Starting phenix.real_space_refine
on Sun May 11 10:41:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t4j_41033/05_2025/8t4j_41033.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t4j_41033/05_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_41033/05_2025/8t4j_41033.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t4j_41033/05_2025/8t4j_41033.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t4j_41033/05_2025/8t4j_41033.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t4j_41033/05_2025/8t4j_41033.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.019
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3}
          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: {'GLN:plan1': 24, 'HIS:plan': 7, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 6, 'GLU:plan': 19, 'ARG:plan': 13}
          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: 6.22, per 1000 atoms: 0.79
  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: 1.75
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.82
  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: 2.41

  Time building geometry restraints manager: 2.09 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:             4.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.860
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.460
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (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
 TRP   0.015   0.001   TRP A 413 
 HIS   0.002   0.001   HIS B 543 
 PHE   0.027   0.001   PHE A 339 
 TYR   0.010   0.001   TYR B 376 
 ARG   0.004   0.000   ARG A 378 

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

*********************** 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  : 0.792 
Fit side-chains
   revert: symmetry clash
REVERT: B  166 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7674 (tt0)
REVERT: B  254 SER cc_start: 0.9012 (t) cc_final: 0.8761 (p)
REVERT: B  260 MET cc_start: 0.8357 (mmm) cc_final: 0.8135 (mmp)
REVERT: B  366 TYR cc_start: 0.8523 (m-80) cc_final: 0.8272 (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: 0.1852
  time to fit residues: 29.6386
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  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.0050
   chunk 82 optimal weight:    0.4980
   chunk 45 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 85 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 51 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9990
   chunk 98 optimal weight:    0.5980
   overall best weight:    0.5394

-------------------------------------------------------------------------------
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 = 0.3963 r_free = 0.3963 target = 0.124326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.096811 restraints weight = 18426.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.096024 restraints weight = 11700.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.096847 restraints weight = 10087.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7950  Z= 0.164
  Angle     :  0.617  10.752  10829  Z= 0.317
  Chirality :  0.042   0.254   1295
  Planarity :  0.004   0.045   1415
  Dihedral  :  3.767  21.410   1174
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.78 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.26), residues: 1095
  helix:  0.96 (0.19), residues: 717
  sheet: -0.28 (0.72), residues: 66
  loop : -0.15 (0.38), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 413 
 HIS   0.003   0.001   HIS B 299 
 PHE   0.013   0.001   PHE B 214 
 TYR   0.019   0.001   TYR A 349 
 ARG   0.004   0.000   ARG B 273 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06807 (  551)
  hydrogen bonds       : angle       4.71508 ( 1605)
  covalent geometry    : bond        0.00301 ( 7950)
  covalent geometry    : angle       0.61678 (10829)

*********************** 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: 13
    poor density    : 102
  time to evaluate  : 0.902 
Fit side-chains
REVERT: B  385 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8518 (tt)
REVERT: B  389 MET cc_start: 0.7946 (tpt) cc_final: 0.7571 (tpt)
REVERT: B  391 MET cc_start: 0.8006 (tpp) cc_final: 0.7789 (tpp)
REVERT: B  413 MET cc_start: 0.8315 (tpp) cc_final: 0.8090 (tpp)
REVERT: B  467 VAL cc_start: 0.8735 (t) cc_final: 0.8426 (p)
REVERT: A  189 LEU cc_start: 0.8183 (mm) cc_final: 0.7881 (tp)
REVERT: A  213 ASP cc_start: 0.8856 (m-30) cc_final: 0.8512 (m-30)
  outliers start: 13
  outliers final: 8
  residues processed: 111
  average time/residue: 0.1579
  time to fit residues: 25.6603
Evaluate side-chains
  89 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  169 ILE
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  385 LEU
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain A residue  194 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 98 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 47 optimal weight:    6.9990
   chunk 64 optimal weight:    7.9990
   chunk 107 optimal weight:   50.0000
   chunk 53 optimal weight:    2.9990
   chunk 89 optimal weight:    0.3980
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
B 350 HIS
B 406 GLN
** B 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 261 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.122518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.095483 restraints weight = 19008.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.093133 restraints weight = 13286.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.094504 restraints weight = 11629.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7950  Z= 0.178
  Angle     :  0.603  10.205  10829  Z= 0.308
  Chirality :  0.042   0.211   1295
  Planarity :  0.004   0.051   1415
  Dihedral  :  3.733  21.140   1174
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 15.05 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.26), residues: 1095
  helix:  1.11 (0.19), residues: 707
  sheet: -0.20 (0.71), residues: 64
  loop : -0.10 (0.38), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 413 
 HIS   0.005   0.001   HIS B 299 
 PHE   0.014   0.001   PHE A 479 
 TYR   0.017   0.001   TYR A 349 
 ARG   0.006   0.000   ARG A 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06183 (  551)
  hydrogen bonds       : angle       4.48546 ( 1605)
  covalent geometry    : bond        0.00387 ( 7950)
  covalent geometry    : angle       0.60329 (10829)

*********************** 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
  107 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 0.895 
Fit side-chains
REVERT: B  260 MET cc_start: 0.8292 (tpp) cc_final: 0.7918 (mtm)
REVERT: B  385 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8491 (tp)
REVERT: B  390 LEU cc_start: 0.8513 (tt) cc_final: 0.8265 (tp)
REVERT: B  413 MET cc_start: 0.8374 (tpp) cc_final: 0.8035 (tpp)
REVERT: B  467 VAL cc_start: 0.8881 (t) cc_final: 0.8513 (p)
REVERT: A  191 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.7614 (mt)
  outliers start: 28
  outliers final: 16
  residues processed: 100
  average time/residue: 0.1371
  time to fit residues: 21.3277
Evaluate side-chains
  94 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
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  195 PHE
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  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  560 VAL
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  307 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 91 optimal weight:    8.9990
   chunk 96 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9980
   chunk 98 optimal weight:    9.9990
   chunk 50 optimal weight:    9.9990
   chunk 31 optimal weight:    0.2980
   chunk 89 optimal weight:    6.9990
   chunk 73 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9980
   chunk 99 optimal weight:    9.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3959 r_free = 0.3959 target = 0.124045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.096214 restraints weight = 18772.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.094595 restraints weight = 12395.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.096115 restraints weight = 9775.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.2409

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= 0.135
  Angle     :  0.558  10.647  10829  Z= 0.280
  Chirality :  0.041   0.254   1295
  Planarity :  0.004   0.048   1415
  Dihedral  :  3.657  23.151   1174
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 16.74 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.26), residues: 1095
  helix:  1.30 (0.19), residues: 714
  sheet: -0.30 (0.69), residues: 69
  loop : -0.19 (0.38), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 413 
 HIS   0.004   0.001   HIS B 299 
 PHE   0.010   0.001   PHE B 588 
 TYR   0.011   0.001   TYR A 309 
 ARG   0.004   0.000   ARG B 319 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05446 (  551)
  hydrogen bonds       : angle       4.16910 ( 1605)
  covalent geometry    : bond        0.00274 ( 7950)
  covalent geometry    : angle       0.55784 (10829)

*********************** 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
  116 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 85
  time to evaluate  : 0.874 
Fit side-chains
REVERT: B  385 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8380 (tt)
REVERT: B  390 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8333 (tp)
REVERT: B  413 MET cc_start: 0.8328 (tpp) cc_final: 0.7978 (tpp)
REVERT: B  467 VAL cc_start: 0.8840 (t) cc_final: 0.8503 (p)
REVERT: A  191 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.7573 (mt)
REVERT: A  213 ASP cc_start: 0.8746 (m-30) cc_final: 0.8440 (m-30)
  outliers start: 31
  outliers final: 20
  residues processed: 106
  average time/residue: 0.1247
  time to fit residues: 21.0366
Evaluate side-chains
  103 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
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  195 PHE
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  261 SER
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  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  307 LEU
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  421 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   chunk 91 optimal weight:    8.9990
   chunk 101 optimal weight:    0.1980
   chunk 66 optimal weight:    0.9980
   chunk 80 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0980
   chunk 64 optimal weight:    8.9990
   chunk 22 optimal weight:    7.9990
   overall best weight:    0.5780

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.124287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.096479 restraints weight = 18761.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.094996 restraints weight = 12747.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.096199 restraints weight = 10488.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7950  Z= 0.127
  Angle     :  0.548  10.424  10829  Z= 0.273
  Chirality :  0.040   0.224   1295
  Planarity :  0.003   0.040   1415
  Dihedral  :  3.564  23.203   1174
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 17.58 %
    Favored  : 78.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.26), residues: 1095
  helix:  1.39 (0.19), residues: 715
  sheet: -0.30 (0.68), residues: 69
  loop : -0.14 (0.39), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 308 
 HIS   0.004   0.001   HIS B 299 
 PHE   0.010   0.001   PHE B 588 
 TYR   0.012   0.001   TYR A 309 
 ARG   0.003   0.000   ARG A 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05120 (  551)
  hydrogen bonds       : angle       3.99721 ( 1605)
  covalent geometry    : bond        0.00257 ( 7950)
  covalent geometry    : angle       0.54769 (10829)

*********************** 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: 30
    poor density    : 83
  time to evaluate  : 0.981 
Fit side-chains
REVERT: B  385 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8321 (tt)
REVERT: B  390 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8274 (tp)
REVERT: B  413 MET cc_start: 0.8306 (tpp) cc_final: 0.7200 (tpp)
REVERT: B  467 VAL cc_start: 0.8709 (t) cc_final: 0.8455 (p)
REVERT: B  493 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6825 (mt)
REVERT: A  191 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.7589 (mt)
REVERT: A  213 ASP cc_start: 0.8682 (m-30) cc_final: 0.8404 (m-30)
  outliers start: 30
  outliers final: 20
  residues processed: 106
  average time/residue: 0.1327
  time to fit residues: 22.2404
Evaluate side-chains
  105 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 81
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  195 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  261 SER
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  453 LEU
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  493 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 99 optimal weight:    7.9990
   chunk 92 optimal weight:    0.9980
   chunk 93 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 89 optimal weight:    0.0980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3955 r_free = 0.3955 target = 0.123801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.095354 restraints weight = 18785.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.094532 restraints weight = 12278.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.095551 restraints weight = 10405.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2726

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= 0.150
  Angle     :  0.575  10.489  10829  Z= 0.286
  Chirality :  0.040   0.214   1295
  Planarity :  0.004   0.040   1415
  Dihedral  :  3.550  22.855   1174
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 18.28 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.26), residues: 1095
  helix:  1.36 (0.19), residues: 716
  sheet: -0.29 (0.67), residues: 67
  loop : -0.20 (0.38), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 308 
 HIS   0.004   0.001   HIS B 299 
 PHE   0.010   0.001   PHE B 588 
 TYR   0.010   0.001   TYR B 376 
 ARG   0.002   0.000   ARG A 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05065 (  551)
  hydrogen bonds       : angle       4.00817 ( 1605)
  covalent geometry    : bond        0.00325 ( 7950)
  covalent geometry    : angle       0.57467 (10829)

*********************** 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
  119 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 83
  time to evaluate  : 0.816 
Fit side-chains
REVERT: B  195 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7181 (t80)
REVERT: B  385 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8324 (tt)
REVERT: B  389 MET cc_start: 0.8051 (tpt) cc_final: 0.7596 (tpt)
REVERT: B  390 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8348 (tp)
REVERT: B  413 MET cc_start: 0.8276 (tpp) cc_final: 0.7756 (tpp)
REVERT: B  467 VAL cc_start: 0.8801 (t) cc_final: 0.8545 (p)
REVERT: B  493 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6786 (mt)
REVERT: A  191 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.7600 (mt)
REVERT: A  213 ASP cc_start: 0.8682 (m-30) cc_final: 0.8428 (m-30)
REVERT: A  253 MET cc_start: 0.8593 (mmm) cc_final: 0.8380 (tpt)
  outliers start: 36
  outliers final: 24
  residues processed: 111
  average time/residue: 0.1389
  time to fit residues: 23.6704
Evaluate side-chains
  111 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 82
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
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  195 PHE
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  246 THR
Chi-restraints excluded: chain B residue  261 SER
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  443 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  493 LEU
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  366 VAL
Chi-restraints excluded: chain A residue  421 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 17 optimal weight:    8.9990
   chunk 63 optimal weight:    0.9990
   chunk 83 optimal weight:    0.0370
   chunk 1 optimal weight:    0.7980
   chunk 60 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 90 optimal weight:   10.0000
   chunk 103 optimal weight:    9.9990
   overall best weight:    0.7060

-------------------------------------------------------------------------------
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 = 0.3970 r_free = 0.3970 target = 0.125038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.097676 restraints weight = 18500.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.096687 restraints weight = 11838.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.098111 restraints weight = 9253.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7950  Z= 0.132
  Angle     :  0.565  11.047  10829  Z= 0.279
  Chirality :  0.040   0.242   1295
  Planarity :  0.004   0.038   1415
  Dihedral  :  3.529  23.488   1174
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 18.85 %
    Favored  : 76.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.26), residues: 1095
  helix:  1.43 (0.19), residues: 717
  sheet: -0.32 (0.67), residues: 67
  loop : -0.20 (0.38), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 308 
 HIS   0.004   0.001   HIS B 299 
 PHE   0.041   0.001   PHE A 447 
 TYR   0.010   0.001   TYR A 309 
 ARG   0.004   0.000   ARG B 319 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04898 (  551)
  hydrogen bonds       : angle       3.92203 ( 1605)
  covalent geometry    : bond        0.00274 ( 7950)
  covalent geometry    : angle       0.56456 (10829)

*********************** 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
  113 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 83
  time to evaluate  : 0.942 
Fit side-chains
REVERT: B  195 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7200 (t80)
REVERT: B  385 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8277 (tt)
REVERT: B  389 MET cc_start: 0.7914 (tpt) cc_final: 0.7457 (tpt)
REVERT: B  390 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8297 (tp)
REVERT: B  413 MET cc_start: 0.8218 (tpp) cc_final: 0.7779 (tpp)
REVERT: B  467 VAL cc_start: 0.8718 (t) cc_final: 0.8472 (p)
REVERT: B  493 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6914 (mt)
REVERT: B  680 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6317 (pt)
REVERT: A  191 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.7631 (mt)
REVERT: A  213 ASP cc_start: 0.8591 (m-30) cc_final: 0.8316 (m-30)
  outliers start: 30
  outliers final: 18
  residues processed: 106
  average time/residue: 0.1405
  time to fit residues: 23.0175
Evaluate side-chains
  106 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  195 PHE
Chi-restraints excluded: chain B residue  199 PHE
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  225 ILE
Chi-restraints excluded: chain B residue  246 THR
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  443 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  493 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  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 78 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 97 optimal weight:   20.0000
   chunk 81 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 20 optimal weight:    9.9990
   chunk 90 optimal weight:    6.9990
   chunk 69 optimal weight:    0.8980
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3967 r_free = 0.3967 target = 0.124877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.097465 restraints weight = 18868.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.096243 restraints weight = 12221.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.097545 restraints weight = 10335.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.3049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7950  Z= 0.134
  Angle     :  0.575  10.673  10829  Z= 0.283
  Chirality :  0.040   0.245   1295
  Planarity :  0.004   0.037   1415
  Dihedral  :  3.518  23.659   1174
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 18.99 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.26), residues: 1095
  helix:  1.46 (0.19), residues: 719
  sheet: -0.38 (0.66), residues: 67
  loop : -0.18 (0.38), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 308 
 HIS   0.005   0.001   HIS B 299 
 PHE   0.034   0.001   PHE A 447 
 TYR   0.010   0.001   TYR B 376 
 ARG   0.007   0.000   ARG B 319 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04846 (  551)
  hydrogen bonds       : angle       3.90880 ( 1605)
  covalent geometry    : bond        0.00281 ( 7950)
  covalent geometry    : angle       0.57500 (10829)

*********************** 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
  115 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 84
  time to evaluate  : 0.892 
Fit side-chains
REVERT: B  195 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7207 (t80)
REVERT: B  385 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8314 (tt)
REVERT: B  389 MET cc_start: 0.7970 (tpt) cc_final: 0.7522 (tpt)
REVERT: B  390 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8266 (tp)
REVERT: B  413 MET cc_start: 0.8225 (tpp) cc_final: 0.7806 (tpp)
REVERT: B  467 VAL cc_start: 0.8746 (t) cc_final: 0.8516 (p)
REVERT: B  493 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6934 (mt)
REVERT: B  680 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6364 (pt)
REVERT: A  191 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.7582 (mt)
REVERT: A  213 ASP cc_start: 0.8583 (m-30) cc_final: 0.8312 (m-30)
  outliers start: 31
  outliers final: 22
  residues processed: 108
  average time/residue: 0.1490
  time to fit residues: 24.5897
Evaluate side-chains
  111 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 83
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
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  195 PHE
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  225 ILE
Chi-restraints excluded: chain B residue  246 THR
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  443 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  493 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 76 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0050
   chunk 28 optimal weight:    0.1980
   chunk 36 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 105 optimal weight:    7.9990
   chunk 74 optimal weight:    0.6980
   chunk 96 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.4994

-------------------------------------------------------------------------------
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 = 0.3979 r_free = 0.3979 target = 0.125407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.097504 restraints weight = 18887.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.097319 restraints weight = 10979.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.098385 restraints weight = 8639.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.3158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7950  Z= 0.121
  Angle     :  0.571  11.372  10829  Z= 0.279
  Chirality :  0.039   0.230   1295
  Planarity :  0.003   0.036   1415
  Dihedral  :  3.442  24.306   1174
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 19.55 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.26), residues: 1095
  helix:  1.55 (0.19), residues: 720
  sheet: -0.56 (0.65), residues: 69
  loop : -0.16 (0.39), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 308 
 HIS   0.005   0.001   HIS B 299 
 PHE   0.029   0.001   PHE A 447 
 TYR   0.009   0.001   TYR A 309 
 ARG   0.007   0.000   ARG B 319 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04654 (  551)
  hydrogen bonds       : angle       3.80187 ( 1605)
  covalent geometry    : bond        0.00244 ( 7950)
  covalent geometry    : angle       0.57145 (10829)

*********************** 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
  115 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 87
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
REVERT: B  195 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7244 (t80)
REVERT: B  319 ARG cc_start: 0.8336 (mmm160) cc_final: 0.7837 (mmm160)
REVERT: B  389 MET cc_start: 0.7886 (tpt) cc_final: 0.7379 (tpt)
REVERT: B  390 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8237 (tp)
REVERT: B  413 MET cc_start: 0.8249 (tpp) cc_final: 0.7837 (tpp)
REVERT: B  493 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6885 (mt)
REVERT: B  680 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6360 (pt)
REVERT: A  191 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.7593 (mt)
REVERT: A  213 ASP cc_start: 0.8520 (m-30) cc_final: 0.8232 (m-30)
  outliers start: 28
  outliers final: 21
  residues processed: 110
  average time/residue: 0.1412
  time to fit residues: 23.6122
Evaluate side-chains
  108 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 82
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
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  195 PHE
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  225 ILE
Chi-restraints excluded: chain B residue  246 THR
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  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  493 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 87 optimal weight:   20.0000
   chunk 35 optimal weight:    0.6980
   chunk 105 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0970
   chunk 26 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 106 optimal weight:    7.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 302 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.124796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.097159 restraints weight = 18886.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.095771 restraints weight = 11793.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.097233 restraints weight = 9572.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.3258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7950  Z= 0.125
  Angle     :  0.602  15.634  10829  Z= 0.289
  Chirality :  0.040   0.231   1295
  Planarity :  0.004   0.036   1415
  Dihedral  :  3.436  24.013   1174
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 20.39 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.26), residues: 1095
  helix:  1.54 (0.19), residues: 720
  sheet: -0.58 (0.65), residues: 69
  loop : -0.17 (0.38), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 308 
 HIS   0.005   0.001   HIS B 299 
 PHE   0.026   0.001   PHE A 447 
 TYR   0.019   0.001   TYR A 349 
 ARG   0.008   0.000   ARG B 319 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04624 (  551)
  hydrogen bonds       : angle       3.79763 ( 1605)
  covalent geometry    : bond        0.00257 ( 7950)
  covalent geometry    : angle       0.60210 (10829)

********************** 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
  112 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 84
  time to evaluate  : 0.895 
Fit side-chains
REVERT: B  195 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7259 (t80)
REVERT: B  319 ARG cc_start: 0.8432 (mmm160) cc_final: 0.7821 (mmm160)
REVERT: B  390 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8241 (tp)
REVERT: B  413 MET cc_start: 0.8209 (tpp) cc_final: 0.7819 (tpp)
REVERT: B  493 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6912 (mt)
REVERT: B  680 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6366 (pt)
REVERT: A  191 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.7593 (mt)
REVERT: A  213 ASP cc_start: 0.8536 (m-30) cc_final: 0.8239 (m-30)
  outliers start: 28
  outliers final: 22
  residues processed: 107
  average time/residue: 0.1401
  time to fit residues: 23.1928
Evaluate side-chains
  108 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 81
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
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  195 PHE
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  225 ILE
Chi-restraints excluded: chain B residue  246 THR
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  493 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 49 optimal weight:    0.0770
   chunk 77 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9980
   chunk 83 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   chunk 54 optimal weight:    0.0170
   chunk 65 optimal weight:    0.9990
   chunk 95 optimal weight:   10.0000
   chunk 50 optimal weight:    7.9990
   chunk 2 optimal weight:    0.6980
   chunk 90 optimal weight:    7.9990
   overall best weight:    0.4376

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.126570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.100330 restraints weight = 19399.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.099755 restraints weight = 11878.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.100732 restraints weight = 9962.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.3365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7950  Z= 0.121
  Angle     :  0.594  13.383  10829  Z= 0.286
  Chirality :  0.039   0.236   1295
  Planarity :  0.003   0.035   1415
  Dihedral  :  3.391  24.449   1174
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 20.96 %
    Favored  : 75.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.26), residues: 1095
  helix:  1.62 (0.19), residues: 721
  sheet: -0.53 (0.66), residues: 69
  loop : -0.19 (0.38), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 308 
 HIS   0.005   0.001   HIS B 299 
 PHE   0.030   0.001   PHE A 447 
 TYR   0.014   0.001   TYR A 450 
 ARG   0.007   0.000   ARG B 319 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04518 (  551)
  hydrogen bonds       : angle       3.73134 ( 1605)
  covalent geometry    : bond        0.00244 ( 7950)
  covalent geometry    : angle       0.59368 (10829)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2526.04 seconds
wall clock time: 45 minutes 2.79 seconds (2702.79 seconds total)