ... (remaining 73799 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.05
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:             4.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     22.190
  Find NCS groups from input model:        0.300
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9726  Z= 0.173
  Angle     :  0.549   7.814  13174  Z= 0.276
  Chirality :  0.039   0.283   1482
  Planarity :  0.003   0.030   1670
  Dihedral  : 13.992  81.363   3576
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  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: -0.76 (0.26), residues: 1184
  helix:  0.49 (0.20), residues: 742
  sheet: -2.64 (0.56), residues: 86
  loop : -1.95 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 524 
 HIS   0.006   0.001   HIS B 283 
 PHE   0.019   0.001   PHE A 619 
 TYR   0.015   0.001   TYR B 532 
 ARG   0.004   0.000   ARG B 464 

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

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

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 1.081 
Fit side-chains
REVERT: B  598 MET cc_start: 0.7515 (mpp) cc_final: 0.7242 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1930
  time to fit residues: 31.1106
Evaluate side-chains
  83 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    0.0000
   chunk 89 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 30 optimal weight:    0.5980
   chunk 60 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 56 optimal weight:    8.9990
   chunk 68 optimal weight:    2.9990
   chunk 107 optimal weight:    8.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.146008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.101136 restraints weight = 13660.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 2.11
r_work: 0.3117 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.1032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9726  Z= 0.175
  Angle     :  0.575   7.574  13174  Z= 0.291
  Chirality :  0.039   0.201   1482
  Planarity :  0.004   0.031   1670
  Dihedral  :  3.987  19.559   1330
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  7.06 %
    Favored  : 92.45 %
  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: -0.18 (0.26), residues: 1184
  helix:  0.90 (0.20), residues: 760
  sheet: -1.69 (0.76), residues: 54
  loop : -2.00 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 524 
 HIS   0.013   0.001   HIS B 587 
 PHE   0.015   0.001   PHE A 619 
 TYR   0.015   0.001   TYR B 532 
 ARG   0.005   0.000   ARG B 418 

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

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

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 1.344 
Fit side-chains
   revert: symmetry clash
REVERT: B  530 VAL cc_start: 0.8175 (t) cc_final: 0.7936 (t)
REVERT: B  548 MET cc_start: 0.8902 (mmp) cc_final: 0.8609 (mmp)
REVERT: B  591 ARG cc_start: 0.6287 (ppt170) cc_final: 0.6015 (ptt90)
REVERT: B  598 MET cc_start: 0.7695 (mpp) cc_final: 0.7418 (mpp)
  outliers start: 5
  outliers final: 1
  residues processed: 102
  average time/residue: 0.2118
  time to fit residues: 31.1671
Evaluate side-chains
  90 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 117 optimal weight:    5.9990
   chunk 3 optimal weight:    0.6980
   chunk 89 optimal weight:   10.0000
   chunk 60 optimal weight:    0.8980
   chunk 69 optimal weight:    0.0050
   chunk 27 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 55 optimal weight:   10.0000
   chunk 64 optimal weight:    0.4980
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.147321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.102714 restraints weight = 13764.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.11
r_work: 0.3148 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3007 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9726  Z= 0.145
  Angle     :  0.537   8.229  13174  Z= 0.266
  Chirality :  0.038   0.188   1482
  Planarity :  0.003   0.028   1670
  Dihedral  :  3.847  17.644   1330
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  9.44 %
    Favored  : 89.76 %
  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:  0.13 (0.26), residues: 1184
  helix:  1.21 (0.20), residues: 758
  sheet: -1.57 (0.78), residues: 54
  loop : -2.03 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 524 
 HIS   0.011   0.001   HIS B 587 
 PHE   0.011   0.001   PHE B 517 
 TYR   0.012   0.001   TYR B 532 
 ARG   0.002   0.000   ARG A 660 

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

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

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 1.172 
Fit side-chains
   revert: symmetry clash
REVERT: B  380 GLU cc_start: 0.8057 (tp30) cc_final: 0.7733 (tp30)
REVERT: B  591 ARG cc_start: 0.6345 (ppt170) cc_final: 0.6128 (ptt90)
REVERT: A  214 ASN cc_start: 0.9290 (m-40) cc_final: 0.8936 (m110)
REVERT: A  328 VAL cc_start: 0.9244 (t) cc_final: 0.8925 (t)
REVERT: A  530 VAL cc_start: 0.8506 (OUTLIER) cc_final: 0.8288 (m)
  outliers start: 8
  outliers final: 5
  residues processed: 104
  average time/residue: 0.1901
  time to fit residues: 29.6128
Evaluate side-chains
  99 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 LYS
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  499 GLU
Chi-restraints excluded: chain B residue  635 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  530 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 76 optimal weight:    0.0050
   chunk 23 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 116 optimal weight:    9.9990
   chunk 73 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 41 optimal weight:   10.0000
   chunk 115 optimal weight:    0.1980
   chunk 111 optimal weight:    0.2980
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.4996

-------------------------------------------------------------------------------
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 = 0.3889 r_free = 0.3889 target = 0.148562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.102748 restraints weight = 13854.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 2.38
r_work: 0.3103 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.1618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9726  Z= 0.134
  Angle     :  0.524   9.294  13174  Z= 0.256
  Chirality :  0.038   0.170   1482
  Planarity :  0.003   0.027   1670
  Dihedral  :  3.724  17.995   1330
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 10.24 %
    Favored  : 88.47 %
  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:  0.40 (0.26), residues: 1184
  helix:  1.45 (0.20), residues: 756
  sheet: -1.56 (0.78), residues: 54
  loop : -1.99 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 679 
 HIS   0.009   0.001   HIS B 587 
 PHE   0.016   0.001   PHE B 619 
 TYR   0.007   0.001   TYR A 310 
 ARG   0.002   0.000   ARG B 401 

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

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

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  598 MET cc_start: 0.7701 (mpp) cc_final: 0.7105 (mpp)
REVERT: B  619 PHE cc_start: 0.8823 (m-80) cc_final: 0.8457 (m-80)
REVERT: A  214 ASN cc_start: 0.9304 (m-40) cc_final: 0.8964 (m110)
REVERT: A  530 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8232 (m)
REVERT: A  596 GLU cc_start: 0.7289 (pt0) cc_final: 0.6827 (pt0)
  outliers start: 13
  outliers final: 7
  residues processed: 109
  average time/residue: 0.1806
  time to fit residues: 29.7037
Evaluate side-chains
  101 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 LYS
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  499 GLU
Chi-restraints excluded: chain B residue  635 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  530 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 110 optimal weight:    1.9990
   chunk 49 optimal weight:   10.0000
   chunk 56 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 103 optimal weight:    0.3980
   chunk 61 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 19 optimal weight:    0.0970
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.3838 r_free = 0.3838 target = 0.143202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.097990 restraints weight = 13857.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 2.18
r_work: 0.3115 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9726  Z= 0.189
  Angle     :  0.537   8.381  13174  Z= 0.264
  Chirality :  0.039   0.159   1482
  Planarity :  0.003   0.027   1670
  Dihedral  :  3.758  18.028   1330
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.93 %
    Favored  : 86.38 %
  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:  0.46 (0.26), residues: 1184
  helix:  1.51 (0.20), residues: 756
  sheet: -1.52 (0.78), residues: 54
  loop : -1.98 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 524 
 HIS   0.007   0.001   HIS B 587 
 PHE   0.017   0.001   PHE B 517 
 TYR   0.015   0.001   TYR B 532 
 ARG   0.003   0.000   ARG B 591 

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

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

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 ASN cc_start: 0.9272 (m-40) cc_final: 0.8939 (m110)
REVERT: A  476 CYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7453 (p)
  outliers start: 17
  outliers final: 8
  residues processed: 111
  average time/residue: 0.1680
  time to fit residues: 28.5179
Evaluate side-chains
  97 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 LYS
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  405 SER
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  499 GLU
Chi-restraints excluded: chain B residue  635 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  476 CYS
Chi-restraints excluded: chain A residue  503 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 73 optimal weight:    5.9990
   chunk 94 optimal weight:    5.9990
   chunk 15 optimal weight:    0.6980
   chunk 58 optimal weight:    0.1980
   chunk 113 optimal weight:    0.6980
   chunk 100 optimal weight:    8.9990
   chunk 64 optimal weight:    3.9990
   chunk 44 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
B 587 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.144515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.099354 restraints weight = 13860.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.20
r_work: 0.3123 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9726  Z= 0.147
  Angle     :  0.545  11.695  13174  Z= 0.262
  Chirality :  0.039   0.154   1482
  Planarity :  0.003   0.026   1670
  Dihedral  :  3.709  18.161   1330
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 12.72 %
    Favored  : 85.59 %
  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:  0.53 (0.26), residues: 1184
  helix:  1.58 (0.20), residues: 760
  sheet: -1.60 (0.77), residues: 54
  loop : -2.01 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 679 
 HIS   0.006   0.001   HIS B 587 
 PHE   0.016   0.001   PHE B 673 
 TYR   0.015   0.001   TYR A 532 
 ARG   0.003   0.000   ARG B 591 

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

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

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 1.203 
Fit side-chains
   revert: symmetry clash
REVERT: B  472 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7911 (pm20)
REVERT: B  598 MET cc_start: 0.7636 (mpp) cc_final: 0.7129 (mpp)
REVERT: A  214 ASN cc_start: 0.9287 (m-40) cc_final: 0.8964 (m110)
REVERT: A  476 CYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7440 (p)
  outliers start: 17
  outliers final: 8
  residues processed: 104
  average time/residue: 0.1985
  time to fit residues: 30.8850
Evaluate side-chains
  98 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 LYS
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  472 GLN
Chi-restraints excluded: chain B residue  499 GLU
Chi-restraints excluded: chain B residue  635 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  283 HIS
Chi-restraints excluded: chain A residue  476 CYS
Chi-restraints excluded: chain A residue  503 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 57 optimal weight:    9.9990
   chunk 15 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 101 optimal weight:    4.9990
   chunk 111 optimal weight:    9.9990
   chunk 94 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 38 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 = 0.3860 r_free = 0.3860 target = 0.144815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.101795 restraints weight = 13842.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.33
r_work: 0.3092 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.1835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9726  Z= 0.205
  Angle     :  0.552   9.578  13174  Z= 0.269
  Chirality :  0.040   0.148   1482
  Planarity :  0.003   0.027   1670
  Dihedral  :  3.748  18.156   1330
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 13.02 %
    Favored  : 85.39 %
  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:  0.55 (0.26), residues: 1184
  helix:  1.61 (0.20), residues: 760
  sheet: -1.59 (0.77), residues: 54
  loop : -2.04 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 137 
 HIS   0.004   0.001   HIS A 669 
 PHE   0.012   0.001   PHE B 517 
 TYR   0.011   0.001   TYR B 666 
 ARG   0.003   0.000   ARG B 591 

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

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

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 1.050 
Fit side-chains
REVERT: B  472 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8176 (pm20)
REVERT: A  214 ASN cc_start: 0.9315 (m-40) cc_final: 0.8996 (m110)
REVERT: A  380 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7780 (tm-30)
REVERT: A  476 CYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7604 (p)
  outliers start: 16
  outliers final: 9
  residues processed: 99
  average time/residue: 0.1676
  time to fit residues: 25.7907
Evaluate side-chains
  101 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 LYS
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  422 MET
Chi-restraints excluded: chain B residue  472 GLN
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  635 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  283 HIS
Chi-restraints excluded: chain A residue  476 CYS
Chi-restraints excluded: chain A residue  503 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 107 optimal weight:    5.9990
   chunk 116 optimal weight:    8.9990
   chunk 39 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 94 optimal weight:    5.9990
   chunk 73 optimal weight:    4.9990
   chunk 17 optimal weight:    0.2980
   chunk 63 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   chunk 117 optimal weight:    4.9990
   overall best weight:    2.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 433 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.142568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.097645 restraints weight = 13997.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 2.33
r_work: 0.3018 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9726  Z= 0.256
  Angle     :  0.579   8.387  13174  Z= 0.285
  Chirality :  0.041   0.146   1482
  Planarity :  0.003   0.029   1670
  Dihedral  :  3.877  18.585   1330
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 13.12 %
    Favored  : 85.29 %
  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:  0.46 (0.26), residues: 1184
  helix:  1.63 (0.20), residues: 750
  sheet: -1.63 (0.76), residues: 54
  loop : -2.20 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 679 
 HIS   0.005   0.001   HIS A 669 
 PHE   0.014   0.001   PHE B 517 
 TYR   0.011   0.001   TYR A 310 
 ARG   0.003   0.000   ARG B 591 

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

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

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 1.106 
Fit side-chains
REVERT: B  380 GLU cc_start: 0.8248 (tp30) cc_final: 0.8040 (tm-30)
REVERT: B  472 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8385 (pm20)
REVERT: B  598 MET cc_start: 0.7729 (mpp) cc_final: 0.7178 (mpp)
REVERT: A  367 LYS cc_start: 0.6811 (pttm) cc_final: 0.6405 (pptt)
REVERT: A  380 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7906 (tm-30)
REVERT: A  476 CYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7542 (p)
  outliers start: 16
  outliers final: 9
  residues processed: 99
  average time/residue: 0.1664
  time to fit residues: 25.4974
Evaluate side-chains
  95 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 1.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 LYS
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  422 MET
Chi-restraints excluded: chain B residue  472 GLN
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  635 VAL
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  283 HIS
Chi-restraints excluded: chain A residue  476 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 114 optimal weight:    8.9990
   chunk 74 optimal weight:    0.9980
   chunk 89 optimal weight:    6.9990
   chunk 95 optimal weight:   10.0000
   chunk 0 optimal weight:    7.9990
   chunk 7 optimal weight:    0.5980
   chunk 109 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.3843 r_free = 0.3843 target = 0.143990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.100899 restraints weight = 13836.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 2.46
r_work: 0.3043 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9726  Z= 0.194
  Angle     :  0.564   8.055  13174  Z= 0.277
  Chirality :  0.040   0.147   1482
  Planarity :  0.003   0.026   1670
  Dihedral  :  3.847  18.340   1330
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 13.82 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.26), residues: 1184
  helix:  1.69 (0.20), residues: 752
  sheet: -1.62 (0.76), residues: 54
  loop : -2.13 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 679 
 HIS   0.006   0.001   HIS A 669 
 PHE   0.017   0.001   PHE A 619 
 TYR   0.011   0.001   TYR B 666 
 ARG   0.003   0.000   ARG B 591 

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

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

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 1.033 
Fit side-chains
REVERT: B  472 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8349 (pm20)
REVERT: B  598 MET cc_start: 0.7703 (mpp) cc_final: 0.7104 (mpp)
REVERT: A  380 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7824 (tm-30)
REVERT: A  476 CYS cc_start: 0.7829 (OUTLIER) cc_final: 0.6968 (p)
REVERT: A  493 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7716 (pp)
  outliers start: 12
  outliers final: 9
  residues processed: 93
  average time/residue: 0.1699
  time to fit residues: 24.4932
Evaluate side-chains
  96 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 LYS
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  422 MET
Chi-restraints excluded: chain B residue  472 GLN
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  635 VAL
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  283 HIS
Chi-restraints excluded: chain A residue  476 CYS
Chi-restraints excluded: chain A residue  493 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 107 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 49 optimal weight:    0.5980
   chunk 80 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 57 optimal weight:    4.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3868 r_free = 0.3868 target = 0.146841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.100746 restraints weight = 14102.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 2.42
r_work: 0.3085 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9726  Z= 0.155
  Angle     :  0.553   9.040  13174  Z= 0.269
  Chirality :  0.039   0.148   1482
  Planarity :  0.003   0.025   1670
  Dihedral  :  3.763  18.945   1330
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.92 %
    Favored  : 84.79 %
  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:  0.68 (0.26), residues: 1184
  helix:  1.77 (0.20), residues: 758
  sheet: -1.56 (0.75), residues: 54
  loop : -2.11 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 679 
 HIS   0.003   0.001   HIS B 667 
 PHE   0.018   0.001   PHE A 619 
 TYR   0.011   0.001   TYR B 666 
 ARG   0.003   0.000   ARG B 591 

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

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

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2368 Ramachandran restraints generated.
    1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 1.078 
Fit side-chains
REVERT: B  472 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8316 (pm20)
REVERT: B  598 MET cc_start: 0.7654 (mpp) cc_final: 0.7167 (mpp)
REVERT: A  214 ASN cc_start: 0.9276 (m-40) cc_final: 0.9015 (m110)
REVERT: A  367 LYS cc_start: 0.6604 (ptpp) cc_final: 0.6314 (pptt)
REVERT: A  476 CYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7468 (p)
  outliers start: 13
  outliers final: 7
  residues processed: 100
  average time/residue: 0.1865
  time to fit residues: 28.5278
Evaluate side-chains
  95 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  422 MET
Chi-restraints excluded: chain B residue  472 GLN
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  283 HIS
Chi-restraints excluded: chain A residue  476 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 99 optimal weight:    8.9990
   chunk 75 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 104 optimal weight:    0.1980
   chunk 5 optimal weight:    0.4980
   chunk 49 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 289 ASN
** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.147893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.101786 restraints weight = 14084.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.43
r_work: 0.3103 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9726  Z= 0.145
  Angle     :  0.553   8.766  13174  Z= 0.268
  Chirality :  0.039   0.150   1482
  Planarity :  0.003   0.026   1670
  Dihedral  :  3.706  19.322   1330
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 14.51 %
    Favored  : 84.39 %
  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:  0.80 (0.26), residues: 1184
  helix:  1.77 (0.20), residues: 764
  sheet: -0.56 (1.00), residues: 34
  loop : -2.01 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 679 
 HIS   0.003   0.001   HIS B 667 
 PHE   0.014   0.001   PHE B 517 
 TYR   0.011   0.001   TYR B 666 
 ARG   0.009   0.000   ARG B 464 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4871.74 seconds
wall clock time: 87 minutes 0.63 seconds (5220.63 seconds total)