Starting phenix.real_space_refine
on Fri Aug 22 21:05:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t4j_41033/08_2025/8t4j_41033.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t4j_41033/08_2025/8t4j_41033.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t4j_41033/08_2025/8t4j_41033.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t4j_41033/08_2025/8t4j_41033.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t4j_41033/08_2025/8t4j_41033.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t4j_41033/08_2025/8t4j_41033.cif"
  }
  resolution = 3.9
  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=   0.019
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      32      5.16       5
     C    4956      2.51       5
     N    1374      2.21       5
     O    1462      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7824
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 4190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 547, 4190
          Classifications: {'peptide': 547}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 20, 'TRANS': 526}
          Unresolved non-hydrogen bonds: 93
          Unresolved non-hydrogen angles: 120
          Unresolved non-hydrogen dihedrals: 75
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 2, 'ASP:plan': 2, 'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 66
    Chain: "A"
      Number of atoms: 3567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 552, 3567
          Classifications: {'peptide': 552}
          Incomplete info: {'truncation_to_alanine': 202}
          Link IDs: {'PTRANS': 18, 'TRANS': 533}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 722
          Unresolved non-hydrogen angles: 930
          Unresolved non-hydrogen dihedrals: 574
          Unresolved non-hydrogen chiralities: 80
          Planarities with less than four sites: {'ARG:plan': 13, 'GLU:plan': 19, 'HIS:plan': 7, 'GLN:plan1': 24, 'PHE:plan': 6, 'ASP:plan': 9, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 422
    Chain: "C"
      Number of atoms: 67
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 67
          Classifications: {'peptide': 8}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 6}
          Chain breaks: 1
  Time building chain proxies: 2.23, per 1000 atoms: 0.29
  Number of scatterers: 7824
  At special positions: 0
  Unit cell: (74.671, 114.104, 132.562, 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      32     16.00
     O    1462      8.00
     N    1374      7.00
     C    4956      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: 0.59
  Conformation dependent library (CDL) restraints added in 424.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2040

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 6 sheets defined
      72.7% alpha, 8.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'B' and resid 136 through 145
      removed outlier: 3.874A  pdb=" N   ARG B 140 " --> pdb=" O   VAL B 136 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   SER B 145 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 167
      removed outlier: 4.508A  pdb=" N   ALA B 154 " --> pdb=" O   PRO B 150 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLY B 165 " --> pdb=" O   LEU B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 181
    Processing helix  chain 'B' and resid 185 through 234
      removed outlier: 3.749A  pdb=" N   SER B 191 " --> pdb=" O   HIS B 187 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   PHE B 214 " --> pdb=" O   ARG B 210 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ARG B 226 " --> pdb=" O   ASN B 222 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   GLU B 227 " --> pdb=" O   LEU B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 244
      removed outlier: 3.868A  pdb=" N   PHE B 241 " --> pdb=" O   ASP B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 255
    Processing helix  chain 'B' and resid 255 through 260
      removed outlier: 4.067A  pdb=" N   LEU B 259 " --> pdb=" O   SER B 255 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   MET B 260 " --> pdb=" O   ASP B 256 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 255 through 260'
    Processing helix  chain 'B' and resid 266 through 289
    Processing helix  chain 'B' and resid 289 through 338
      removed outlier: 3.851A  pdb=" N   LEU B 294 " --> pdb=" O   PRO B 290 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   LEU B 295 " --> pdb=" O   ARG B 291 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   SER B 296 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
      Proline residue:  B 301  - end of helix
      removed outlier: 3.898A  pdb=" N   GLN B 315 " --> pdb=" O   ASN B 311 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLY B 338 " --> pdb=" O   GLU B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 344
      removed outlier: 3.572A  pdb=" N   VAL B 342 " --> pdb=" O   GLY B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 402
      removed outlier: 3.672A  pdb=" N   GLU B 351 " --> pdb=" O   ALA B 347 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU B 385 " --> pdb=" O   ARG B 381 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   LEU B 390 " --> pdb=" O   GLY B 386 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   SER B 393 " --> pdb=" O   MET B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 448
      removed outlier: 4.048A  pdb=" N   GLU B 417 " --> pdb=" O   MET B 413 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   SER B 418 " --> pdb=" O   ILE B 414 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   SER B 421 " --> pdb=" O   GLU B 417 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   VAL B 427 " --> pdb=" O   VAL B 423 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   TYR B 430 " --> pdb=" O   LEU B 426 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   GLY B 431 " --> pdb=" O   VAL B 427 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ASP B 432 " --> pdb=" O   TYR B 428 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   GLU B 441 " --> pdb=" O   VAL B 437 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   LYS B 442 " --> pdb=" O   GLY B 438 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   VAL B 443 " --> pdb=" O   ALA B 439 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   TYR B 446 " --> pdb=" O   LYS B 442 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 508
    Processing helix  chain 'B' and resid 509 through 517
      removed outlier: 3.966A  pdb=" N   ALA B 513 " --> pdb=" O   LYS B 509 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   GLN B 517 " --> pdb=" O   ALA B 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 535 through 537
      No H-bonds generated for 'chain 'B' and resid 535 through 537'
    Processing helix  chain 'B' and resid 538 through 543
      removed outlier: 3.699A  pdb=" N   HIS B 543 " --> pdb=" O   HIS B 539 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 565
      removed outlier: 3.822A  pdb=" N   ALA B 565 " --> pdb=" O   ARG B 561 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 583
    Processing helix  chain 'B' and resid 585 through 590
      removed outlier: 3.619A  pdb=" N   GLN B 590 " --> pdb=" O   ASP B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 594 through 597
    Processing helix  chain 'B' and resid 601 through 605
    Processing helix  chain 'B' and resid 608 through 622
      removed outlier: 3.569A  pdb=" N   ARG B 614 " --> pdb=" O   GLY B 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 633 through 636
      removed outlier: 3.902A  pdb=" N   ALA B 636 " --> pdb=" O   ALA B 633 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 633 through 636'
    Processing helix  chain 'B' and resid 638 through 647
      removed outlier: 3.579A  pdb=" N   LEU B 645 " --> pdb=" O   CYS B 641 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 653
      removed outlier: 4.163A  pdb=" N   ASP B 653 " --> pdb=" O   ASN B 649 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 662 through 668
      removed outlier: 4.161A  pdb=" N   THR B 665 " --> pdb=" O   ARG B 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 182
      removed outlier: 4.249A  pdb=" N   GLY A 181 " --> pdb=" O   GLY A 178 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   SER A 182 " --> pdb=" O   CYS A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 202
      removed outlier: 3.653A  pdb=" N   LEU A 187 " --> pdb=" O   GLU A 183 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   MET A 202 " --> pdb=" O   SER A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 218
      removed outlier: 3.525A  pdb=" N   PHE A 206 " --> pdb=" O   MET A 202 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   THR A 208 " --> pdb=" O   ILE A 204 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ARG A 210 " --> pdb=" O   PHE A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 269
      removed outlier: 4.428A  pdb=" N   ARG A 226 " --> pdb=" O   ASP A 222 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   MET A 231 " --> pdb=" O   ASN A 227 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   THR A 235 " --> pdb=" O   MET A 231 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE A 248 " --> pdb=" O   VAL A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 324
      removed outlier: 4.147A  pdb=" N   THR A 292 " --> pdb=" O   VAL A 288 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   ASP A 297 " --> pdb=" O   SER A 293 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   SER A 304 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   TRP A 322 " --> pdb=" O   GLY A 318 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   SER A 324 " --> pdb=" O   MET A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 373
      removed outlier: 3.560A  pdb=" N   THR A 328 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   MET A 329 " --> pdb=" O   VAL A 325 " (cutoff:3.500A)
      Proline residue:  A 336  - end of helix
      Proline residue:  A 342  - end of helix
      removed outlier: 3.797A  pdb=" N   TRP A 348 " --> pdb=" O   LYS A 344 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL A 354 " --> pdb=" O   GLN A 350 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ALA A 367 " --> pdb=" O   SER A 363 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ALA A 373 " --> pdb=" O   GLU A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 381
    Processing helix  chain 'A' and resid 382 through 436
      removed outlier: 3.740A  pdb=" N   ALA A 387 " --> pdb=" O   GLU A 383 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LYS A 393 " --> pdb=" O   LYS A 389 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLU A 396 " --> pdb=" O   GLU A 392 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ILE A 397 " --> pdb=" O   LYS A 393 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LEU A 400 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LYS A 403 " --> pdb=" O   THR A 399 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   VAL A 406 " --> pdb=" O   GLN A 402 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ALA A 407 " --> pdb=" O   LYS A 403 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ALA A 409 " --> pdb=" O   ALA A 405 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   VAL A 410 " --> pdb=" O   VAL A 406 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU A 422 " --> pdb=" O   SER A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 476
      removed outlier: 3.556A  pdb=" N   LEU A 444 " --> pdb=" O   SER A 440 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLN A 456 " --> pdb=" O   MET A 452 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   TYR A 465 " --> pdb=" O   LEU A 461 " (cutoff:3.500A)
      Proline residue:  A 466  - end of helix
      removed outlier: 3.636A  pdb=" N   GLU A 476 " --> pdb=" O   VAL A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 483
      removed outlier: 4.260A  pdb=" N   TYR A 481 " --> pdb=" O   LYS A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 517
      No H-bonds generated for 'chain 'A' and resid 515 through 517'
    Processing helix  chain 'A' and resid 543 through 552
    Processing helix  chain 'A' and resid 568 through 572
      removed outlier: 3.871A  pdb=" N   TYR A 572 " --> pdb=" O   LEU A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 581
      removed outlier: 3.693A  pdb=" N   VAL A 581 " --> pdb=" O   LEU A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 619
    Processing helix  chain 'A' and resid 621 through 626
    Processing helix  chain 'A' and resid 630 through 634
    Processing helix  chain 'A' and resid 637 through 641
    Processing helix  chain 'A' and resid 644 through 660
      removed outlier: 4.169A  pdb=" N   ALA A 650 " --> pdb=" O   GLY A 646 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ARG A 659 " --> pdb=" O   ARG A 655 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 669 through 672
      removed outlier: 3.510A  pdb=" N   ALA A 672 " --> pdb=" O   ALA A 669 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 669 through 672'
    Processing helix  chain 'A' and resid 674 through 688
    Processing helix  chain 'A' and resid 689 through 694
    Processing helix  chain 'A' and resid 702 through 709
    Processing helix  chain 'A' and resid 725 through 732
    Processing helix  chain 'A' and resid 734 through 739
    Processing sheet with id=AA1, first strand: chain 'B' and resid 486 through 489
      removed outlier: 6.233A  pdb=" N   LYS B 487 " --> pdb=" O   PHE B 475 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   PHE B 475 " --> pdb=" O   LYS B 487 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 486 through 489
      removed outlier: 6.233A  pdb=" N   LYS B 487 " --> pdb=" O   PHE B 475 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   PHE B 475 " --> pdb=" O   LYS B 487 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLN B 471 " --> pdb=" O   GLN B 526 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLN B 526 " --> pdb=" O   GLN B 471 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   VAL B 473 " --> pdb=" O   GLY B 524 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   GLY B 524 " --> pdb=" O   VAL B 473 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 546 through 549
      removed outlier: 6.656A  pdb=" N   VAL B 498 " --> pdb=" O   GLN B 671 " (cutoff:3.500A)
      removed outlier: 7.949A  pdb=" N   LEU B 673 " --> pdb=" O   VAL B 498 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ALA B 500 " --> pdb=" O   LEU B 673 " (cutoff:3.500A)
      removed outlier: 7.476A  pdb=" N   LEU B 675 " --> pdb=" O   ALA B 500 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   VAL B 502 " --> pdb=" O   LEU B 675 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 558 through 559
      removed outlier: 3.551A  pdb=" N   GLY B 558 " --> pdb=" O   VAL B 600 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 519 through 524
      removed outlier: 5.251A  pdb=" N   GLN A 522 " --> pdb=" O   PHE A 510 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   PHE A 510 " --> pdb=" O   GLN A 522 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   VAL A 508 " --> pdb=" O   GLY A 559 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   GLY A 559 " --> pdb=" O   VAL A 508 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 582 through 584
      removed outlier: 3.658A  pdb=" N   ILE A 665 " --> pdb=" O   ALA A 582 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ASP A 667 " --> pdb=" O   VAL A 584 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   LEU A 664 " --> pdb=" O   LEU A 697 " (cutoff:3.500A)
      removed outlier: 8.016A  pdb=" N   ILE A 699 " --> pdb=" O   LEU A 664 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   LEU A 666 " --> pdb=" O   ILE A 699 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   VAL A 533 " --> pdb=" O   HIS A 711 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   LEU A 713 " --> pdb=" O   VAL A 533 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   ALA A 535 " --> pdb=" O   LEU A 713 " (cutoff:3.500A)
      removed outlier: 8.190A  pdb=" N   LEU A 715 " --> pdb=" O   ALA A 535 " (cutoff:3.500A)
      removed outlier: 5.708A  pdb=" N   GLU A 716 " --> pdb=" O   ILE A 720 " (cutoff:3.500A)
      removed outlier: 5.415A  pdb=" N   ILE A 720 " --> pdb=" O   GLU A 716 " (cutoff:3.500A)

    553 hydrogen bonds defined for protein.
    1605 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: 0.90

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2659
        1.34 -     1.46: 1728
        1.46 -     1.58: 3508
        1.58 -     1.70: 0
        1.70 -     1.81: 55
  Bond restraints: 7950
  Sorted by residual:
  bond pdb=" CA  ILE B 169 "
       pdb=" CB  ILE B 169 "
    ideal  model  delta    sigma   weight residual
    1.534  1.545 -0.010 6.80e-03 2.16e+04 2.38e+00
  bond pdb=" CB  GLU B 166 "
       pdb=" CG  GLU B 166 "
    ideal  model  delta    sigma   weight residual
    1.520  1.557 -0.037 3.00e-02 1.11e+03 1.54e+00
  bond pdb=" CA  ILE B 169 "
       pdb=" C   ILE B 169 "
    ideal  model  delta    sigma   weight residual
    1.520  1.530 -0.010 8.80e-03 1.29e+04 1.35e+00
  bond pdb=" CA  ILE A 665 "
       pdb=" CB  ILE A 665 "
    ideal  model  delta    sigma   weight residual
    1.551  1.540  0.011 1.08e-02 8.57e+03 1.05e+00
  bond pdb=" C   LYS A 660 "
       pdb=" O   LYS A 660 "
    ideal  model  delta    sigma   weight residual
    1.235  1.230  0.005 4.70e-03 4.53e+04 9.37e-01
  ... (remaining 7945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 10628
        1.72 -     3.43: 154
        3.43 -     5.15: 27
        5.15 -     6.87: 13
        6.87 -     8.58: 7
  Bond angle restraints: 10829
  Sorted by residual:
  angle pdb=" CA  GLU B 166 "
        pdb=" CB  GLU B 166 "
        pdb=" CG  GLU B 166 "
      ideal   model   delta    sigma   weight residual
     114.10  121.34   -7.24 2.00e+00 2.50e-01 1.31e+01
  angle pdb=" CB  GLU B 166 "
        pdb=" CG  GLU B 166 "
        pdb=" CD  GLU B 166 "
      ideal   model   delta    sigma   weight residual
     112.60  117.94   -5.34 1.70e+00 3.46e-01 9.88e+00
  angle pdb=" N   TYR A 692 "
        pdb=" CA  TYR A 692 "
        pdb=" C   TYR A 692 "
      ideal   model   delta    sigma   weight residual
     114.04  110.17    3.87 1.24e+00 6.50e-01 9.72e+00
  angle pdb=" N   VAL A 520 "
        pdb=" CA  VAL A 520 "
        pdb=" C   VAL A 520 "
      ideal   model   delta    sigma   weight residual
     113.20  110.34    2.86 9.60e-01 1.09e+00 8.86e+00
  angle pdb=" N   ILE B 169 "
        pdb=" CA  ILE B 169 "
        pdb=" CB  ILE B 169 "
      ideal   model   delta    sigma   weight residual
     110.50  112.20   -1.70 6.30e-01 2.52e+00 7.29e+00
  ... (remaining 10824 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 4339
       18.00 -    36.00: 313
       36.00 -    54.00: 78
       54.00 -    71.99: 7
       71.99 -    89.99: 5
  Dihedral angle restraints: 4742
    sinusoidal: 1574
      harmonic: 3168
  Sorted by residual:
  dihedral pdb=" CA  VAL B 387 "
           pdb=" C   VAL B 387 "
           pdb=" N   GLN B 388 "
           pdb=" CA  GLN B 388 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.23  -15.77     0      5.00e+00 4.00e-02 9.95e+00
  dihedral pdb=" CA  ASN B 267 "
           pdb=" CB  ASN B 267 "
           pdb=" CG  ASN B 267 "
           pdb=" OD1 ASN B 267 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -177.32  -62.68     2      2.00e+01 2.50e-03 9.47e+00
  dihedral pdb=" CA  ARG B 561 "
           pdb=" CB  ARG B 561 "
           pdb=" CG  ARG B 561 "
           pdb=" CD  ARG B 561 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.76  -57.76     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 4739 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1010
       0.042 -    0.084: 231
       0.084 -    0.126: 51
       0.126 -    0.167: 1
       0.167 -    0.209: 2
  Chirality restraints: 1295
  Sorted by residual:
  chirality pdb=" CG  LEU A 211 "
            pdb=" CB  LEU A 211 "
            pdb=" CD1 LEU A 211 "
            pdb=" CD2 LEU A 211 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CB  ILE B 169 "
            pdb=" CA  ILE B 169 "
            pdb=" CG1 ILE B 169 "
            pdb=" CG2 ILE B 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.72e-01
  chirality pdb=" CG  LEU B 295 "
            pdb=" CB  LEU B 295 "
            pdb=" CD1 LEU B 295 "
            pdb=" CD2 LEU B 295 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.93e-01
  ... (remaining 1292 not shown)

  Planarity restraints: 1415
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 146 "   -0.030 5.00e-02 4.00e+02   4.49e-02 3.22e+00
        pdb=" N   PRO B 147 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B 147 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 147 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 204 "    0.029 5.00e-02 4.00e+02   4.35e-02 3.03e+00
        pdb=" N   PRO A 205 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A 205 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 205 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 339 "    0.008 2.00e-02 2.50e+03   1.17e-02 2.38e+00
        pdb=" CG  PHE A 339 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 339 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 339 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 339 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 339 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 339 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1412 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2144
        2.80 -     3.33: 8273
        3.33 -     3.85: 12472
        3.85 -     4.38: 13803
        4.38 -     4.90: 23172
  Nonbonded interactions: 59864
  Sorted by model distance:
  nonbonded pdb=" O   THR A 289 "
            pdb=" OG  SER A 293 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OH  TYR A 249 "
            pdb=" O   SER A 300 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" N   GLU B 417 "
            pdb=" OE1 GLU B 417 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" O   MET A 452 "
            pdb=" OG1 THR A 455 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" O   LEU B 253 "
            pdb=" OG1 THR B 257 "
     model   vdw
     2.318 3.040
  ... (remaining 59859 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             10.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.060
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
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      :  0.002   0.037   7950  Z= 0.118
  Angle     :  0.600   8.583  10829  Z= 0.326
  Chirality :  0.037   0.209   1295
  Planarity :  0.003   0.045   1415
  Dihedral  : 13.692  89.993   2702
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 12.94 %
    Favored  : 86.78 %
  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 aren not related in a simple way.
  whole:  0.48 (0.26), residues: 1095
  helix:  0.58 (0.20), residues: 698
  sheet: -0.35 (0.73), residues: 66
  loop :  0.20 (0.38), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 378 
 TYR   0.010   0.001   TYR B 376 
 PHE   0.027   0.001   PHE A 339 
 TRP   0.015   0.001   TRP A 413 
 HIS   0.002   0.001   HIS B 543 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 7950)
  covalent geometry    : angle       0.60018 (10829)
  hydrogen bonds       : bond        0.26407 (  551)
  hydrogen bonds       : angle       7.61521 ( 1605)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 115
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: B  166 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7675 (tt0)
REVERT: B  254 SER cc_start: 0.9012 (t) cc_final: 0.8762 (p)
REVERT: B  260 MET cc_start: 0.8357 (mmm) cc_final: 0.8134 (mmp)
REVERT: B  366 TYR cc_start: 0.8523 (m-80) cc_final: 0.8273 (m-10)
REVERT: B  467 VAL cc_start: 0.8277 (t) cc_final: 0.7924 (p)
REVERT: A  189 LEU cc_start: 0.8072 (mm) cc_final: 0.7798 (tp)
REVERT: A  191 LEU cc_start: 0.8771 (tt) cc_final: 0.7843 (mm)
  outliers start: 2
  outliers final: 0
  residues processed: 116
  average time/residue: 0.0753
  time to fit residues: 12.1963
Evaluate side-chains
  89 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    6.9990
   chunk 106 optimal weight:   40.0000
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
B 267 ASN
B 350 HIS
B 406 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.122045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.093693 restraints weight = 18791.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.092965 restraints weight = 11935.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.093895 restraints weight = 10110.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.094617 restraints weight = 8312.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.094830 restraints weight = 7464.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.1640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7950  Z= 0.211
  Angle     :  0.664  10.037  10829  Z= 0.348
  Chirality :  0.044   0.221   1295
  Planarity :  0.005   0.051   1415
  Dihedral  :  3.828  20.185   1174
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 13.78 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.26), residues: 1095
  helix:  0.88 (0.19), residues: 713
  sheet: -0.50 (0.71), residues: 66
  loop : -0.09 (0.39), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 391 
 TYR   0.016   0.001   TYR A 349 
 PHE   0.015   0.002   PHE B 214 
 TRP   0.011   0.002   TRP A 413 
 HIS   0.003   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 7950)
  covalent geometry    : angle       0.66401 (10829)
  hydrogen bonds       : bond        0.07363 (  551)
  hydrogen bonds       : angle       5.00997 ( 1605)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.264 
Fit side-chains
REVERT: B  391 MET cc_start: 0.8037 (tpp) cc_final: 0.7821 (tpp)
REVERT: B  413 MET cc_start: 0.8357 (tpp) cc_final: 0.8059 (tpp)
REVERT: B  433 MET cc_start: 0.8215 (mmt) cc_final: 0.7907 (mmt)
REVERT: B  467 VAL cc_start: 0.8886 (t) cc_final: 0.8495 (p)
REVERT: A  189 LEU cc_start: 0.8250 (mm) cc_final: 0.8049 (tp)
REVERT: A  191 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.7622 (mt)
  outliers start: 20
  outliers final: 11
  residues processed: 108
  average time/residue: 0.0560
  time to fit residues: 9.2232
Evaluate side-chains
  95 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  307 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9980
   chunk 50 optimal weight:    7.9990
   chunk 34 optimal weight:    3.9990
   chunk 80 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 102 optimal weight:   20.0000
   chunk 23 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 267 ASN
B 314 HIS
B 350 HIS
** B 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.123898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.092043 restraints weight = 18775.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.094439 restraints weight = 10891.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.096152 restraints weight = 7611.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.097219 restraints weight = 5925.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.097925 restraints weight = 5003.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.2198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7950  Z= 0.152
  Angle     :  0.587  10.424  10829  Z= 0.298
  Chirality :  0.041   0.188   1295
  Planarity :  0.004   0.049   1415
  Dihedral  :  3.735  21.562   1174
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 14.91 %
    Favored  : 81.58 %
  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 aren not related in a simple way.
  whole:  0.94 (0.26), residues: 1095
  helix:  1.12 (0.19), residues: 710
  sheet: -0.48 (0.70), residues: 66
  loop : -0.04 (0.38), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 668 
 TYR   0.011   0.001   TYR A 309 
 PHE   0.012   0.001   PHE A 339 
 TRP   0.011   0.001   TRP A 413 
 HIS   0.004   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7950)
  covalent geometry    : angle       0.58691 (10829)
  hydrogen bonds       : bond        0.05974 (  551)
  hydrogen bonds       : angle       4.41618 ( 1605)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 91
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: B  385 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8469 (tt)
REVERT: B  390 LEU cc_start: 0.8539 (tt) cc_final: 0.8287 (tp)
REVERT: B  413 MET cc_start: 0.8288 (tpp) cc_final: 0.7980 (tpp)
REVERT: B  467 VAL cc_start: 0.8869 (t) cc_final: 0.8516 (p)
REVERT: B  680 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6239 (pt)
REVERT: A  191 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.7642 (mt)
REVERT: A  213 ASP cc_start: 0.8722 (m-30) cc_final: 0.8428 (m-30)
  outliers start: 25
  outliers final: 14
  residues processed: 108
  average time/residue: 0.0596
  time to fit residues: 9.6399
Evaluate side-chains
  95 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  285 MET
Chi-restraints excluded: chain B residue  314 HIS
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  656 VAL
Chi-restraints excluded: chain B residue  680 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  356 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 50 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9990
   chunk 100 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 101 optimal weight:    0.8980
   chunk 103 optimal weight:    9.9990
   chunk 85 optimal weight:   20.0000
   chunk 21 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
B 350 HIS
A 261 GLN
A 401 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.122508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.090537 restraints weight = 19231.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.093010 restraints weight = 10840.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.094754 restraints weight = 7469.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.095954 restraints weight = 5788.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.096657 restraints weight = 4834.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7950  Z= 0.183
  Angle     :  0.619  12.466  10829  Z= 0.310
  Chirality :  0.042   0.214   1295
  Planarity :  0.004   0.050   1415
  Dihedral  :  3.737  22.572   1174
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 17.02 %
    Favored  : 78.48 %
  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 aren not related in a simple way.
  whole:  0.95 (0.26), residues: 1095
  helix:  1.14 (0.19), residues: 707
  sheet: -0.37 (0.70), residues: 64
  loop : -0.10 (0.38), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 313 
 TYR   0.012   0.001   TYR A 309 
 PHE   0.011   0.001   PHE B 588 
 TRP   0.009   0.001   TRP A 308 
 HIS   0.004   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 7950)
  covalent geometry    : angle       0.61858 (10829)
  hydrogen bonds       : bond        0.05700 (  551)
  hydrogen bonds       : angle       4.36223 ( 1605)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 78
  time to evaluate  : 0.307 
Fit side-chains
REVERT: B  385 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8438 (tt)
REVERT: B  390 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8409 (tp)
REVERT: B  413 MET cc_start: 0.8298 (tpp) cc_final: 0.7938 (tpp)
REVERT: B  467 VAL cc_start: 0.8901 (t) cc_final: 0.8548 (p)
REVERT: A  191 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.7660 (mt)
  outliers start: 32
  outliers final: 22
  residues processed: 102
  average time/residue: 0.0507
  time to fit residues: 8.3381
Evaluate side-chains
  102 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  285 MET
Chi-restraints excluded: chain B residue  314 HIS
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  656 VAL
Chi-restraints excluded: chain B residue  680 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 70 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 101 optimal weight:    0.0050
   chunk 95 optimal weight:   20.0000
   chunk 106 optimal weight:    6.9990
   chunk 85 optimal weight:   40.0000
   chunk 50 optimal weight:    8.9990
   chunk 86 optimal weight:    0.0170
   overall best weight:    1.3836

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

Flipped N/Q/H residues before XYZ refinement:
B 350 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.121922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.093930 restraints weight = 19188.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.092478 restraints weight = 12694.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.093776 restraints weight = 10405.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.095274 restraints weight = 7976.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.095280 restraints weight = 6933.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7950  Z= 0.184
  Angle     :  0.614  12.141  10829  Z= 0.308
  Chirality :  0.042   0.234   1295
  Planarity :  0.004   0.051   1415
  Dihedral  :  3.781  23.196   1174
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 18.14 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.26), residues: 1095
  helix:  1.15 (0.19), residues: 705
  sheet: -0.51 (0.69), residues: 64
  loop : -0.13 (0.37), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 333 
 TYR   0.011   0.001   TYR B 376 
 PHE   0.014   0.001   PHE A 306 
 TRP   0.009   0.001   TRP A 308 
 HIS   0.005   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 7950)
  covalent geometry    : angle       0.61361 (10829)
  hydrogen bonds       : bond        0.05545 (  551)
  hydrogen bonds       : angle       4.31635 ( 1605)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 81
  time to evaluate  : 0.321 
Fit side-chains
REVERT: B  385 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8421 (tt)
REVERT: B  413 MET cc_start: 0.8363 (tpp) cc_final: 0.7254 (tpp)
REVERT: B  467 VAL cc_start: 0.8933 (t) cc_final: 0.8595 (p)
REVERT: A  191 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.7608 (mt)
  outliers start: 32
  outliers final: 24
  residues processed: 105
  average time/residue: 0.0542
  time to fit residues: 9.2188
Evaluate side-chains
  105 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 79
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  285 MET
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  628 LEU
Chi-restraints excluded: chain B residue  656 VAL
Chi-restraints excluded: chain B residue  680 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 20 optimal weight:    8.9990
   chunk 106 optimal weight:   30.0000
   chunk 91 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 69 optimal weight:    3.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B 350 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.123132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.095271 restraints weight = 18813.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.093918 restraints weight = 12358.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.095291 restraints weight = 9800.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.096627 restraints weight = 7703.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.096815 restraints weight = 6457.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7950  Z= 0.148
  Angle     :  0.599  12.321  10829  Z= 0.295
  Chirality :  0.041   0.249   1295
  Planarity :  0.004   0.047   1415
  Dihedral  :  3.721  24.152   1174
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 18.99 %
    Favored  : 76.23 %
  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 aren not related in a simple way.
  whole:  1.01 (0.26), residues: 1095
  helix:  1.28 (0.19), residues: 701
  sheet: -0.54 (0.64), residues: 73
  loop : -0.22 (0.38), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 319 
 TYR   0.011   0.001   TYR A 309 
 PHE   0.043   0.002   PHE A 447 
 TRP   0.008   0.001   TRP A 308 
 HIS   0.005   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 7950)
  covalent geometry    : angle       0.59936 (10829)
  hydrogen bonds       : bond        0.05293 (  551)
  hydrogen bonds       : angle       4.14400 ( 1605)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 84
  time to evaluate  : 0.286 
Fit side-chains
REVERT: B  385 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8386 (tp)
REVERT: B  389 MET cc_start: 0.7981 (tpt) cc_final: 0.7555 (tpt)
REVERT: B  390 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8408 (tp)
REVERT: B  413 MET cc_start: 0.8287 (tpp) cc_final: 0.7802 (tpp)
REVERT: B  467 VAL cc_start: 0.8899 (t) cc_final: 0.8568 (p)
REVERT: A  191 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.7648 (mt)
REVERT: A  213 ASP cc_start: 0.8664 (m-30) cc_final: 0.8396 (m-30)
  outliers start: 34
  outliers final: 21
  residues processed: 110
  average time/residue: 0.0505
  time to fit residues: 9.0120
Evaluate side-chains
  107 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 83
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  285 MET
Chi-restraints excluded: chain B residue  314 HIS
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  429 ILE
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  628 LEU
Chi-restraints excluded: chain B residue  656 VAL
Chi-restraints excluded: chain B residue  680 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  307 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:   30.0000
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 104 optimal weight:    0.0670
   chunk 58 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 94 optimal weight:   20.0000
   chunk 8 optimal weight:    0.6980
   chunk 95 optimal weight:    7.9990
   chunk 54 optimal weight:   20.0000
   overall best weight:    1.0722

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

Flipped N/Q/H residues before XYZ refinement:
B 262 ASN
B 350 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.123141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.095192 restraints weight = 18777.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.093795 restraints weight = 12760.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.095210 restraints weight = 9969.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.096586 restraints weight = 7797.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.096762 restraints weight = 6641.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7950  Z= 0.160
  Angle     :  0.609  11.708  10829  Z= 0.302
  Chirality :  0.041   0.258   1295
  Planarity :  0.004   0.047   1415
  Dihedral  :  3.694  22.188   1174
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 18.71 %
    Favored  : 76.51 %
  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 aren not related in a simple way.
  whole:  0.99 (0.26), residues: 1095
  helix:  1.29 (0.19), residues: 703
  sheet: -0.66 (0.63), residues: 73
  loop : -0.29 (0.37), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 319 
 TYR   0.011   0.001   TYR B 376 
 PHE   0.033   0.002   PHE A 447 
 TRP   0.009   0.001   TRP A 308 
 HIS   0.005   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 7950)
  covalent geometry    : angle       0.60922 (10829)
  hydrogen bonds       : bond        0.05211 (  551)
  hydrogen bonds       : angle       4.11033 ( 1605)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 80
  time to evaluate  : 0.295 
Fit side-chains
REVERT: B  389 MET cc_start: 0.7986 (tpt) cc_final: 0.7514 (tpt)
REVERT: B  390 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8420 (tp)
REVERT: B  413 MET cc_start: 0.8263 (tpp) cc_final: 0.7819 (tpp)
REVERT: B  467 VAL cc_start: 0.8911 (t) cc_final: 0.8585 (p)
REVERT: A  191 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.7601 (mt)
REVERT: A  213 ASP cc_start: 0.8655 (m-30) cc_final: 0.8428 (m-30)
  outliers start: 34
  outliers final: 26
  residues processed: 106
  average time/residue: 0.0492
  time to fit residues: 8.4531
Evaluate side-chains
  108 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 80
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  199 PHE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  285 MET
Chi-restraints excluded: chain B residue  314 HIS
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  429 ILE
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  628 LEU
Chi-restraints excluded: chain B residue  656 VAL
Chi-restraints excluded: chain B residue  680 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  421 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 37 optimal weight:    0.1980
   chunk 74 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 95 optimal weight:    0.8980
   chunk 108 optimal weight:   20.0000
   chunk 87 optimal weight:   30.0000
   chunk 35 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 76 optimal weight:    0.7980
   chunk 45 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 350 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.124398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.098709 restraints weight = 19348.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.097335 restraints weight = 13107.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.098964 restraints weight = 10685.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.099334 restraints weight = 7878.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.099456 restraints weight = 7331.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7950  Z= 0.135
  Angle     :  0.611  13.830  10829  Z= 0.296
  Chirality :  0.041   0.238   1295
  Planarity :  0.003   0.039   1415
  Dihedral  :  3.638  23.724   1174
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 19.55 %
    Favored  : 76.09 %
  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 aren not related in a simple way.
  whole:  1.05 (0.26), residues: 1095
  helix:  1.34 (0.19), residues: 711
  sheet: -0.74 (0.63), residues: 75
  loop : -0.27 (0.38), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 319 
 TYR   0.012   0.001   TYR B 376 
 PHE   0.029   0.001   PHE A 447 
 TRP   0.008   0.001   TRP A 308 
 HIS   0.005   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7950)
  covalent geometry    : angle       0.61100 (10829)
  hydrogen bonds       : bond        0.04992 (  551)
  hydrogen bonds       : angle       3.99605 ( 1605)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 83
  time to evaluate  : 0.212 
Fit side-chains
REVERT: B  389 MET cc_start: 0.7932 (tpt) cc_final: 0.7474 (tpt)
REVERT: B  390 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8398 (tp)
REVERT: B  413 MET cc_start: 0.8228 (tpp) cc_final: 0.7812 (tpp)
REVERT: B  467 VAL cc_start: 0.8765 (t) cc_final: 0.8525 (p)
REVERT: B  680 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6379 (pt)
REVERT: A  191 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.7587 (mt)
REVERT: A  213 ASP cc_start: 0.8601 (m-30) cc_final: 0.8349 (m-30)
  outliers start: 31
  outliers final: 24
  residues processed: 108
  average time/residue: 0.0525
  time to fit residues: 8.9052
Evaluate side-chains
  106 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 79
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  199 PHE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  285 MET
Chi-restraints excluded: chain B residue  314 HIS
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  628 LEU
Chi-restraints excluded: chain B residue  656 VAL
Chi-restraints excluded: chain B residue  674 VAL
Chi-restraints excluded: chain B residue  680 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 87 optimal weight:   20.0000
   chunk 101 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 93 optimal weight:    2.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
B 350 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.121857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.093211 restraints weight = 18970.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.092218 restraints weight = 12780.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.093444 restraints weight = 10270.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.094685 restraints weight = 8129.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.094753 restraints weight = 6889.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   7950  Z= 0.201
  Angle     :  0.666  13.055  10829  Z= 0.328
  Chirality :  0.043   0.243   1295
  Planarity :  0.004   0.043   1415
  Dihedral  :  3.739  20.992   1174
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 19.55 %
    Favored  : 75.81 %
  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 aren not related in a simple way.
  whole:  0.91 (0.26), residues: 1095
  helix:  1.25 (0.19), residues: 704
  sheet: -0.75 (0.62), residues: 73
  loop : -0.36 (0.37), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 319 
 TYR   0.014   0.001   TYR B 376 
 PHE   0.026   0.002   PHE A 306 
 TRP   0.010   0.002   TRP A 308 
 HIS   0.005   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 7950)
  covalent geometry    : angle       0.66578 (10829)
  hydrogen bonds       : bond        0.05200 (  551)
  hydrogen bonds       : angle       4.17180 ( 1605)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 81
  time to evaluate  : 0.189 
Fit side-chains
REVERT: B  390 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8490 (tp)
REVERT: B  413 MET cc_start: 0.8268 (tpp) cc_final: 0.8008 (tpp)
REVERT: B  467 VAL cc_start: 0.8961 (t) cc_final: 0.8654 (p)
REVERT: A  191 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.7546 (mt)
REVERT: A  213 ASP cc_start: 0.8660 (m-30) cc_final: 0.8414 (m-30)
  outliers start: 33
  outliers final: 27
  residues processed: 105
  average time/residue: 0.0489
  time to fit residues: 8.0261
Evaluate side-chains
  108 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 79
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  199 PHE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  246 THR
Chi-restraints excluded: chain B residue  285 MET
Chi-restraints excluded: chain B residue  314 HIS
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  628 LEU
Chi-restraints excluded: chain B residue  656 VAL
Chi-restraints excluded: chain B residue  674 VAL
Chi-restraints excluded: chain B residue  680 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  421 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 92 optimal weight:    7.9990
   chunk 53 optimal weight:    0.0570
   chunk 48 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 91 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0970
   overall best weight:    0.4696

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

Flipped N/Q/H residues before XYZ refinement:
B 350 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.124165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.096486 restraints weight = 18834.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.094744 restraints weight = 13055.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.096202 restraints weight = 10691.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.097433 restraints weight = 8208.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.097395 restraints weight = 7204.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7950  Z= 0.129
  Angle     :  0.635  12.941  10829  Z= 0.305
  Chirality :  0.041   0.226   1295
  Planarity :  0.003   0.037   1415
  Dihedral  :  3.634  24.502   1174
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 21.10 %
    Favored  : 75.67 %
  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 aren not related in a simple way.
  whole:  1.12 (0.26), residues: 1095
  helix:  1.41 (0.20), residues: 711
  sheet: -0.76 (0.63), residues: 75
  loop : -0.29 (0.38), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 210 
 TYR   0.013   0.001   TYR A 349 
 PHE   0.029   0.001   PHE A 447 
 TRP   0.007   0.001   TRP A 308 
 HIS   0.005   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 7950)
  covalent geometry    : angle       0.63525 (10829)
  hydrogen bonds       : bond        0.04877 (  551)
  hydrogen bonds       : angle       3.95299 ( 1605)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 84
  time to evaluate  : 0.226 
Fit side-chains
REVERT: B  319 ARG cc_start: 0.8449 (mmm160) cc_final: 0.7769 (mmm160)
REVERT: B  389 MET cc_start: 0.8074 (tpt) cc_final: 0.7603 (tpt)
REVERT: B  390 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8368 (tp)
REVERT: B  467 VAL cc_start: 0.8688 (t) cc_final: 0.8485 (p)
REVERT: B  680 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6406 (pt)
REVERT: A  191 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.7540 (mt)
REVERT: A  213 ASP cc_start: 0.8568 (m-30) cc_final: 0.8335 (m-30)
REVERT: A  335 LEU cc_start: 0.8646 (mt) cc_final: 0.8400 (mt)
  outliers start: 23
  outliers final: 19
  residues processed: 100
  average time/residue: 0.0507
  time to fit residues: 7.9424
Evaluate side-chains
  101 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  177 ILE
Chi-restraints excluded: chain B residue  199 PHE
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  246 THR
Chi-restraints excluded: chain B residue  285 MET
Chi-restraints excluded: chain B residue  314 HIS
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain B residue  628 LEU
Chi-restraints excluded: chain B residue  656 VAL
Chi-restraints excluded: chain B residue  674 VAL
Chi-restraints excluded: chain B residue  680 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  421 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9990
   chunk 108 optimal weight:   20.0000
   chunk 75 optimal weight:    2.9990
   chunk 87 optimal weight:   40.0000
   chunk 101 optimal weight:    0.0980
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.2186

-------------------------------------------------------------------------------
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 = 0.3936 r_free = 0.3936 target = 0.122567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.094098 restraints weight = 18882.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.093500 restraints weight = 12646.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.094769 restraints weight = 9945.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.095478 restraints weight = 8131.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.095694 restraints weight = 6981.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.3184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7950  Z= 0.174
  Angle     :  0.645  12.869  10829  Z= 0.318
  Chirality :  0.042   0.240   1295
  Planarity :  0.004   0.040   1415
  Dihedral  :  3.653  22.061   1174
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 20.82 %
    Favored  : 75.67 %
  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 aren not related in a simple way.
  whole:  1.05 (0.26), residues: 1095
  helix:  1.35 (0.20), residues: 714
  sheet: -0.69 (0.63), residues: 73
  loop : -0.36 (0.37), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 319 
 TYR   0.017   0.001   TYR A 249 
 PHE   0.028   0.001   PHE A 447 
 TRP   0.009   0.001   TRP A 413 
 HIS   0.004   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 7950)
  covalent geometry    : angle       0.64509 (10829)
  hydrogen bonds       : bond        0.04984 (  551)
  hydrogen bonds       : angle       4.03068 ( 1605)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1264.54 seconds
wall clock time: 22 minutes 33.56 seconds (1353.56 seconds total)