Starting phenix.real_space_refine
on Wed Mar 12 11:42:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t4f_41029/03_2025/8t4f_41029.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t4f_41029/03_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_41029/03_2025/8t4f_41029.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t4f_41029/03_2025/8t4f_41029.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t4f_41029/03_2025/8t4f_41029.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t4f_41029/03_2025/8t4f_41029.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.018
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 24, 'ARG:plan': 11, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 6, 'GLU:plan': 16, 'HIS:plan': 7}
          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: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3}
          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: 6.61, per 1000 atoms: 0.85
  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: 2.20
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.92
  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: 2.31

  Time building geometry restraints manager: 2.60 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:             5.930
  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:          0.400
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     24.490
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.970
-------------------------------------------------------------------------------
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= 0.216
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (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
 TRP   0.009   0.001   TRP A 348 
 HIS   0.002   0.001   HIS B 543 
 PHE   0.031   0.001   PHE B 588 
 TYR   0.012   0.001   TYR B 428 
 ARG   0.005   0.000   ARG A 270 

*********************** 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  : 0.799 
Fit side-chains
  outliers start: 4
  outliers final: 0
  residues processed: 113
  average time/residue: 0.2598
  time to fit residues: 37.4837
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  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.6980
   chunk 81 optimal weight:    0.8980
   chunk 45 optimal weight:   20.0000
   chunk 27 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9980
   chunk 43 optimal weight:    7.9990
   chunk 84 optimal weight:    3.9990
   chunk 32 optimal weight:   20.0000
   chunk 51 optimal weight:    5.9990
   chunk 63 optimal weight:    0.6980
   chunk 98 optimal weight:    5.9990
   overall best weight:    1.4582

-------------------------------------------------------------------------------
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 = 0.4117 r_free = 0.4117 target = 0.181035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.138166 restraints weight = 9445.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.136956 restraints weight = 9846.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.138669 restraints weight = 7673.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3649
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3649
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.1192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7916  Z= 0.280
  Angle     :  0.550   6.957  10777  Z= 0.280
  Chirality :  0.038   0.136   1288
  Planarity :  0.004   0.040   1407
  Dihedral  :  3.366  17.275   1164
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 19.83 %
    Favored  : 76.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.27), residues: 1083
  helix:  2.29 (0.20), residues: 720
  sheet: -1.34 (0.64), residues: 64
  loop : -0.53 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 348 
 HIS   0.004   0.001   HIS B 384 
 PHE   0.012   0.002   PHE A 207 
 TYR   0.012   0.001   TYR A 309 
 ARG   0.004   0.000   ARG A 270 

*********************** 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
  127 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 0.815 
Fit side-chains
REVERT: A  432 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7594 (tt0)
REVERT: B  135 LYS cc_start: 0.5121 (tptt) cc_final: 0.4645 (tptt)
REVERT: B  166 GLU cc_start: 0.7555 (tp30) cc_final: 0.7188 (tp30)
REVERT: B  536 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7942 (tm-30)
  outliers start: 28
  outliers final: 20
  residues processed: 117
  average time/residue: 0.2655
  time to fit residues: 40.6706
Evaluate side-chains
  113 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
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  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  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  527 VAL
Chi-restraints excluded: chain B residue  536 GLN
Chi-restraints excluded: chain B residue  547 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 65 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 83 optimal weight:    0.5980
   chunk 104 optimal weight:   10.0000
   chunk 21 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 32 optimal weight:    8.9990
   chunk 58 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4232 r_free = 0.4232 target = 0.192681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.150704 restraints weight = 9503.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.150211 restraints weight = 9767.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.151144 restraints weight = 6643.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3796
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3796 r_free = 0.3796    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3796 r_free = 0.3796    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3796
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.1231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7916  Z= 0.182
  Angle     :  0.480   7.630  10777  Z= 0.244
  Chirality :  0.036   0.133   1288
  Planarity :  0.003   0.039   1407
  Dihedral  :  3.156  17.849   1164
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 20.53 %
    Favored  : 76.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.27), residues: 1083
  helix:  2.56 (0.20), residues: 720
  sheet: -1.34 (0.64), residues: 64
  loop : -0.45 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 348 
 HIS   0.002   0.001   HIS B 543 
 PHE   0.010   0.001   PHE A 447 
 TYR   0.014   0.001   TYR B 541 
 ARG   0.005   0.000   ARG A 270 

*********************** 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
  123 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.699 
Fit side-chains
REVERT: B  135 LYS cc_start: 0.5028 (tptt) cc_final: 0.4499 (tptt)
REVERT: B  166 GLU cc_start: 0.7543 (tp30) cc_final: 0.7101 (tp30)
  outliers start: 23
  outliers final: 18
  residues processed: 114
  average time/residue: 0.2834
  time to fit residues: 42.4657
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  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  168 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  387 VAL
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  433 MET
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  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 103 optimal weight:    4.9990
   chunk 40 optimal weight:    5.9990
   chunk 25 optimal weight:    0.5980
   chunk 24 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 102 optimal weight:    0.3980
   chunk 4 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 36 optimal weight:    9.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.189847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.145604 restraints weight = 9428.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.144679 restraints weight = 9854.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.144884 restraints weight = 5997.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3714
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3714 r_free = 0.3714    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3714 r_free = 0.3714    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3714
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.1339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7916  Z= 0.173
  Angle     :  0.485   8.408  10777  Z= 0.241
  Chirality :  0.036   0.129   1288
  Planarity :  0.003   0.037   1407
  Dihedral  :  3.038  17.477   1164
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 21.23 %
    Favored  : 75.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.43 (0.27), residues: 1083
  helix:  2.69 (0.20), residues: 720
  sheet: -1.29 (0.64), residues: 64
  loop : -0.44 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 348 
 HIS   0.002   0.000   HIS B 384 
 PHE   0.010   0.001   PHE B 588 
 TYR   0.012   0.001   TYR B 541 
 ARG   0.003   0.000   ARG B 343 

*********************** 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
  124 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.896 
Fit side-chains
REVERT: B  135 LYS cc_start: 0.5139 (tptt) cc_final: 0.4726 (tptt)
REVERT: B  166 GLU cc_start: 0.7648 (tp30) cc_final: 0.7337 (tp30)
REVERT: B  679 LYS cc_start: 0.8389 (tmtt) cc_final: 0.8140 (mttp)
  outliers start: 26
  outliers final: 21
  residues processed: 115
  average time/residue: 0.2369
  time to fit residues: 35.6057
Evaluate side-chains
  115 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  421 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  159 LEU
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  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  560 VAL
Chi-restraints excluded: chain B residue  584 HIS
Chi-restraints excluded: chain B residue  592 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 101 optimal weight:    9.9990
   chunk 67 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 52 optimal weight:    7.9990
   chunk 65 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0070
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.6198

-------------------------------------------------------------------------------
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 = 0.4217 r_free = 0.4217 target = 0.191106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.149151 restraints weight = 9429.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.149560 restraints weight = 9816.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.150130 restraints weight = 6504.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3786
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3786 r_free = 0.3786    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3786 r_free = 0.3786    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3786
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.1491

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= 0.163
  Angle     :  0.476   9.181  10777  Z= 0.235
  Chirality :  0.036   0.128   1288
  Planarity :  0.003   0.036   1407
  Dihedral  :  2.964  17.273   1164
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 21.93 %
    Favored  : 74.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.55 (0.27), residues: 1083
  helix:  2.75 (0.20), residues: 724
  sheet: -1.23 (0.65), residues: 64
  loop : -0.37 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 348 
 HIS   0.002   0.000   HIS B 543 
 PHE   0.009   0.001   PHE A 447 
 TYR   0.013   0.001   TYR B 541 
 ARG   0.003   0.000   ARG B 343 

*********************** 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
  123 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 1.580 
Fit side-chains
REVERT: B  135 LYS cc_start: 0.5153 (tptt) cc_final: 0.4795 (tptt)
REVERT: B  166 GLU cc_start: 0.7573 (tp30) cc_final: 0.7266 (tp30)
REVERT: B  679 LYS cc_start: 0.8381 (tmtt) cc_final: 0.8012 (tptt)
  outliers start: 24
  outliers final: 22
  residues processed: 116
  average time/residue: 0.3690
  time to fit residues: 55.0582
Evaluate side-chains
  116 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 1.322 
-------------------------------------------------------------------------------
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  421 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain B residue  159 LEU
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  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  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
Chi-restraints excluded: chain B residue  598 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 80 optimal weight:    0.0000
   chunk 37 optimal weight:    0.0370
   chunk 7 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0020
   chunk 97 optimal weight:    0.0060
   chunk 43 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.1886

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.198192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.158316 restraints weight = 9393.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.156498 restraints weight = 7976.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.158749 restraints weight = 6258.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3876
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3876 r_free = 0.3876    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3876 r_free = 0.3876    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3876
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7916  Z= 0.132
  Angle     :  0.466   9.424  10777  Z= 0.226
  Chirality :  0.035   0.120   1288
  Planarity :  0.003   0.035   1407
  Dihedral  :  2.830  23.159   1164
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 23.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.93 (0.27), residues: 1083
  helix:  3.04 (0.20), residues: 721
  sheet: -1.09 (0.65), residues: 64
  loop : -0.17 (0.37), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 308 
 HIS   0.003   0.001   HIS B 670 
 PHE   0.013   0.001   PHE B 588 
 TYR   0.010   0.001   TYR A 309 
 ARG   0.005   0.000   ARG B 343 

*********************** 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
  119 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 1.436 
Fit side-chains
REVERT: B  135 LYS cc_start: 0.4928 (tptt) cc_final: 0.4479 (tptt)
REVERT: B  532 LYS cc_start: 0.6637 (mmpt) cc_final: 0.5897 (mttm)
REVERT: B  679 LYS cc_start: 0.8429 (tmtt) cc_final: 0.8183 (tptp)
  outliers start: 20
  outliers final: 13
  residues processed: 110
  average time/residue: 0.5225
  time to fit residues: 74.9171
Evaluate side-chains
  102 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 1.197 
-------------------------------------------------------------------------------
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  421 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain B residue  159 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  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  674 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 93 optimal weight:    4.9990
   chunk 81 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 34 optimal weight:    7.9990
   chunk 48 optimal weight:    5.9990
   chunk 107 optimal weight:    7.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B 521 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.189162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.145800 restraints weight = 9442.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.145141 restraints weight = 11078.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.146975 restraints weight = 6859.882|
|-----------------------------------------------------------------------------|
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) = 0.145         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3757 r_free = 0.3757    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3757
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7916  Z= 0.191
  Angle     :  0.520  10.788  10777  Z= 0.249
  Chirality :  0.037   0.123   1288
  Planarity :  0.003   0.033   1407
  Dihedral  :  2.904  16.993   1164
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 23.60 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.79 (0.27), residues: 1083
  helix:  2.92 (0.20), residues: 721
  sheet: -1.01 (0.64), residues: 62
  loop : -0.27 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 322 
 HIS   0.004   0.001   HIS B 670 
 PHE   0.010   0.001   PHE A 207 
 TYR   0.014   0.001   TYR B 541 
 ARG   0.008   0.000   ARG C   2 

*********************** 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
  117 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 91
  time to evaluate  : 0.822 
Fit side-chains
REVERT: B  135 LYS cc_start: 0.5047 (tptt) cc_final: 0.4750 (tptt)
REVERT: B  532 LYS cc_start: 0.6812 (mmpt) cc_final: 0.5916 (mttm)
REVERT: B  679 LYS cc_start: 0.8481 (tmtt) cc_final: 0.8065 (tptt)
  outliers start: 26
  outliers final: 20
  residues processed: 105
  average time/residue: 0.2457
  time to fit residues: 33.4742
Evaluate side-chains
  110 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  168 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  387 VAL
Chi-restraints excluded: chain B residue  421 SER
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  584 HIS
Chi-restraints excluded: chain B residue  592 MET
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 103 optimal weight:    0.0270
   chunk 39 optimal weight:    8.9990
   chunk 59 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 29 optimal weight:   20.0000
   chunk 77 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 41 optimal weight:    8.9990
   chunk 28 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.9444

-------------------------------------------------------------------------------
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 = 0.4189 r_free = 0.4189 target = 0.188267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.146588 restraints weight = 9492.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.145688 restraints weight = 10235.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.147354 restraints weight = 8398.069|
|-----------------------------------------------------------------------------|
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 = 0.81   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 = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3757
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7916  Z= 0.205
  Angle     :  0.522   9.633  10777  Z= 0.252
  Chirality :  0.037   0.125   1288
  Planarity :  0.003   0.036   1407
  Dihedral  :  2.981  17.222   1164
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 24.30 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.70 (0.27), residues: 1083
  helix:  2.84 (0.20), residues: 721
  sheet: -1.18 (0.63), residues: 64
  loop : -0.20 (0.38), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 348 
 HIS   0.002   0.000   HIS B 543 
 PHE   0.010   0.001   PHE A 207 
 TYR   0.015   0.001   TYR B 541 
 ARG   0.007   0.000   ARG C   2 

*********************** 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
  116 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 0.934 
Fit side-chains
REVERT: B  135 LYS cc_start: 0.5152 (tptt) cc_final: 0.4806 (tptt)
REVERT: B  532 LYS cc_start: 0.6879 (mmpt) cc_final: 0.5964 (mttm)
REVERT: B  679 LYS cc_start: 0.8486 (tmtt) cc_final: 0.8160 (tmtt)
  outliers start: 24
  outliers final: 23
  residues processed: 110
  average time/residue: 0.2758
  time to fit residues: 39.4357
Evaluate side-chains
  113 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
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  411 ASN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue  159 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  421 SER
Chi-restraints excluded: chain B residue  429 ILE
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 88 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 70 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 77 optimal weight:    0.3980
   chunk 78 optimal weight:    0.6980
   chunk 61 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9990
   chunk 85 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4214 r_free = 0.4214 target = 0.191034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.149086 restraints weight = 9644.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.149314 restraints weight = 9984.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.150689 restraints weight = 6899.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3791
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3791 r_free = 0.3791    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3791 r_free = 0.3791    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3791
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   7916  Z= 0.168
  Angle     :  0.511   9.802  10777  Z= 0.246
  Chirality :  0.036   0.122   1288
  Planarity :  0.003   0.035   1407
  Dihedral  :  2.905  17.695   1164
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 25.56 %
    Favored  : 71.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.85 (0.27), residues: 1083
  helix:  2.96 (0.20), residues: 720
  sheet: -1.15 (0.63), residues: 64
  loop : -0.14 (0.38), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 322 
 HIS   0.003   0.000   HIS B 670 
 PHE   0.009   0.001   PHE A 207 
 TYR   0.013   0.001   TYR B 541 
 ARG   0.008   0.000   ARG C   2 

*********************** 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
  106 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.899 
Fit side-chains
REVERT: B  135 LYS cc_start: 0.5081 (tptt) cc_final: 0.4781 (tptt)
REVERT: B  532 LYS cc_start: 0.6805 (mmpt) cc_final: 0.5941 (mttm)
  outliers start: 20
  outliers final: 20
  residues processed: 101
  average time/residue: 0.2546
  time to fit residues: 33.2854
Evaluate side-chains
  104 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
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  411 ASN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  168 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  389 MET
Chi-restraints excluded: chain B residue  421 SER
Chi-restraints excluded: chain B residue  429 ILE
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  674 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 49 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 66 optimal weight:    0.4980
   chunk 41 optimal weight:    6.9990
   chunk 39 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 107 optimal weight:    0.0470
   overall best weight:    0.5478

-------------------------------------------------------------------------------
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 = 0.4217 r_free = 0.4217 target = 0.191504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.149023 restraints weight = 9524.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.148881 restraints weight = 10208.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.150956 restraints weight = 6818.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3800
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3800 r_free = 0.3800    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3800 r_free = 0.3800    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3800
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.1992

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= 0.163
  Angle     :  0.511   9.610  10777  Z= 0.245
  Chirality :  0.036   0.119   1288
  Planarity :  0.003   0.036   1407
  Dihedral  :  2.865  17.945   1164
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 24.86 %
    Favored  : 71.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.92 (0.27), residues: 1083
  helix:  3.00 (0.20), residues: 720
  sheet: -1.09 (0.63), residues: 64
  loop : -0.09 (0.38), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 322 
 HIS   0.003   0.000   HIS B 670 
 PHE   0.008   0.001   PHE A 207 
 TYR   0.013   0.001   TYR B 428 
 ARG   0.010   0.000   ARG C   1 

********************** 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
  110 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 86
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
REVERT: B  135 LYS cc_start: 0.5072 (tptt) cc_final: 0.4781 (tptt)
REVERT: B  532 LYS cc_start: 0.6785 (mmpt) cc_final: 0.5936 (mttm)
  outliers start: 24
  outliers final: 23
  residues processed: 105
  average time/residue: 0.2525
  time to fit residues: 34.6860
Evaluate side-chains
  107 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 84
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
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  411 ASN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain B residue  269 ASN
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  421 SER
Chi-restraints excluded: chain B residue  429 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 99 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4203 r_free = 0.4203 target = 0.189809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.147800 restraints weight = 9492.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.146374 restraints weight = 11367.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.148578 restraints weight = 8423.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3773
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3773 r_free = 0.3773    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3773 r_free = 0.3773    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3773
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.1967

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= 0.186
  Angle     :  0.525   9.501  10777  Z= 0.254
  Chirality :  0.036   0.121   1288
  Planarity :  0.003   0.040   1407
  Dihedral  :  2.918  17.104   1164
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 24.30 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.85 (0.27), residues: 1083
  helix:  2.95 (0.20), residues: 717
  sheet: -1.08 (0.63), residues: 64
  loop : -0.11 (0.38), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 322 
 HIS   0.003   0.001   HIS B 670 
 PHE   0.010   0.001   PHE A 207 
 TYR   0.014   0.001   TYR B 541 
 ARG   0.009   0.000   ARG C   2 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3283.51 seconds
wall clock time: 59 minutes 38.65 seconds (3578.65 seconds total)