Starting phenix.real_space_refine
on Tue Mar  3 20:58:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rxb_24727/03_2026/7rxb_24727.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rxb_24727/03_2026/7rxb_24727.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rxb_24727/03_2026/7rxb_24727.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rxb_24727/03_2026/7rxb_24727.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rxb_24727/03_2026/7rxb_24727.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rxb_24727/03_2026/7rxb_24727.cif"
  }
  resolution = 3.07
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
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=   0.005
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: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      32      5.16       5
     C    5660      2.51       5
     N    1382      2.21       5
     O    1426      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8506
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 548, 4153
          Classifications: {'peptide': 548}
          Incomplete info: {'truncation_to_alanine': 91}
          Link IDs: {'PTRANS': 21, 'TRANS': 526}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 389
          Unresolved non-hydrogen angles: 471
          Unresolved non-hydrogen dihedrals: 323
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 29, 'ASP:plan': 12, 'ASN:plan1': 2, 'ARG:plan': 16, 'HIS:plan': 2, 'PHE:plan': 3, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 292
    Chain: "B"
      Number of atoms: 4153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 548, 4153
          Classifications: {'peptide': 548}
          Incomplete info: {'truncation_to_alanine': 91}
          Link IDs: {'PTRANS': 21, 'TRANS': 526}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 389
          Unresolved non-hydrogen angles: 471
          Unresolved non-hydrogen dihedrals: 323
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 29, 'ASP:plan': 12, 'ASN:plan1': 2, 'ARG:plan': 16, 'HIS:plan': 2, 'PHE:plan': 3, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 292
    Chain: "A"
      Number of atoms: 100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 100
          Unusual residues: {'PGW': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 104
          Unresolved non-hydrogen angles: 112
          Unresolved non-hydrogen dihedrals: 115
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PGW:plan-1': 1, 'PGW:plan-3': 4}
          Unresolved non-hydrogen planarities: 19
    Chain: "B"
      Number of atoms: 100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 100
          Unusual residues: {'PGW': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 104
          Unresolved non-hydrogen angles: 112
          Unresolved non-hydrogen dihedrals: 115
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PGW:plan-3': 4, 'PGW:plan-1': 1}
          Unresolved non-hydrogen planarities: 19
  Time building chain proxies: 2.17, per 1000 atoms: 0.26
  Number of scatterers: 8506
  At special positions: 0
  Unit cell: (115.02, 74.124, 100.536, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     P       6     15.00
     O    1426      8.00
     N    1382      7.00
     C    5660      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: 0.67
  Conformation dependent library (CDL) restraints added in 347.0 milliseconds
  

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2108

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 2 sheets defined
      63.7% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 46
      removed outlier: 4.045A  pdb=" N   VAL A  46 " --> pdb=" O   GLU A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 85
      removed outlier: 3.843A  pdb=" N   LYS A  73 " --> pdb=" O   LYS A  69 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ARG A  74 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 113
      removed outlier: 3.777A  pdb=" N   LEU A 109 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 153
    Processing helix  chain 'A' and resid 165 through 169
    Processing helix  chain 'A' and resid 174 through 191
      removed outlier: 3.629A  pdb=" N   GLY A 178 " --> pdb=" O   GLY A 174 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   TYR A 180 " --> pdb=" O   HIS A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 198
    Processing helix  chain 'A' and resid 209 through 238
      removed outlier: 3.599A  pdb=" N   THR A 213 " --> pdb=" O   SER A 209 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   CYS A 220 " --> pdb=" O   ASN A 216 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ILE A 221 " --> pdb=" O   CYS A 217 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ILE A 224 " --> pdb=" O   CYS A 220 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ARG A 229 " --> pdb=" O   GLU A 225 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   GLU A 232 " --> pdb=" O   LYS A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 280
      removed outlier: 3.621A  pdb=" N   ARG A 279 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 311
      removed outlier: 3.820A  pdb=" N   PHE A 286 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   VAL A 292 " --> pdb=" O   LEU A 288 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ILE A 297 " --> pdb=" O   ALA A 293 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE A 306 " --> pdb=" O   PHE A 302 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   VAL A 311 " --> pdb=" O   PHE A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 330
      removed outlier: 3.627A  pdb=" N   ILE A 326 " --> pdb=" O   PHE A 322 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   VAL A 328 " --> pdb=" O   PRO A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 336
    Processing helix  chain 'A' and resid 338 through 350
      removed outlier: 3.596A  pdb=" N   VAL A 342 " --> pdb=" O   VAL A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 380
      removed outlier: 3.599A  pdb=" N   TYR A 358 " --> pdb=" O   THR A 354 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LYS A 359 " --> pdb=" O   GLN A 355 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   VAL A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL A 368 " --> pdb=" O   GLN A 364 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL A 369 " --> pdb=" O   LYS A 365 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   LEU A 376 " --> pdb=" O   ILE A 372 " (cutoff:3.500A)
      Proline residue:  A 377  - end of helix
    Processing helix  chain 'A' and resid 392 through 397
    Processing helix  chain 'A' and resid 423 through 435
      removed outlier: 3.901A  pdb=" N   ARG A 427 " --> pdb=" O   PRO A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 441
    Processing helix  chain 'A' and resid 492 through 501
      removed outlier: 3.710A  pdb=" N   ARG A 496 " --> pdb=" O   ARG A 492 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ARG A 498 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 525
      removed outlier: 3.810A  pdb=" N   MET A 515 " --> pdb=" O   ASP A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 543
      removed outlier: 3.589A  pdb=" N   ASN A 539 " --> pdb=" O   SER A 535 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   GLU A 543 " --> pdb=" O   ASN A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 552
    Processing helix  chain 'A' and resid 568 through 573
      removed outlier: 3.585A  pdb=" N   SER A 572 " --> pdb=" O   PRO A 568 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU A 573 " --> pdb=" O   TRP A 569 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 568 through 573'
    Processing helix  chain 'A' and resid 574 through 592
      removed outlier: 3.619A  pdb=" N   TRP A 578 " --> pdb=" O   GLY A 574 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ILE A 582 " --> pdb=" O   TRP A 578 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   SER A 585 " --> pdb=" O   SER A 581 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   VAL A 588 " --> pdb=" O   SER A 584 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   TYR A 589 " --> pdb=" O   SER A 585 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   MET A 590 " --> pdb=" O   ALA A 586 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER A 592 " --> pdb=" O   VAL A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 630
      removed outlier: 3.570A  pdb=" N   LEU A 610 " --> pdb=" O   ARG A 606 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   PHE A 615 " --> pdb=" O   LEU A 611 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ILE A 623 " --> pdb=" O   HIS A 619 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   TYR A 626 " --> pdb=" O   LEU A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 656
      removed outlier: 3.797A  pdb=" N   ARG A 642 " --> pdb=" O   PRO A 638 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLU A 643 " --> pdb=" O   ASN A 639 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ASP A 656 " --> pdb=" O   LYS A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 711 through 717
      removed outlier: 4.170A  pdb=" N   SER A 715 " --> pdb=" O   GLY A 711 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ALA A 716 " --> pdb=" O   TRP A 712 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 46
      removed outlier: 4.044A  pdb=" N   VAL B  46 " --> pdb=" O   GLU B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 85
      removed outlier: 3.843A  pdb=" N   LYS B  73 " --> pdb=" O   LYS B  69 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ARG B  74 " --> pdb=" O   LYS B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 113
      removed outlier: 3.779A  pdb=" N   LEU B 109 " --> pdb=" O   ALA B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 153
    Processing helix  chain 'B' and resid 165 through 169
    Processing helix  chain 'B' and resid 174 through 191
      removed outlier: 3.630A  pdb=" N   GLY B 178 " --> pdb=" O   GLY B 174 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   TYR B 180 " --> pdb=" O   HIS B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 198
    Processing helix  chain 'B' and resid 209 through 238
      removed outlier: 3.599A  pdb=" N   THR B 213 " --> pdb=" O   SER B 209 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   CYS B 220 " --> pdb=" O   ASN B 216 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ILE B 221 " --> pdb=" O   CYS B 217 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ILE B 224 " --> pdb=" O   CYS B 220 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ARG B 229 " --> pdb=" O   GLU B 225 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   GLU B 232 " --> pdb=" O   LYS B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 280
      removed outlier: 3.620A  pdb=" N   ARG B 279 " --> pdb=" O   LYS B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 311
      removed outlier: 3.820A  pdb=" N   PHE B 286 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   VAL B 292 " --> pdb=" O   LEU B 288 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ILE B 297 " --> pdb=" O   ALA B 293 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ILE B 306 " --> pdb=" O   PHE B 302 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   VAL B 311 " --> pdb=" O   PHE B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 330
      removed outlier: 3.627A  pdb=" N   ILE B 326 " --> pdb=" O   PHE B 322 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   VAL B 328 " --> pdb=" O   PRO B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 336
    Processing helix  chain 'B' and resid 338 through 350
      removed outlier: 3.596A  pdb=" N   VAL B 342 " --> pdb=" O   VAL B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 380
      removed outlier: 3.598A  pdb=" N   TYR B 358 " --> pdb=" O   THR B 354 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LYS B 359 " --> pdb=" O   GLN B 355 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   VAL B 360 " --> pdb=" O   ASP B 356 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL B 368 " --> pdb=" O   GLN B 364 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL B 369 " --> pdb=" O   LYS B 365 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   LEU B 376 " --> pdb=" O   ILE B 372 " (cutoff:3.500A)
      Proline residue:  B 377  - end of helix
    Processing helix  chain 'B' and resid 392 through 397
    Processing helix  chain 'B' and resid 423 through 435
      removed outlier: 3.901A  pdb=" N   ARG B 427 " --> pdb=" O   PRO B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 441
    Processing helix  chain 'B' and resid 492 through 501
      removed outlier: 3.709A  pdb=" N   ARG B 496 " --> pdb=" O   ARG B 492 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ARG B 498 " --> pdb=" O   LEU B 494 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 511 through 525
      removed outlier: 3.810A  pdb=" N   MET B 515 " --> pdb=" O   ASP B 511 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 531 through 543
      removed outlier: 3.590A  pdb=" N   ASN B 539 " --> pdb=" O   SER B 535 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLU B 543 " --> pdb=" O   ASN B 539 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 546 through 552
    Processing helix  chain 'B' and resid 568 through 573
      removed outlier: 3.586A  pdb=" N   SER B 572 " --> pdb=" O   PRO B 568 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU B 573 " --> pdb=" O   TRP B 569 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 568 through 573'
    Processing helix  chain 'B' and resid 574 through 592
      removed outlier: 3.618A  pdb=" N   TRP B 578 " --> pdb=" O   GLY B 574 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ILE B 582 " --> pdb=" O   TRP B 578 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   SER B 585 " --> pdb=" O   SER B 581 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   VAL B 588 " --> pdb=" O   SER B 584 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   TYR B 589 " --> pdb=" O   SER B 585 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   MET B 590 " --> pdb=" O   ALA B 586 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER B 592 " --> pdb=" O   VAL B 588 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 606 through 630
      removed outlier: 3.571A  pdb=" N   LEU B 610 " --> pdb=" O   ARG B 606 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   PHE B 615 " --> pdb=" O   LEU B 611 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ILE B 623 " --> pdb=" O   HIS B 619 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   TYR B 626 " --> pdb=" O   LEU B 622 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 637 through 656
      removed outlier: 3.798A  pdb=" N   ARG B 642 " --> pdb=" O   PRO B 638 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLU B 643 " --> pdb=" O   ASN B 639 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ASP B 656 " --> pdb=" O   LYS B 652 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 711 through 717
      removed outlier: 4.170A  pdb=" N   SER B 715 " --> pdb=" O   GLY B 711 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ALA B 716 " --> pdb=" O   TRP B 712 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 54
      removed outlier: 6.807A  pdb=" N   VAL A  19 " --> pdb=" O   ILE A 139 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   ILE A 139 " --> pdb=" O   VAL A  19 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   ARG A  21 " --> pdb=" O   ASP A 137 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 54
      removed outlier: 6.807A  pdb=" N   VAL B  19 " --> pdb=" O   ILE B 139 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   ILE B 139 " --> pdb=" O   VAL B  19 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   ARG B  21 " --> pdb=" O   ASP B 137 " (cutoff:3.500A)

    410 hydrogen bonds defined for protein.
    1212 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: 1.24

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1230
        1.30 -     1.43: 2566
        1.43 -     1.56: 4866
        1.56 -     1.68: 12
        1.68 -     1.81: 44
  Bond restraints: 8718
  Sorted by residual:
  bond pdb=" C1  PGW B1003 "
       pdb=" O01 PGW B1003 "
    ideal  model  delta    sigma   weight residual
    1.332  1.419 -0.087 2.00e-02 2.50e+03 1.91e+01
  bond pdb=" C1  PGW A 802 "
       pdb=" O01 PGW A 802 "
    ideal  model  delta    sigma   weight residual
    1.332  1.419 -0.087 2.00e-02 2.50e+03 1.89e+01
  bond pdb=" C1  PGW A 803 "
       pdb=" O01 PGW A 803 "
    ideal  model  delta    sigma   weight residual
    1.332  1.417 -0.085 2.00e-02 2.50e+03 1.82e+01
  bond pdb=" C1  PGW B1004 "
       pdb=" O01 PGW B1004 "
    ideal  model  delta    sigma   weight residual
    1.332  1.417 -0.085 2.00e-02 2.50e+03 1.81e+01
  bond pdb=" C1  PGW B1001 "
       pdb=" O01 PGW B1001 "
    ideal  model  delta    sigma   weight residual
    1.332  1.416 -0.084 2.00e-02 2.50e+03 1.74e+01
  ... (remaining 8713 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.34: 11368
        2.34 -     4.69: 395
        4.69 -     7.03: 83
        7.03 -     9.38: 26
        9.38 -    11.72: 18
  Bond angle restraints: 11890
  Sorted by residual:
  angle pdb=" N   ILE A 169 "
        pdb=" CA  ILE A 169 "
        pdb=" C   ILE A 169 "
      ideal   model   delta    sigma   weight residual
     111.91  105.97    5.94 8.90e-01 1.26e+00 4.46e+01
  angle pdb=" N   ILE B 169 "
        pdb=" CA  ILE B 169 "
        pdb=" C   ILE B 169 "
      ideal   model   delta    sigma   weight residual
     111.91  106.00    5.91 8.90e-01 1.26e+00 4.40e+01
  angle pdb=" C   LYS A 158 "
        pdb=" N   THR A 159 "
        pdb=" CA  THR A 159 "
      ideal   model   delta    sigma   weight residual
     121.54  132.10  -10.56 1.91e+00 2.74e-01 3.06e+01
  angle pdb=" C   LYS B 158 "
        pdb=" N   THR B 159 "
        pdb=" CA  THR B 159 "
      ideal   model   delta    sigma   weight residual
     121.54  132.09  -10.55 1.91e+00 2.74e-01 3.05e+01
  angle pdb=" O11 PGW B1001 "
        pdb=" P   PGW B1001 "
        pdb=" O12 PGW B1001 "
      ideal   model   delta    sigma   weight residual
      98.90  110.62  -11.72 3.00e+00 1.11e-01 1.53e+01
  ... (remaining 11885 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.26: 4856
       30.26 -    60.53: 160
       60.53 -    90.79: 10
       90.79 -   121.05: 4
      121.05 -   151.32: 4
  Dihedral angle restraints: 5034
    sinusoidal: 1804
      harmonic: 3230
  Sorted by residual:
  dihedral pdb=" CA  PHE B 399 "
           pdb=" C   PHE B 399 "
           pdb=" N   HIS B 400 "
           pdb=" CA  HIS B 400 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.67  -23.33     0      5.00e+00 4.00e-02 2.18e+01
  dihedral pdb=" CA  PHE A 399 "
           pdb=" C   PHE A 399 "
           pdb=" N   HIS A 400 "
           pdb=" CA  HIS A 400 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.74  -23.26     0      5.00e+00 4.00e-02 2.16e+01
  dihedral pdb=" CA  ASN A 171 "
           pdb=" C   ASN A 171 "
           pdb=" N   THR A 172 "
           pdb=" CA  THR A 172 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.57   22.43     0      5.00e+00 4.00e-02 2.01e+01
  ... (remaining 5031 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 663
       0.037 -    0.073: 527
       0.073 -    0.110: 130
       0.110 -    0.146: 68
       0.146 -    0.183: 12
  Chirality restraints: 1400
  Sorted by residual:
  chirality pdb=" CA  THR B 159 "
            pdb=" N   THR B 159 "
            pdb=" C   THR B 159 "
            pdb=" CB  THR B 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.18 2.00e-01 2.50e+01 8.36e-01
  chirality pdb=" CA  THR A 159 "
            pdb=" N   THR A 159 "
            pdb=" C   THR A 159 "
            pdb=" CB  THR A 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.18 2.00e-01 2.50e+01 8.33e-01
  chirality pdb=" CA  SER A 526 "
            pdb=" N   SER A 526 "
            pdb=" C   SER A 526 "
            pdb=" CB  SER A 526 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.24e-01
  ... (remaining 1397 not shown)

  Planarity restraints: 1438
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 422 "   -0.053 5.00e-02 4.00e+02   7.94e-02 1.01e+01
        pdb=" N   PRO B 423 "    0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO B 423 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 423 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 422 "    0.052 5.00e-02 4.00e+02   7.90e-02 9.98e+00
        pdb=" N   PRO A 423 "   -0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO A 423 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 423 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 376 "    0.048 5.00e-02 4.00e+02   7.16e-02 8.20e+00
        pdb=" N   PRO A 377 "   -0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO A 377 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 377 "    0.040 5.00e-02 4.00e+02
  ... (remaining 1435 not shown)

  Histogram of nonbonded interaction distances:
        2.44 -     2.93: 3351
        2.93 -     3.42: 7552
        3.42 -     3.91: 12800
        3.91 -     4.41: 14692
        4.41 -     4.90: 25955
  Nonbonded interactions: 64350
  Sorted by model distance:
  nonbonded pdb=" O   SER A 209 "
            pdb=" OG1 THR A 213 "
     model   vdw
     2.437 3.040
  nonbonded pdb=" O   SER B 209 "
            pdb=" OG1 THR B 213 "
     model   vdw
     2.437 3.040
  nonbonded pdb=" O   THR B 613 "
            pdb=" OG  SER B 617 "
     model   vdw
     2.448 3.040
  nonbonded pdb=" O   THR A 613 "
            pdb=" OG  SER A 617 "
     model   vdw
     2.448 3.040
  nonbonded pdb=" O01 PGW B1002 "
            pdb=" O11 PGW B1002 "
     model   vdw
     2.452 2.432
  ... (remaining 64345 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: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 11 through 717 or (resid 801 and (name C01 or name C02 or  \ 
name C03 or name C19 or name O03 or name O04 or name O11 or name O12 or name O13 \ 
 or name O14 or name P )) or (resid 802 and (name C01 or name C02 or name C03 or \ 
 name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name O0 \ 
3 or name O04)) or (resid 803 and (name C01 or name C02 or name C03 or name C1 o \ 
r name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C2 \ 
4 or name C25 or name C3 or name C4 or name C5 or name C6 or name O01 or name O0 \ 
2 or name O03 or name O04)) or resid 804))
  selection = (chain 'B' and (resid 11 through 717 or (resid 1001 and (name C01 or name C02 or \ 
 name C03 or name C19 or name O03 or name O04 or name O11 or name O12 or name O1 \ 
3 or name O14 or name P )) or (resid 1002 and (name C01 or name C02 or name C03  \ 
or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name  \ 
O03 or name O04)) or resid 1003 or (resid 1004 and (name C01 or name C02 or name \ 
 C03 or name C1 or name C19 or name C2 or name C20 or name C3 or name C4 or name \ 
 C5 or name C6 or name C7 or name O01 or name O02 or name O03 or name O04 or nam \ 
e O11 or name O12 or name O13 or name O14 or name P ))))
}

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:             1.290
  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:          0.150
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     9.190
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
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   0.087   8718  Z= 0.390
  Angle     :  1.151  11.724  11890  Z= 0.569
  Chirality :  0.055   0.183   1400
  Planarity :  0.008   0.079   1438
  Dihedral  : 16.228 151.317   2926
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 0.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.88 (0.18), residues: 1060
  helix: -3.22 (0.13), residues: 710
  sheet: -0.67 (0.61), residues: 44
  loop : -3.09 (0.28), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 496 
 TYR   0.014   0.002   TYR A 589 
 PHE   0.016   0.002   PHE A 140 
 TRP   0.022   0.002   TRP A 227 
 HIS   0.008   0.002   HIS A 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00944 ( 8718)
  covalent geometry    : angle       1.15124 (11890)
  hydrogen bonds       : bond        0.16702 (  410)
  hydrogen bonds       : angle       5.53769 ( 1212)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A  551 ILE cc_start: 0.8368 (tt) cc_final: 0.7892 (tp)
REVERT: B   21 ARG cc_start: 0.8288 (ttp80) cc_final: 0.8075 (ttp-170)
REVERT: B  551 ILE cc_start: 0.8344 (tt) cc_final: 0.7954 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.0745
  time to fit residues: 9.0038
Evaluate side-chains
  64 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:    9.9990
   chunk 38 optimal weight:    7.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 280 GLN
A 370 ASN
A 518 GLN
B 280 GLN
B 370 ASN
B 518 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.114017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.084288 restraints weight = 10490.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.2801 rms_B_bonded: 1.58
r_work: 0.2672 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2547 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.0894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8718  Z= 0.140
  Angle     :  0.565   8.043  11890  Z= 0.302
  Chirality :  0.040   0.122   1400
  Planarity :  0.006   0.061   1438
  Dihedral  : 15.391 126.311   1326
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 1.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  6.42 %
    Favored  : 93.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.81 (0.24), residues: 1060
  helix: -1.52 (0.18), residues: 714
  sheet: -0.55 (0.58), residues: 44
  loop : -2.53 (0.33), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 496 
 TYR   0.014   0.001   TYR B 589 
 PHE   0.009   0.001   PHE A 286 
 TRP   0.012   0.001   TRP A 227 
 HIS   0.004   0.001   HIS B 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 8718)
  covalent geometry    : angle       0.56456 (11890)
  hydrogen bonds       : bond        0.05368 (  410)
  hydrogen bonds       : angle       3.55251 ( 1212)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.358 
Fit side-chains
REVERT: B   21 ARG cc_start: 0.8358 (ttp80) cc_final: 0.8137 (ttp-170)
  outliers start: 4
  outliers final: 2
  residues processed: 74
  average time/residue: 0.0620
  time to fit residues: 7.4129
Evaluate side-chains
  69 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 67
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain B residue   19 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 105 optimal weight:    5.9990
   chunk 2 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 88 optimal weight:    0.0570
   chunk 18 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.9702

-------------------------------------------------------------------------------
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 = 0.3242 r_free = 0.3242 target = 0.116409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.086579 restraints weight = 10419.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 1.59
r_work: 0.2713 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2587 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.1306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8718  Z= 0.110
  Angle     :  0.504   7.703  11890  Z= 0.267
  Chirality :  0.039   0.122   1400
  Planarity :  0.005   0.049   1438
  Dihedral  : 13.775 115.825   1326
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 1.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 10.33 %
    Favored  : 89.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.76 (0.26), residues: 1060
  helix: -0.69 (0.20), residues: 714
  sheet: -0.39 (0.58), residues: 44
  loop : -2.17 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 496 
 TYR   0.010   0.001   TYR B 589 
 PHE   0.006   0.001   PHE A 286 
 TRP   0.011   0.001   TRP A 227 
 HIS   0.003   0.001   HIS A 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 8718)
  covalent geometry    : angle       0.50362 (11890)
  hydrogen bonds       : bond        0.03961 (  410)
  hydrogen bonds       : angle       3.15501 ( 1212)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.328 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 74
  average time/residue: 0.0707
  time to fit residues: 8.1638
Evaluate side-chains
  65 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 87 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 84 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 94 optimal weight:    1.9990
   chunk 102 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 = 0.3234 r_free = 0.3234 target = 0.115728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.085856 restraints weight = 10444.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.2810 rms_B_bonded: 1.58
r_work: 0.2682 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2555 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.1394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8718  Z= 0.139
  Angle     :  0.523   7.527  11890  Z= 0.277
  Chirality :  0.040   0.130   1400
  Planarity :  0.005   0.044   1438
  Dihedral  : 13.418 112.544   1326
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 1.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 10.71 %
    Favored  : 88.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.39 (0.26), residues: 1060
  helix: -0.40 (0.20), residues: 718
  sheet:  0.30 (0.64), residues: 44
  loop : -2.16 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 496 
 TYR   0.011   0.001   TYR A 589 
 PHE   0.008   0.001   PHE B 286 
 TRP   0.012   0.001   TRP A 227 
 HIS   0.005   0.001   HIS B 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8718)
  covalent geometry    : angle       0.52305 (11890)
  hydrogen bonds       : bond        0.04502 (  410)
  hydrogen bonds       : angle       3.15500 ( 1212)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.301 
Fit side-chains
  outliers start: 8
  outliers final: 5
  residues processed: 68
  average time/residue: 0.0574
  time to fit residues: 6.5930
Evaluate side-chains
  67 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  509 THR
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  509 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 106 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0170
   chunk 65 optimal weight:    0.7980
   chunk 4 optimal weight:    8.9990
   chunk 29 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0670
   chunk 87 optimal weight:    4.9990
   chunk 98 optimal weight:    0.8980
   overall best weight:    0.4956

-------------------------------------------------------------------------------
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 = 0.3278 r_free = 0.3278 target = 0.119536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.089793 restraints weight = 10381.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.2878 rms_B_bonded: 1.60
r_work: 0.2753 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2628 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8718  Z= 0.085
  Angle     :  0.463   7.344  11890  Z= 0.244
  Chirality :  0.038   0.140   1400
  Planarity :  0.004   0.042   1438
  Dihedral  : 12.330 103.473   1326
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 1.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 11.08 %
    Favored  : 88.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.27), residues: 1060
  helix:  0.15 (0.21), residues: 708
  sheet:  0.49 (0.67), residues: 44
  loop : -1.92 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 629 
 TYR   0.008   0.001   TYR B 180 
 PHE   0.007   0.001   PHE A 615 
 TRP   0.010   0.001   TRP B 227 
 HIS   0.002   0.001   HIS A 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.00186 ( 8718)
  covalent geometry    : angle       0.46258 (11890)
  hydrogen bonds       : bond        0.02961 (  410)
  hydrogen bonds       : angle       2.86497 ( 1212)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.314 
Fit side-chains
REVERT: B  241 LYS cc_start: 0.8672 (tptp) cc_final: 0.8470 (tttm)
  outliers start: 5
  outliers final: 2
  residues processed: 70
  average time/residue: 0.0776
  time to fit residues: 8.1317
Evaluate side-chains
  64 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  509 THR
Chi-restraints excluded: chain B residue  509 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 45 optimal weight:    0.0970
   chunk 2 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 105 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 47 optimal weight:    4.9990
   chunk 107 optimal weight:    9.9990
   overall best weight:    1.4184

-------------------------------------------------------------------------------
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 = 0.3234 r_free = 0.3234 target = 0.115937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.086042 restraints weight = 10341.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.2821 rms_B_bonded: 1.58
r_work: 0.2690 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2565 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8718  Z= 0.129
  Angle     :  0.503   7.371  11890  Z= 0.266
  Chirality :  0.040   0.132   1400
  Planarity :  0.004   0.039   1438
  Dihedral  : 12.250 105.081   1326
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 1.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 10.83 %
    Favored  : 88.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.27), residues: 1060
  helix:  0.18 (0.21), residues: 718
  sheet:  0.81 (0.69), residues: 44
  loop : -1.97 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  65 
 TYR   0.011   0.001   TYR A 589 
 PHE   0.007   0.001   PHE A 615 
 TRP   0.011   0.001   TRP A 227 
 HIS   0.005   0.001   HIS B 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8718)
  covalent geometry    : angle       0.50328 (11890)
  hydrogen bonds       : bond        0.04199 (  410)
  hydrogen bonds       : angle       2.99219 ( 1212)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.358 
Fit side-chains
  outliers start: 9
  outliers final: 5
  residues processed: 74
  average time/residue: 0.0567
  time to fit residues: 7.0591
Evaluate side-chains
  76 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  509 THR
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain B residue  509 THR
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 95 optimal weight:    0.0770
   chunk 64 optimal weight:    7.9990
   chunk 54 optimal weight:    5.9990
   chunk 97 optimal weight:    0.7980
   chunk 59 optimal weight:    9.9990
   chunk 98 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.9140

-------------------------------------------------------------------------------
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 = 0.3258 r_free = 0.3258 target = 0.117854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.088085 restraints weight = 10412.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.2848 rms_B_bonded: 1.59
r_work: 0.2720 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2593 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8718  Z= 0.101
  Angle     :  0.478   7.346  11890  Z= 0.252
  Chirality :  0.039   0.122   1400
  Planarity :  0.004   0.039   1438
  Dihedral  : 11.712 101.842   1326
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 1.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 11.46 %
    Favored  : 87.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.27), residues: 1060
  helix:  0.41 (0.21), residues: 716
  sheet:  1.20 (0.74), residues: 44
  loop : -1.83 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  65 
 TYR   0.008   0.001   TYR B 180 
 PHE   0.007   0.001   PHE A 615 
 TRP   0.010   0.001   TRP A 227 
 HIS   0.003   0.001   HIS B 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8718)
  covalent geometry    : angle       0.47819 (11890)
  hydrogen bonds       : bond        0.03516 (  410)
  hydrogen bonds       : angle       2.88298 ( 1212)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.312 
Fit side-chains
  outliers start: 6
  outliers final: 5
  residues processed: 69
  average time/residue: 0.0583
  time to fit residues: 6.7619
Evaluate side-chains
  73 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  509 THR
Chi-restraints excluded: chain B residue  327 LEU
Chi-restraints excluded: chain B residue  509 THR
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 59 optimal weight:    9.9990
   chunk 45 optimal weight:    0.0170
   chunk 92 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 106 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    2.2026

-------------------------------------------------------------------------------
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 = 0.3203 r_free = 0.3203 target = 0.113534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.083751 restraints weight = 10400.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.2785 rms_B_bonded: 1.57
r_work: 0.2653 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2526 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.1555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   8718  Z= 0.180
  Angle     :  0.554   7.410  11890  Z= 0.292
  Chirality :  0.042   0.133   1400
  Planarity :  0.004   0.039   1438
  Dihedral  : 12.215 106.420   1326
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 1.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 11.08 %
    Favored  : 87.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.27), residues: 1060
  helix:  0.21 (0.21), residues: 718
  sheet:  1.55 (0.81), residues: 44
  loop : -1.94 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  65 
 TYR   0.012   0.001   TYR A 589 
 PHE   0.009   0.001   PHE B 616 
 TRP   0.012   0.001   TRP A 227 
 HIS   0.006   0.002   HIS B 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 8718)
  covalent geometry    : angle       0.55365 (11890)
  hydrogen bonds       : bond        0.05173 (  410)
  hydrogen bonds       : angle       3.15182 ( 1212)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.303 
Fit side-chains
  outliers start: 10
  outliers final: 7
  residues processed: 70
  average time/residue: 0.0561
  time to fit residues: 6.6499
Evaluate side-chains
  73 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  509 THR
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  327 LEU
Chi-restraints excluded: chain B residue  509 THR
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   chunk 75 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0370
   chunk 103 optimal weight:    4.9990
   overall best weight:    1.4062

-------------------------------------------------------------------------------
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 = 0.3228 r_free = 0.3228 target = 0.115405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.085681 restraints weight = 10408.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.2811 rms_B_bonded: 1.58
r_work: 0.2681 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2553 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8718  Z= 0.129
  Angle     :  0.509   7.325  11890  Z= 0.269
  Chirality :  0.040   0.132   1400
  Planarity :  0.004   0.040   1438
  Dihedral  : 11.907 104.385   1326
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 1.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 11.59 %
    Favored  : 87.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.27), residues: 1060
  helix:  0.35 (0.21), residues: 718
  sheet:  1.66 (0.82), residues: 44
  loop : -1.90 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  65 
 TYR   0.009   0.001   TYR A 589 
 PHE   0.007   0.001   PHE A 615 
 TRP   0.011   0.001   TRP A 227 
 HIS   0.004   0.001   HIS A 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8718)
  covalent geometry    : angle       0.50884 (11890)
  hydrogen bonds       : bond        0.04287 (  410)
  hydrogen bonds       : angle       3.02917 ( 1212)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.306 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 66
  average time/residue: 0.0603
  time to fit residues: 6.7122
Evaluate side-chains
  70 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  509 THR
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain B residue  327 LEU
Chi-restraints excluded: chain B residue  509 THR
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 1 optimal weight:   10.0000
   chunk 102 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 104 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 75 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    2.1186

-------------------------------------------------------------------------------
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 = 0.3199 r_free = 0.3199 target = 0.113260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.083509 restraints weight = 10369.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.2786 rms_B_bonded: 1.57
r_work: 0.2655 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2527 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8718  Z= 0.173
  Angle     :  0.549   7.365  11890  Z= 0.290
  Chirality :  0.042   0.139   1400
  Planarity :  0.004   0.040   1438
  Dihedral  : 12.160 106.908   1326
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 1.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 11.71 %
    Favored  : 87.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.27), residues: 1060
  helix:  0.24 (0.21), residues: 718
  sheet:  1.58 (0.81), residues: 44
  loop : -1.93 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  65 
 TYR   0.011   0.001   TYR A 589 
 PHE   0.009   0.001   PHE A 616 
 TRP   0.011   0.001   TRP A 227 
 HIS   0.005   0.002   HIS B 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 8718)
  covalent geometry    : angle       0.54928 (11890)
  hydrogen bonds       : bond        0.05046 (  410)
  hydrogen bonds       : angle       3.15184 ( 1212)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.269 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 66
  average time/residue: 0.0549
  time to fit residues: 6.1855
Evaluate side-chains
  72 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  509 THR
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain B residue  327 LEU
Chi-restraints excluded: chain B residue  509 THR
Chi-restraints excluded: chain B residue  551 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 98 optimal weight:    0.3980
   chunk 68 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 90 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3256 r_free = 0.3256 target = 0.117732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.088193 restraints weight = 10279.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.2848 rms_B_bonded: 1.57
r_work: 0.2721 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2595 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.1804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8718  Z= 0.095
  Angle     :  0.475   7.283  11890  Z= 0.252
  Chirality :  0.039   0.127   1400
  Planarity :  0.004   0.040   1438
  Dihedral  : 11.474 101.431   1326
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 1.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 11.96 %
    Favored  : 87.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.27), residues: 1060
  helix:  0.66 (0.21), residues: 710
  sheet:  1.60 (0.82), residues: 44
  loop : -1.87 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  65 
 TYR   0.008   0.001   TYR A 180 
 PHE   0.008   0.001   PHE A 615 
 TRP   0.011   0.001   TRP A 227 
 HIS   0.003   0.001   HIS A 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 8718)
  covalent geometry    : angle       0.47547 (11890)
  hydrogen bonds       : bond        0.03376 (  410)
  hydrogen bonds       : angle       2.89346 ( 1212)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2030.98 seconds
wall clock time: 35 minutes 19.11 seconds (2119.11 seconds total)