Starting phenix.real_space_refine
on Fri Aug 22 20:42:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t4f_41029/08_2025/8t4f_41029.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t4f_41029/08_2025/8t4f_41029.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t4f_41029/08_2025/8t4f_41029.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t4f_41029/08_2025/8t4f_41029.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t4f_41029/08_2025/8t4f_41029.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t4f_41029/08_2025/8t4f_41029.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.018
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      31      5.16       5
     C    4932      2.51       5
     N    1372      2.21       5
     O    1458      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7793
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 540, 3508
          Classifications: {'peptide': 540}
          Incomplete info: {'truncation_to_alanine': 191}
          Link IDs: {'PTRANS': 18, 'TRANS': 521}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 686
          Unresolved non-hydrogen angles: 885
          Unresolved non-hydrogen dihedrals: 547
          Unresolved non-hydrogen chiralities: 76
          Planarities with less than four sites: {'HIS:plan': 7, 'GLU:plan': 16, 'GLN:plan1': 24, 'PHE:plan': 6, 'ASP:plan': 9, 'TYR:plan': 9, 'ASN:plan1': 5, 'ARG:plan': 11, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 400
    Chain: "B"
      Number of atoms: 4202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 548, 4202
          Classifications: {'peptide': 548}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 20, 'TRANS': 527}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 90
          Unresolved non-hydrogen angles: 117
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 4, 'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 62
    Chain: "C"
      Number of atoms: 83
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 83
          Classifications: {'peptide': 9}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 8}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   ARG A 529 " occ=0.62
      ... (3 atoms not shown)
      pdb=" CB  ARG A 529 " occ=0.62
  Time building chain proxies: 2.14, per 1000 atoms: 0.27
  Number of scatterers: 7793
  At special positions: 0
  Unit cell: (69.628, 100.048, 136.552, 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      31     16.00
     O    1458      8.00
     N    1372      7.00
     C    4932      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 412.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2026

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 6 sheets defined
      73.9% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 180 through 182
      No H-bonds generated for 'chain 'A' and resid 180 through 182'
    Processing helix  chain 'A' and resid 183 through 201
      removed outlier: 3.518A  pdb=" N   SER A 188 " --> pdb=" O   THR A 184 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   VAL A 195 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 216
      removed outlier: 3.520A  pdb=" N   PHE A 207 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 272
      removed outlier: 3.631A  pdb=" N   HIS A 255 " --> pdb=" O   ASN A 251 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLU A 272 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 324
      removed outlier: 3.547A  pdb=" N   SER A 293 " --> pdb=" O   THR A 289 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   ASP A 297 " --> pdb=" O   SER A 293 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   SER A 298 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 338
      Proline residue:  A 336  - end of helix
    Processing helix  chain 'A' and resid 340 through 372
      removed outlier: 3.502A  pdb=" N   TRP A 348 " --> pdb=" O   LYS A 344 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ALA A 370 " --> pdb=" O   VAL A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 381
    Processing helix  chain 'A' and resid 382 through 437
      removed outlier: 3.587A  pdb=" N   GLU A 386 " --> pdb=" O   ASN A 382 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   GLU A 396 " --> pdb=" O   GLU A 392 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ILE A 397 " --> pdb=" O   LYS A 393 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   THR A 399 " --> pdb=" O   GLN A 395 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LEU A 400 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   GLN A 402 " --> pdb=" O   LYS A 398 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   LYS A 403 " --> pdb=" O   THR A 399 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LYS A 423 " --> pdb=" O   GLY A 419 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ILE A 426 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ILE A 429 " --> pdb=" O   GLY A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 484
      removed outlier: 3.609A  pdb=" N   LEU A 444 " --> pdb=" O   SER A 440 " (cutoff:3.500A)
      Proline residue:  A 466  - end of helix
      removed outlier: 3.765A  pdb=" N   GLU A 476 " --> pdb=" O   VAL A 472 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   LYS A 477 " --> pdb=" O   GLY A 473 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ILE A 478 " --> pdb=" O   SER A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 519
      removed outlier: 3.878A  pdb=" N   LEU A 519 " --> pdb=" O   PRO A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 544
      removed outlier: 3.844A  pdb=" N   GLY A 543 " --> pdb=" O   ASN A 540 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   LYS A 544 " --> pdb=" O   GLY A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 552
      removed outlier: 3.558A  pdb=" N   ALA A 549 " --> pdb=" O   SER A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 572
      removed outlier: 4.032A  pdb=" N   TYR A 572 " --> pdb=" O   LEU A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 578
    Processing helix  chain 'A' and resid 594 through 599
    Processing helix  chain 'A' and resid 608 through 619
    Processing helix  chain 'A' and resid 621 through 628
    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 658
    Processing helix  chain 'A' and resid 668 through 673
      removed outlier: 3.587A  pdb=" N   ALA A 672 " --> pdb=" O   ASP A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 674 through 687
    Processing helix  chain 'A' and resid 690 through 694
      removed outlier: 3.930A  pdb=" N   ARG A 694 " --> pdb=" O   ARG A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 702 through 707
      removed outlier: 3.792A  pdb=" N   VAL A 706 " --> pdb=" O   HIS A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 731
    Processing helix  chain 'A' and resid 734 through 742
    Processing helix  chain 'B' and resid 132 through 145
      removed outlier: 3.586A  pdb=" N   SER B 145 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 168
      removed outlier: 3.844A  pdb=" N   ALA B 154 " --> pdb=" O   PRO B 150 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL B 160 " --> pdb=" O   PHE B 156 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LEU B 168 " --> pdb=" O   LEU B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 181
      removed outlier: 3.579A  pdb=" N   TYR B 172 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 234
      removed outlier: 3.754A  pdb=" N   GLY B 208 " --> pdb=" O   SER B 204 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   GLY B 211 " --> pdb=" O   ALA B 207 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   GLU B 227 " --> pdb=" O   LEU B 223 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLN B 228 " --> pdb=" O   ARG B 224 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU B 234 " --> pdb=" O   PHE B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 244
      removed outlier: 3.879A  pdb=" N   PHE B 241 " --> pdb=" O   ASP B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 255
      removed outlier: 3.621A  pdb=" N   LEU B 249 " --> pdb=" O   LYS B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 260
    Processing helix  chain 'B' and resid 261 through 263
      No H-bonds generated for 'chain 'B' and resid 261 through 263'
    Processing helix  chain 'B' and resid 266 through 289
      removed outlier: 3.786A  pdb=" N   LEU B 272 " --> pdb=" O   ALA B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 338
      removed outlier: 4.306A  pdb=" N   LEU B 295 " --> pdb=" O   ARG B 291 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   SER B 296 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
      Proline residue:  B 301  - end of helix
      removed outlier: 3.827A  pdb=" N   ALA B 306 " --> pdb=" O   PHE B 302 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLU B 316 " --> pdb=" O   THR B 312 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ARG B 319 " --> pdb=" O   GLN B 315 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL B 331 " --> pdb=" O   ARG B 327 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   VAL B 332 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 346
    Processing helix  chain 'B' and resid 347 through 402
      removed outlier: 3.831A  pdb=" N   CYS B 353 " --> pdb=" O   GLU B 349 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   GLN B 364 " --> pdb=" O   GLU B 360 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   LEU B 365 " --> pdb=" O   GLN B 361 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ALA B 374 " --> pdb=" O   ASP B 370 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ASP B 401 " --> pdb=" O   GLN B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 448
      removed outlier: 4.450A  pdb=" N   GLY B 420 " --> pdb=" O   GLN B 416 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   SER B 421 " --> pdb=" O   GLU B 417 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   TYR B 422 " --> pdb=" O   SER B 418 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   VAL B 427 " --> pdb=" O   VAL B 423 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   LEU B 434 " --> pdb=" O   TYR B 430 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   SER B 435 " --> pdb=" O   GLY B 431 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ASN B 436 " --> pdb=" O   ASP B 432 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   TYR B 446 " --> pdb=" O   LYS B 442 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   MET B 447 " --> pdb=" O   VAL B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 507
    Processing helix  chain 'B' and resid 508 through 516
      removed outlier: 3.528A  pdb=" N   VAL B 512 " --> pdb=" O   GLY B 508 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU B 516 " --> pdb=" O   VAL B 512 " (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 545
      removed outlier: 3.817A  pdb=" N   HIS B 543 " --> pdb=" O   HIS B 539 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   SER B 544 " --> pdb=" O   CYS B 540 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLN B 545 " --> pdb=" O   TYR B 541 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 565
    Processing helix  chain 'B' and resid 572 through 582
    Processing helix  chain 'B' and resid 585 through 590
    Processing helix  chain 'B' and resid 594 through 598
      removed outlier: 3.798A  pdb=" N   TYR B 597 " --> pdb=" O   HIS B 594 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   THR B 598 " --> pdb=" O   GLY B 595 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 594 through 598'
    Processing helix  chain 'B' and resid 608 through 622
      removed outlier: 3.731A  pdb=" N   ALA B 620 " --> pdb=" O   ALA B 616 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU B 621 " --> pdb=" O   ILE B 617 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL B 622 " --> pdb=" O   ALA B 618 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 633 through 636
    Processing helix  chain 'B' and resid 638 through 646
    Processing helix  chain 'B' and resid 648 through 653
      removed outlier: 4.598A  pdb=" N   ASP B 653 " --> pdb=" O   ASN B 649 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 662 through 668
      removed outlier: 4.123A  pdb=" N   THR B 665 " --> pdb=" O   ARG B 662 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLN B 667 " --> pdb=" O   GLN B 664 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 503 through 504
      removed outlier: 3.833A  pdb=" N   VAL A 503 " --> pdb=" O   LEU A 528 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU A 528 " --> pdb=" O   VAL A 503 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 506 through 509
      removed outlier: 3.694A  pdb=" N   GLN A 506 " --> pdb=" O   GLN A 561 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   GLN A 561 " --> pdb=" O   GLN A 506 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   VAL A 508 " --> pdb=" O   GLY A 559 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   GLY A 559 " --> pdb=" O   VAL A 508 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 536 through 537
      removed outlier: 6.787A  pdb=" N   VAL A 537 " --> pdb=" O   LEU A 715 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ILE A 712 " --> pdb=" O   GLY A 723 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   GLY A 723 " --> pdb=" O   ILE A 712 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   PHE A 714 " --> pdb=" O   ARG A 721 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 663 through 664
    Processing sheet with id=AA5, first strand: chain 'B' and resid 486 through 493
      removed outlier: 6.920A  pdb=" N   LYS B 487 " --> pdb=" O   SER B 474 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   SER B 474 " --> pdb=" O   LYS B 487 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   LEU B 489 " --> pdb=" O   ASP B 472 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL B 468 " --> pdb=" O   LEU B 493 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   PHE B 470 " --> pdb=" O   LEU B 528 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   LEU B 528 " --> pdb=" O   PHE B 470 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   ASP B 472 " --> pdb=" O   GLN B 526 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   GLN B 526 " --> pdb=" O   ASP B 472 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 546 through 548
      removed outlier: 6.292A  pdb=" N   ALA B 500 " --> pdb=" O   LEU B 673 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   LEU B 675 " --> pdb=" O   ALA B 500 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   VAL B 502 " --> pdb=" O   LEU B 675 " (cutoff:3.500A)

    547 hydrogen bonds defined for protein.
    1590 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.35

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2645
        1.34 -     1.46: 1248
        1.46 -     1.58: 3970
        1.58 -     1.69: 0
        1.69 -     1.81: 53
  Bond restraints: 7916
  Sorted by residual:
  bond pdb=" N   VAL A 460 "
       pdb=" CA  VAL A 460 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.17e-02 7.31e+03 7.72e+00
  bond pdb=" N   VAL A 366 "
       pdb=" CA  VAL A 366 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.25e-02 6.40e+03 7.58e+00
  bond pdb=" N   VAL B 387 "
       pdb=" CA  VAL B 387 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.17e-02 7.31e+03 7.46e+00
  bond pdb=" N   VAL B 276 "
       pdb=" CA  VAL B 276 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.17e-02 7.31e+03 7.45e+00
  bond pdb=" N   LEU B 383 "
       pdb=" CA  LEU B 383 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.21e-02 6.83e+03 7.09e+00
  ... (remaining 7911 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 10504
        1.55 -     3.09: 229
        3.09 -     4.64: 32
        4.64 -     6.18: 9
        6.18 -     7.73: 3
  Bond angle restraints: 10777
  Sorted by residual:
  angle pdb=" C   GLN B 450 "
        pdb=" N   PRO B 451 "
        pdb=" CA  PRO B 451 "
      ideal   model   delta    sigma   weight residual
     120.98  125.12   -4.14 1.07e+00 8.73e-01 1.50e+01
  angle pdb=" CA  LEU B 272 "
        pdb=" C   LEU B 272 "
        pdb=" O   LEU B 272 "
      ideal   model   delta    sigma   weight residual
     121.00  117.81    3.19 1.05e+00 9.07e-01 9.22e+00
  angle pdb=" CA  VAL B 387 "
        pdb=" C   VAL B 387 "
        pdb=" O   VAL B 387 "
      ideal   model   delta    sigma   weight residual
     121.17  118.03    3.14 1.06e+00 8.90e-01 8.79e+00
  angle pdb=" CA  HIS B 384 "
        pdb=" C   HIS B 384 "
        pdb=" O   HIS B 384 "
      ideal   model   delta    sigma   weight residual
     120.82  117.80    3.02 1.05e+00 9.07e-01 8.30e+00
  angle pdb=" CA  VAL A 460 "
        pdb=" C   VAL A 460 "
        pdb=" O   VAL A 460 "
      ideal   model   delta    sigma   weight residual
     121.17  118.14    3.03 1.06e+00 8.90e-01 8.15e+00
  ... (remaining 10772 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 4204
       17.63 -    35.26: 401
       35.26 -    52.89: 98
       52.89 -    70.52: 20
       70.52 -    88.15: 8
  Dihedral angle restraints: 4731
    sinusoidal: 1588
      harmonic: 3143
  Sorted by residual:
  dihedral pdb=" CA  THR B 167 "
           pdb=" C   THR B 167 "
           pdb=" N   LEU B 168 "
           pdb=" CA  LEU B 168 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.67  -17.33     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CB  GLU B 227 "
           pdb=" CG  GLU B 227 "
           pdb=" CD  GLU B 227 "
           pdb=" OE1 GLU B 227 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.15   88.15     1      3.00e+01 1.11e-03 1.03e+01
  dihedral pdb=" CB  GLU C   8 "
           pdb=" CG  GLU C   8 "
           pdb=" CD  GLU C   8 "
           pdb=" OE1 GLU C   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.63  -87.63     1      3.00e+01 1.11e-03 1.02e+01
  ... (remaining 4728 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 933
       0.037 -    0.075: 264
       0.075 -    0.112: 69
       0.112 -    0.149: 14
       0.149 -    0.186: 8
  Chirality restraints: 1288
  Sorted by residual:
  chirality pdb=" CA  VAL B 276 "
            pdb=" N   VAL B 276 "
            pdb=" C   VAL B 276 "
            pdb=" CB  VAL B 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.68e-01
  chirality pdb=" CA  VAL A 366 "
            pdb=" N   VAL A 366 "
            pdb=" C   VAL A 366 "
            pdb=" CB  VAL A 366 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.00e-01
  chirality pdb=" CA  VAL B 387 "
            pdb=" N   VAL B 387 "
            pdb=" C   VAL B 387 "
            pdb=" CB  VAL B 387 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.16 2.00e-01 2.50e+01 6.75e-01
  ... (remaining 1285 not shown)

  Planarity restraints: 1407
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 588 "    0.010 2.00e-02 2.50e+03   1.35e-02 3.20e+00
        pdb=" CG  PHE B 588 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 588 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 588 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 588 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 588 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 588 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 146 "   -0.024 5.00e-02 4.00e+02   3.61e-02 2.08e+00
        pdb=" N   PRO B 147 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B 147 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 147 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 374 "   -0.022 5.00e-02 4.00e+02   3.26e-02 1.70e+00
        pdb=" N   PRO A 375 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 375 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 375 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1404 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1582
        2.77 -     3.31: 7665
        3.31 -     3.84: 12385
        3.84 -     4.37: 12461
        4.37 -     4.90: 23078
  Nonbonded interactions: 57171
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN B 517 "
            pdb=" OG  SER B 548 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OD2 ASP B 256 "
            pdb=" NZ  LYS B 442 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" O   PHE B 284 "
            pdb=" OG  SER B 287 "
     model   vdw
     2.348 3.040
  nonbonded pdb=" OE2 GLU B 307 "
            pdb=" ND2 ASN B 311 "
     model   vdw
     2.351 3.120
  nonbonded pdb=" NH1 ARG B 140 "
            pdb=" OD2 ASP B 448 "
     model   vdw
     2.354 3.120
  ... (remaining 57166 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=0.62 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:             7.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.370
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7916  Z= 0.208
  Angle     :  0.571   7.728  10777  Z= 0.344
  Chirality :  0.040   0.186   1288
  Planarity :  0.003   0.036   1407
  Dihedral  : 15.367  88.146   2705
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 19.41 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.27), residues: 1083
  helix:  2.25 (0.20), residues: 707
  sheet: -1.01 (0.66), residues: 64
  loop : -0.31 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 270 
 TYR   0.012   0.001   TYR B 428 
 PHE   0.031   0.001   PHE B 588 
 TRP   0.009   0.001   TRP A 348 
 HIS   0.002   0.001   HIS B 543 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7916)
  covalent geometry    : angle       0.57094 (10777)
  hydrogen bonds       : bond        0.15909 (  547)
  hydrogen bonds       : angle       4.68124 ( 1590)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 109
  time to evaluate  : 0.291 
Fit side-chains
  outliers start: 4
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1273
  time to fit residues: 18.2483
Evaluate side-chains
  95 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 97 optimal weight:    0.2980
   chunk 53 optimal weight:    0.0980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
B 536 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.186369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.144964 restraints weight = 9484.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.144105 restraints weight = 8752.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.145521 restraints weight = 7014.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.143824 restraints weight = 5588.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.144660 restraints weight = 5155.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3711
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3711 r_free = 0.3711    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3711 r_free = 0.3711    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3711
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.0964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7916  Z= 0.136
  Angle     :  0.495   6.431  10777  Z= 0.251
  Chirality :  0.037   0.131   1288
  Planarity :  0.003   0.038   1407
  Dihedral  :  3.180  17.810   1164
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 19.83 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.27), residues: 1083
  helix:  2.52 (0.20), residues: 720
  sheet: -1.24 (0.65), residues: 64
  loop : -0.40 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 270 
 TYR   0.011   0.001   TYR A 309 
 PHE   0.009   0.001   PHE A 207 
 TRP   0.009   0.001   TRP A 348 
 HIS   0.002   0.001   HIS B 384 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7916)
  covalent geometry    : angle       0.49455 (10777)
  hydrogen bonds       : bond        0.06685 (  547)
  hydrogen bonds       : angle       3.44981 ( 1590)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A  432 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7532 (tt0)
REVERT: B  135 LYS cc_start: 0.5074 (tptt) cc_final: 0.4612 (tptt)
REVERT: B  166 GLU cc_start: 0.7525 (tp30) cc_final: 0.7195 (tp30)
  outliers start: 22
  outliers final: 12
  residues processed: 117
  average time/residue: 0.1123
  time to fit residues: 17.1723
Evaluate side-chains
  107 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  598 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 88 optimal weight:    6.9990
   chunk 57 optimal weight:    2.9990
   chunk 64 optimal weight:    0.4980
   chunk 0 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:   50.0000
   chunk 5 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   chunk 106 optimal weight:    0.1980
   chunk 96 optimal weight:    4.9990
   chunk 40 optimal weight:    0.4980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.4218 r_free = 0.4218 target = 0.191217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.149115 restraints weight = 9359.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.148711 restraints weight = 9520.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.150820 restraints weight = 6773.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.149894 restraints weight = 5233.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.150721 restraints weight = 4463.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3787
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3787 r_free = 0.3787    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3787 r_free = 0.3787    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3787
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.1305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7916  Z= 0.148
  Angle     :  0.500   7.379  10777  Z= 0.252
  Chirality :  0.037   0.133   1288
  Planarity :  0.003   0.038   1407
  Dihedral  :  3.156  17.036   1164
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 19.97 %
    Favored  : 75.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.26 (0.27), residues: 1083
  helix:  2.53 (0.20), residues: 720
  sheet: -1.30 (0.64), residues: 64
  loop : -0.43 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 270 
 TYR   0.013   0.001   TYR B 541 
 PHE   0.009   0.001   PHE B 588 
 TRP   0.010   0.001   TRP A 348 
 HIS   0.002   0.001   HIS B 384 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 7916)
  covalent geometry    : angle       0.50030 (10777)
  hydrogen bonds       : bond        0.07019 (  547)
  hydrogen bonds       : angle       3.36225 ( 1590)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 99
  time to evaluate  : 0.314 
Fit side-chains
REVERT: B  135 LYS cc_start: 0.5129 (tptt) cc_final: 0.4568 (tptt)
REVERT: B  166 GLU cc_start: 0.7593 (tp30) cc_final: 0.7095 (tp30)
  outliers start: 34
  outliers final: 25
  residues processed: 120
  average time/residue: 0.1117
  time to fit residues: 17.5611
Evaluate side-chains
  121 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  416 SER
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  584 HIS
Chi-restraints excluded: chain B residue  592 MET
Chi-restraints excluded: chain B residue  598 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 101 optimal weight:   10.0000
   chunk 66 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0980
   chunk 49 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 89 optimal weight:    5.9990
   chunk 93 optimal weight:    4.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.4176 r_free = 0.4176 target = 0.186785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.144020 restraints weight = 9633.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.143041 restraints weight = 10304.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.145318 restraints weight = 7503.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.143934 restraints weight = 5559.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.144394 restraints weight = 4878.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3721
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3721 r_free = 0.3721    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3721 r_free = 0.3721    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3721
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.1416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7916  Z= 0.154
  Angle     :  0.521   8.586  10777  Z= 0.260
  Chirality :  0.037   0.130   1288
  Planarity :  0.003   0.039   1407
  Dihedral  :  3.169  17.283   1164
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 20.81 %
    Favored  : 74.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.26 (0.27), residues: 1083
  helix:  2.54 (0.20), residues: 720
  sheet: -1.36 (0.64), residues: 64
  loop : -0.47 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 343 
 TYR   0.014   0.001   TYR B 541 
 PHE   0.010   0.001   PHE B 588 
 TRP   0.009   0.001   TRP A 348 
 HIS   0.003   0.001   HIS B 384 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 7916)
  covalent geometry    : angle       0.52149 (10777)
  hydrogen bonds       : bond        0.07116 (  547)
  hydrogen bonds       : angle       3.33772 ( 1590)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 97
  time to evaluate  : 0.315 
Fit side-chains
REVERT: B  166 GLU cc_start: 0.7625 (tp30) cc_final: 0.7227 (tp30)
  outliers start: 31
  outliers final: 27
  residues processed: 116
  average time/residue: 0.1115
  time to fit residues: 16.8889
Evaluate side-chains
  119 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  416 SER
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  429 ILE
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  584 HIS
Chi-restraints excluded: chain B residue  592 MET
Chi-restraints excluded: chain B residue  598 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0670
   chunk 90 optimal weight:    3.9990
   chunk 103 optimal weight:    4.9990
   chunk 93 optimal weight:    1.9990
   chunk 37 optimal weight:    0.2980
   chunk 22 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 33 optimal weight:   20.0000
   overall best weight:    0.8724

-------------------------------------------------------------------------------
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 = 0.4185 r_free = 0.4185 target = 0.187953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.143792 restraints weight = 9520.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.143926 restraints weight = 9160.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.144453 restraints weight = 5707.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.144030 restraints weight = 5091.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.144175 restraints weight = 4355.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3724
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3724 r_free = 0.3724    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3724 r_free = 0.3724    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3724
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7916  Z= 0.137
  Angle     :  0.496   9.461  10777  Z= 0.245
  Chirality :  0.036   0.127   1288
  Planarity :  0.003   0.038   1407
  Dihedral  :  3.127  19.346   1164
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 21.93 %
    Favored  : 74.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.38 (0.27), residues: 1083
  helix:  2.64 (0.20), residues: 720
  sheet: -1.31 (0.64), residues: 64
  loop : -0.45 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 270 
 TYR   0.015   0.001   TYR B 541 
 PHE   0.009   0.001   PHE A 207 
 TRP   0.009   0.001   TRP A 322 
 HIS   0.002   0.001   HIS B 543 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 7916)
  covalent geometry    : angle       0.49571 (10777)
  hydrogen bonds       : bond        0.06701 (  547)
  hydrogen bonds       : angle       3.23987 ( 1590)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 93
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: B  166 GLU cc_start: 0.7657 (tp30) cc_final: 0.7389 (tp30)
  outliers start: 29
  outliers final: 27
  residues processed: 113
  average time/residue: 0.1175
  time to fit residues: 17.1012
Evaluate side-chains
  117 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 90
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain A residue  304 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  416 SER
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  429 ILE
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  584 HIS
Chi-restraints excluded: chain B residue  592 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 35 optimal weight:   30.0000
   chunk 104 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 63 optimal weight:    0.6980
   chunk 90 optimal weight:    5.9990
   chunk 76 optimal weight:    0.8980
   chunk 80 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 97 optimal weight:    0.1980
   chunk 9 optimal weight:    0.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4207 r_free = 0.4207 target = 0.190246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.145825 restraints weight = 9526.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.146603 restraints weight = 9042.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.146417 restraints weight = 5336.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.145931 restraints weight = 4772.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.146141 restraints weight = 4215.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3738
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3738 r_free = 0.3738    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3738 r_free = 0.3738    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3738
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.1543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7916  Z= 0.124
  Angle     :  0.485   9.782  10777  Z= 0.239
  Chirality :  0.036   0.125   1288
  Planarity :  0.003   0.037   1407
  Dihedral  :  2.987  17.288   1164
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 22.77 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.55 (0.27), residues: 1083
  helix:  2.78 (0.20), residues: 720
  sheet: -1.25 (0.63), residues: 64
  loop : -0.39 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C   2 
 TYR   0.013   0.001   TYR B 541 
 PHE   0.014   0.001   PHE B 588 
 TRP   0.010   0.001   TRP A 322 
 HIS   0.002   0.001   HIS B 543 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7916)
  covalent geometry    : angle       0.48487 (10777)
  hydrogen bonds       : bond        0.06179 (  547)
  hydrogen bonds       : angle       3.11594 ( 1590)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
REVERT: B  166 GLU cc_start: 0.7607 (tp30) cc_final: 0.7350 (tp30)
  outliers start: 24
  outliers final: 18
  residues processed: 108
  average time/residue: 0.1071
  time to fit residues: 14.9607
Evaluate side-chains
  106 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  416 SER
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  584 HIS
Chi-restraints excluded: chain B residue  592 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 88 optimal weight:    6.9990
   chunk 97 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   chunk 16 optimal weight:    6.9990
   chunk 51 optimal weight:   20.0000
   chunk 100 optimal weight:    9.9990
   chunk 32 optimal weight:   20.0000
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
B 521 GLN
** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.187875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.147187 restraints weight = 9613.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.147177 restraints weight = 10020.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.146588 restraints weight = 6628.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.145268 restraints weight = 7408.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.146738 restraints weight = 5394.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3750
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3750 r_free = 0.3750    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3750 r_free = 0.3750    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3750
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053   7916  Z= 0.278
  Angle     :  0.650  10.570  10777  Z= 0.328
  Chirality :  0.041   0.149   1288
  Planarity :  0.004   0.039   1407
  Dihedral  :  3.561  16.542   1164
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 21.79 %
    Favored  : 73.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.79 (0.27), residues: 1083
  helix:  2.17 (0.20), residues: 720
  sheet: -1.42 (0.63), residues: 64
  loop : -0.65 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 273 
 TYR   0.030   0.002   TYR B 541 
 PHE   0.015   0.002   PHE A 243 
 TRP   0.016   0.002   TRP A 322 
 HIS   0.004   0.001   HIS B 384 

Details of bonding type rmsd
  covalent geometry    : bond        0.00671 ( 7916)
  covalent geometry    : angle       0.65010 (10777)
  hydrogen bonds       : bond        0.08937 (  547)
  hydrogen bonds       : angle       3.69637 ( 1590)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 97
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 ARG cc_start: 0.6920 (ttt90) cc_final: 0.6576 (ttt-90)
REVERT: A  215 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8589 (tt)
REVERT: B  166 GLU cc_start: 0.7674 (tp30) cc_final: 0.7265 (tp30)
  outliers start: 36
  outliers final: 25
  residues processed: 123
  average time/residue: 0.1200
  time to fit residues: 19.0236
Evaluate side-chains
  122 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  304 SER
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  416 SER
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  429 ILE
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  584 HIS
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  674 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 20 optimal weight:    0.0170
   chunk 68 optimal weight:    0.6980
   chunk 97 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0170
   chunk 11 optimal weight:    0.7980
   chunk 90 optimal weight:    0.6980
   chunk 95 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 44 optimal weight:   20.0000
   chunk 33 optimal weight:   20.0000
   overall best weight:    0.4056

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

Flipped N/Q/H residues before XYZ refinement:
B 543 HIS
** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.191844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.149746 restraints weight = 9519.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.149446 restraints weight = 10362.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.150280 restraints weight = 6421.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.149561 restraints weight = 5282.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.150126 restraints weight = 4387.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3779
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3779 r_free = 0.3779    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3779 r_free = 0.3779    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3779
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7916  Z= 0.120
  Angle     :  0.508  11.028  10777  Z= 0.247
  Chirality :  0.035   0.119   1288
  Planarity :  0.003   0.040   1407
  Dihedral  :  3.052  18.738   1164
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 24.58 %
    Favored  : 72.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.51 (0.27), residues: 1083
  helix:  2.77 (0.20), residues: 716
  sheet: -1.28 (0.63), residues: 64
  loop : -0.41 (0.37), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 333 
 TYR   0.015   0.001   TYR B 541 
 PHE   0.009   0.001   PHE A 207 
 TRP   0.014   0.001   TRP A 322 
 HIS   0.003   0.001   HIS B 670 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 7916)
  covalent geometry    : angle       0.50822 (10777)
  hydrogen bonds       : bond        0.05927 (  547)
  hydrogen bonds       : angle       3.13190 ( 1590)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A  215 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8467 (tt)
  outliers start: 19
  outliers final: 17
  residues processed: 110
  average time/residue: 0.1242
  time to fit residues: 17.6745
Evaluate side-chains
  111 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  304 SER
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  479 PHE
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  380 ARG
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain B residue  446 TYR
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  584 HIS
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  674 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 44 optimal weight:   20.0000
   chunk 90 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 52 optimal weight:    9.9990
   chunk 63 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 106 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.192471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.149726 restraints weight = 9685.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.149055 restraints weight = 10048.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.149152 restraints weight = 5759.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.149038 restraints weight = 4644.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.149911 restraints weight = 4167.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3767
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3767 r_free = 0.3767    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3767 r_free = 0.3767    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3767
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7916  Z= 0.188
  Angle     :  0.579  10.990  10777  Z= 0.284
  Chirality :  0.038   0.131   1288
  Planarity :  0.003   0.037   1407
  Dihedral  :  3.242  17.227   1164
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 23.60 %
    Favored  : 72.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.26 (0.27), residues: 1083
  helix:  2.54 (0.20), residues: 720
  sheet: -1.34 (0.62), residues: 64
  loop : -0.48 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 333 
 TYR   0.019   0.001   TYR B 541 
 PHE   0.011   0.002   PHE A 207 
 TRP   0.028   0.002   TRP A 322 
 HIS   0.005   0.001   HIS B 670 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 7916)
  covalent geometry    : angle       0.57854 (10777)
  hydrogen bonds       : bond        0.07654 (  547)
  hydrogen bonds       : angle       3.39765 ( 1590)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 94
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A  215 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8593 (tt)
REVERT: B  552 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7793 (mm-30)
  outliers start: 28
  outliers final: 23
  residues processed: 117
  average time/residue: 0.1234
  time to fit residues: 18.2984
Evaluate side-chains
  118 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  304 SER
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  416 SER
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  479 PHE
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  429 ILE
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  584 HIS
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  674 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 75 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 95 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.187986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.147000 restraints weight = 9494.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.145402 restraints weight = 11059.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.147707 restraints weight = 8676.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.146959 restraints weight = 5583.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.147043 restraints weight = 5038.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3757
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3757 r_free = 0.3757    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3757 r_free = 0.3757    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3757
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7916  Z= 0.136
  Angle     :  0.531  11.192  10777  Z= 0.259
  Chirality :  0.036   0.124   1288
  Planarity :  0.003   0.039   1407
  Dihedral  :  3.115  18.011   1164
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 24.58 %
    Favored  : 72.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.46 (0.27), residues: 1083
  helix:  2.71 (0.20), residues: 720
  sheet: -1.28 (0.63), residues: 64
  loop : -0.42 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C   1 
 TYR   0.016   0.001   TYR B 541 
 PHE   0.019   0.001   PHE B 588 
 TRP   0.023   0.001   TRP A 322 
 HIS   0.003   0.001   HIS B 670 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7916)
  covalent geometry    : angle       0.53129 (10777)
  hydrogen bonds       : bond        0.06594 (  547)
  hydrogen bonds       : angle       3.18864 ( 1590)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.317 
Fit side-chains
REVERT: B  135 LYS cc_start: 0.4878 (tptt) cc_final: 0.4523 (tptt)
REVERT: B  552 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7776 (mm-30)
REVERT: B  584 HIS cc_start: 0.5937 (OUTLIER) cc_final: 0.5504 (t-90)
REVERT: B  679 LYS cc_start: 0.8231 (tmtt) cc_final: 0.7916 (tmtt)
  outliers start: 23
  outliers final: 21
  residues processed: 109
  average time/residue: 0.1253
  time to fit residues: 17.5570
Evaluate side-chains
  113 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  304 SER
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  416 SER
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  479 PHE
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  287 SER
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  380 ARG
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  429 ILE
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  546 VAL
Chi-restraints excluded: chain B residue  560 VAL
Chi-restraints excluded: chain B residue  584 HIS
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  674 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 102 optimal weight:    0.4980
   chunk 101 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 103 optimal weight:    3.9990
   chunk 90 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0870
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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 = 0.4218 r_free = 0.4218 target = 0.191498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.149356 restraints weight = 9486.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.150058 restraints weight = 9245.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.150560 restraints weight = 6077.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.149522 restraints weight = 5410.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.149838 restraints weight = 4734.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3784
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3784 r_free = 0.3784    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3784 r_free = 0.3784    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3784
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   7916  Z= 0.120
  Angle     :  0.512  10.965  10777  Z= 0.247
  Chirality :  0.036   0.119   1288
  Planarity :  0.003   0.038   1407
  Dihedral  :  2.938  18.268   1164
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 24.86 %
    Favored  : 72.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.71 (0.27), residues: 1083
  helix:  2.91 (0.20), residues: 717
  sheet: -1.20 (0.63), residues: 64
  loop : -0.34 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C   1 
 TYR   0.015   0.001   TYR B 541 
 PHE   0.017   0.001   PHE B 588 
 TRP   0.021   0.001   TRP A 322 
 HIS   0.005   0.001   HIS B 670 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 7916)
  covalent geometry    : angle       0.51228 (10777)
  hydrogen bonds       : bond        0.05795 (  547)
  hydrogen bonds       : angle       3.01220 ( 1590)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1724.22 seconds
wall clock time: 30 minutes 19.76 seconds (1819.76 seconds total)