Starting phenix.real_space_refine
on Fri Feb 14 19:40:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qm4_4587/02_2025/6qm4_4587.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qm4_4587/02_2025/6qm4_4587.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qm4_4587/02_2025/6qm4_4587.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qm4_4587/02_2025/6qm4_4587.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qm4_4587/02_2025/6qm4_4587.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qm4_4587/02_2025/6qm4_4587.cif"
  }
  resolution = 3.8
  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=   0.006
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      40      5.16       5
     C    6886      2.51       5
     N    1760      2.21       5
     O    1894      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10580
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 654, 5290
          Classifications: {'peptide': 654}
          Link IDs: {'PTRANS': 28, 'TRANS': 625}
          Chain breaks: 5
  Restraints were copied for chains:
    B
  Time building chain proxies: 9.78, per 1000 atoms: 0.92
  Number of scatterers: 10580
  At special positions: 0
  Unit cell: (118.404, 108.284, 106.26, 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      40     16.00
     O    1894      8.00
     N    1760      7.00
     C    6886      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: 2.61
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2480

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 4 sheets defined
      72.6% alpha, 2.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 50
      removed outlier: 3.743A  pdb=" N   THR A  48 " --> pdb=" O   ILE A  44 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   VAL A  50 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 90
      removed outlier: 3.890A  pdb=" N   HIS A  90 " --> pdb=" O   GLY A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 111 through 125
      removed outlier: 3.734A  pdb=" N   LEU A 118 " --> pdb=" O   GLU A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 165
      removed outlier: 3.861A  pdb=" N   GLU A 158 " --> pdb=" O   SER A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 182
      removed outlier: 3.747A  pdb=" N   ILE A 177 " --> pdb=" O   ASP A 173 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG A 178 " --> pdb=" O   ILE A 174 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LYS A 180 " --> pdb=" O   ASN A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 197
      removed outlier: 3.750A  pdb=" N   TYR A 188 " --> pdb=" O   SER A 184 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   PHE A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 212
      removed outlier: 3.581A  pdb=" N   TRP A 210 " --> pdb=" O   GLY A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 246
      removed outlier: 4.097A  pdb=" N   ALA A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   VAL A 229 " --> pdb=" O   GLY A 225 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   PHE A 232 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   VAL A 240 " --> pdb=" O   LYS A 236 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL A 244 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 289
      removed outlier: 3.879A  pdb=" N   ARG A 284 " --> pdb=" O   PRO A 280 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   THR A 287 " --> pdb=" O   LYS A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 320
      removed outlier: 3.900A  pdb=" N   LEU A 312 " --> pdb=" O   THR A 308 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASN A 317 " --> pdb=" O   GLU A 313 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   GLU A 318 " --> pdb=" O   VAL A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 330
    Processing helix  chain 'A' and resid 330 through 358
      Proline residue:  A 341  - end of helix
      removed outlier: 3.629A  pdb=" N   LEU A 347 " --> pdb=" O   ILE A 343 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ASN A 355 " --> pdb=" O   ALA A 351 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLU A 358 " --> pdb=" O   LEU A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 392
      removed outlier: 3.513A  pdb=" N   ASP A 367 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ALA A 369 " --> pdb=" O   ALA A 365 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   GLN A 372 " --> pdb=" O   ALA A 368 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LYS A 373 " --> pdb=" O   ALA A 369 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   VAL A 376 " --> pdb=" O   GLN A 372 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   THR A 381 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   SER A 382 " --> pdb=" O   ASN A 378 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   TYR A 383 " --> pdb=" O   PHE A 379 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   ALA A 385 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
      removed outlier: 5.286A  pdb=" N   LEU A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   THR A 389 " --> pdb=" O   ALA A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 416
      removed outlier: 3.708A  pdb=" N   THR A 410 " --> pdb=" O   PHE A 406 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLN A 412 " --> pdb=" O   ARG A 408 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   THR A 413 " --> pdb=" O   ALA A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 460
      removed outlier: 3.878A  pdb=" N   ASN A 435 " --> pdb=" O   ALA A 431 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ALA A 444 " --> pdb=" O   PHE A 440 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   VAL A 455 " --> pdb=" O   THR A 451 " (cutoff:3.500A)
      Proline residue:  A 456  - end of helix
      removed outlier: 3.714A  pdb=" N   GLN A 460 " --> pdb=" O   PRO A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 493
      removed outlier: 3.529A  pdb=" N   VAL A 489 " --> pdb=" O   PHE A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 516
      removed outlier: 4.304A  pdb=" N   GLU A 506 " --> pdb=" O   GLY A 502 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   VAL A 514 " --> pdb=" O   GLN A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 545
      removed outlier: 3.736A  pdb=" N   VAL A 530 " --> pdb=" O   CYS A 526 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ASN A 531 " --> pdb=" O   CYS A 527 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   VAL A 534 " --> pdb=" O   VAL A 530 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ARG A 537 " --> pdb=" O   TRP A 533 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   ALA A 540 " --> pdb=" O   LEU A 536 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ALA A 544 " --> pdb=" O   ALA A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 583
      removed outlier: 3.501A  pdb=" N   ALA A 564 " --> pdb=" O   PRO A 560 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU A 568 " --> pdb=" O   ALA A 564 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ILE A 574 " --> pdb=" O   TRP A 570 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   SER A 576 " --> pdb=" O   GLY A 572 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   SER A 577 " --> pdb=" O   SER A 573 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE A 579 " --> pdb=" O   THR A 575 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   VAL A 580 " --> pdb=" O   SER A 576 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU A 582 " --> pdb=" O   ALA A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 624
      removed outlier: 3.628A  pdb=" N   ALA A 609 " --> pdb=" O   SER A 605 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU A 614 " --> pdb=" O   GLU A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 628
      removed outlier: 4.207A  pdb=" N   ASP A 628 " --> pdb=" O   SER A 625 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 625 through 628'
    Processing helix  chain 'A' and resid 629 through 650
      removed outlier: 3.739A  pdb=" N   GLU A 635 " --> pdb=" O   GLY A 631 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   PHE A 640 " --> pdb=" O   ARG A 636 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   THR A 642 " --> pdb=" O   GLU A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 684
      removed outlier: 4.043A  pdb=" N   ILE A 670 " --> pdb=" O   HIS A 666 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   THR A 671 " --> pdb=" O   SER A 667 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   ARG A 672 " --> pdb=" O   GLU A 668 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   GLU A 673 " --> pdb=" O   LYS A 669 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ALA A 674 " --> pdb=" O   ILE A 670 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ALA A 682 " --> pdb=" O   GLU A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 690 through 696
      removed outlier: 3.544A  pdb=" N   TRP A 695 " --> pdb=" O   GLU A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 718
      removed outlier: 3.722A  pdb=" N   ILE A 712 " --> pdb=" O   GLY A 708 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 50
      removed outlier: 3.744A  pdb=" N   THR B  48 " --> pdb=" O   ILE B  44 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   VAL B  50 " --> pdb=" O   ALA B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 90
      removed outlier: 3.890A  pdb=" N   HIS B  90 " --> pdb=" O   GLY B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 108
    Processing helix  chain 'B' and resid 111 through 125
      removed outlier: 3.734A  pdb=" N   LEU B 118 " --> pdb=" O   GLU B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 165
      removed outlier: 3.861A  pdb=" N   GLU B 158 " --> pdb=" O   SER B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 182
      removed outlier: 3.748A  pdb=" N   ILE B 177 " --> pdb=" O   ASP B 173 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG B 178 " --> pdb=" O   ILE B 174 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LYS B 180 " --> pdb=" O   ASN B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 197
      removed outlier: 3.750A  pdb=" N   TYR B 188 " --> pdb=" O   SER B 184 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   PHE B 189 " --> pdb=" O   VAL B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 212
      removed outlier: 3.581A  pdb=" N   TRP B 210 " --> pdb=" O   GLY B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 246
      removed outlier: 4.097A  pdb=" N   ALA B 221 " --> pdb=" O   SER B 217 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   VAL B 229 " --> pdb=" O   GLY B 225 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   PHE B 232 " --> pdb=" O   SER B 228 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   VAL B 240 " --> pdb=" O   LYS B 236 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL B 244 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 289
      removed outlier: 3.880A  pdb=" N   ARG B 284 " --> pdb=" O   PRO B 280 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   THR B 287 " --> pdb=" O   LYS B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 320
      removed outlier: 3.900A  pdb=" N   LEU B 312 " --> pdb=" O   THR B 308 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ASN B 317 " --> pdb=" O   GLU B 313 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLU B 318 " --> pdb=" O   VAL B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 330
    Processing helix  chain 'B' and resid 330 through 358
      Proline residue:  B 341  - end of helix
      removed outlier: 3.629A  pdb=" N   LEU B 347 " --> pdb=" O   ILE B 343 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ASN B 355 " --> pdb=" O   ALA B 351 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLU B 358 " --> pdb=" O   LEU B 354 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 392
      removed outlier: 3.513A  pdb=" N   ASP B 367 " --> pdb=" O   VAL B 363 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ALA B 369 " --> pdb=" O   ALA B 365 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   GLN B 372 " --> pdb=" O   ALA B 368 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LYS B 373 " --> pdb=" O   ALA B 369 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   VAL B 376 " --> pdb=" O   GLN B 372 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   THR B 381 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   SER B 382 " --> pdb=" O   ASN B 378 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   TYR B 383 " --> pdb=" O   PHE B 379 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   ALA B 385 " --> pdb=" O   THR B 381 " (cutoff:3.500A)
      removed outlier: 5.286A  pdb=" N   LEU B 386 " --> pdb=" O   SER B 382 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   THR B 389 " --> pdb=" O   ALA B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 416
      removed outlier: 3.708A  pdb=" N   THR B 410 " --> pdb=" O   PHE B 406 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLN B 412 " --> pdb=" O   ARG B 408 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   THR B 413 " --> pdb=" O   ALA B 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 460
      removed outlier: 3.879A  pdb=" N   ASN B 435 " --> pdb=" O   ALA B 431 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ALA B 444 " --> pdb=" O   PHE B 440 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   VAL B 455 " --> pdb=" O   THR B 451 " (cutoff:3.500A)
      Proline residue:  B 456  - end of helix
      removed outlier: 3.714A  pdb=" N   GLN B 460 " --> pdb=" O   PRO B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 493
      removed outlier: 3.529A  pdb=" N   VAL B 489 " --> pdb=" O   PHE B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 516
      removed outlier: 4.305A  pdb=" N   GLU B 506 " --> pdb=" O   GLY B 502 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL B 514 " --> pdb=" O   GLN B 510 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 545
      removed outlier: 3.735A  pdb=" N   VAL B 530 " --> pdb=" O   CYS B 526 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ASN B 531 " --> pdb=" O   CYS B 527 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   VAL B 534 " --> pdb=" O   VAL B 530 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ARG B 537 " --> pdb=" O   TRP B 533 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   ALA B 540 " --> pdb=" O   LEU B 536 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ALA B 544 " --> pdb=" O   ALA B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 583
      removed outlier: 3.500A  pdb=" N   ALA B 564 " --> pdb=" O   PRO B 560 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU B 568 " --> pdb=" O   ALA B 564 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE B 574 " --> pdb=" O   TRP B 570 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   SER B 576 " --> pdb=" O   GLY B 572 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   SER B 577 " --> pdb=" O   SER B 573 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE B 579 " --> pdb=" O   THR B 575 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   VAL B 580 " --> pdb=" O   SER B 576 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU B 582 " --> pdb=" O   ALA B 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 598 through 624
      removed outlier: 3.628A  pdb=" N   ALA B 609 " --> pdb=" O   SER B 605 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU B 614 " --> pdb=" O   GLU B 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 625 through 628
      removed outlier: 4.207A  pdb=" N   ASP B 628 " --> pdb=" O   SER B 625 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 625 through 628'
    Processing helix  chain 'B' and resid 629 through 650
      removed outlier: 3.739A  pdb=" N   GLU B 635 " --> pdb=" O   GLY B 631 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   PHE B 640 " --> pdb=" O   ARG B 636 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   THR B 642 " --> pdb=" O   GLU B 638 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 666 through 684
      removed outlier: 4.043A  pdb=" N   ILE B 670 " --> pdb=" O   HIS B 666 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   THR B 671 " --> pdb=" O   SER B 667 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   ARG B 672 " --> pdb=" O   GLU B 668 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   GLU B 673 " --> pdb=" O   LYS B 669 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ALA B 674 " --> pdb=" O   ILE B 670 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ALA B 682 " --> pdb=" O   GLU B 678 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 690 through 696
      removed outlier: 3.544A  pdb=" N   TRP B 695 " --> pdb=" O   GLU B 691 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 700 through 718
      removed outlier: 3.722A  pdb=" N   ILE B 712 " --> pdb=" O   GLY B 708 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56
      removed outlier: 3.825A  pdb=" N   PHE A  22 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 266
      removed outlier: 3.912A  pdb=" N   HIS A 265 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 56
      removed outlier: 3.825A  pdb=" N   PHE B  22 " --> pdb=" O   VAL B  68 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 266
      removed outlier: 3.912A  pdb=" N   HIS B 265 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)

    606 hydrogen bonds defined for protein.
    1812 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: 3.29

  Time building geometry restraints manager: 3.03 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: 3319
        1.34 -     1.46: 2219
        1.46 -     1.57: 5254
        1.57 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 10858
  Sorted by residual:
  bond pdb=" C   ILE B 394 "
       pdb=" N   PRO B 395 "
    ideal  model  delta    sigma   weight residual
    1.336  1.384 -0.048 1.20e-02 6.94e+03 1.57e+01
  bond pdb=" C   ILE A 394 "
       pdb=" N   PRO A 395 "
    ideal  model  delta    sigma   weight residual
    1.336  1.383 -0.047 1.20e-02 6.94e+03 1.56e+01
  bond pdb=" N   GLU A 480 "
       pdb=" CA  GLU A 480 "
    ideal  model  delta    sigma   weight residual
    1.459  1.482 -0.023 1.15e-02 7.56e+03 3.88e+00
  bond pdb=" N   GLU B 480 "
       pdb=" CA  GLU B 480 "
    ideal  model  delta    sigma   weight residual
    1.459  1.481 -0.022 1.15e-02 7.56e+03 3.72e+00
  bond pdb=" C   THR B 340 "
       pdb=" N   PRO B 341 "
    ideal  model  delta    sigma   weight residual
    1.336  1.359 -0.023 1.25e-02 6.40e+03 3.46e+00
  ... (remaining 10853 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 14050
        2.05 -     4.10: 596
        4.10 -     6.16: 56
        6.16 -     8.21: 22
        8.21 -    10.26: 10
  Bond angle restraints: 14734
  Sorted by residual:
  angle pdb=" C   SER B 584 "
        pdb=" N   ASN B 585 "
        pdb=" CA  ASN B 585 "
      ideal   model   delta    sigma   weight residual
     121.70  129.34   -7.64 1.80e+00 3.09e-01 1.80e+01
  angle pdb=" C   SER A 584 "
        pdb=" N   ASN A 585 "
        pdb=" CA  ASN A 585 "
      ideal   model   delta    sigma   weight residual
     121.70  129.33   -7.63 1.80e+00 3.09e-01 1.80e+01
  angle pdb=" N   VAL A 248 "
        pdb=" CA  VAL A 248 "
        pdb=" CB  VAL A 248 "
      ideal   model   delta    sigma   weight residual
     112.15  106.12    6.03 1.47e+00 4.63e-01 1.68e+01
  angle pdb=" N   VAL B 248 "
        pdb=" CA  VAL B 248 "
        pdb=" CB  VAL B 248 "
      ideal   model   delta    sigma   weight residual
     112.15  106.15    6.00 1.47e+00 4.63e-01 1.67e+01
  angle pdb=" C   PRO B  97 "
        pdb=" N   HIS B  98 "
        pdb=" CA  HIS B  98 "
      ideal   model   delta    sigma   weight residual
     121.54  128.24   -6.70 1.91e+00 2.74e-01 1.23e+01
  ... (remaining 14729 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 5566
       17.83 -    35.67: 662
       35.67 -    53.50: 116
       53.50 -    71.33: 20
       71.33 -    89.17: 10
  Dihedral angle restraints: 6374
    sinusoidal: 2554
      harmonic: 3820
  Sorted by residual:
  dihedral pdb=" CA  ASN A 138 "
           pdb=" C   ASN A 138 "
           pdb=" N   ALA A 139 "
           pdb=" CA  ALA A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.38  -25.62     0      5.00e+00 4.00e-02 2.63e+01
  dihedral pdb=" CA  ASN B 138 "
           pdb=" C   ASN B 138 "
           pdb=" N   ALA B 139 "
           pdb=" CA  ALA B 139 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.42  -25.58     0      5.00e+00 4.00e-02 2.62e+01
  dihedral pdb=" CA  HIS A 479 "
           pdb=" C   HIS A 479 "
           pdb=" N   GLU A 480 "
           pdb=" CA  GLU A 480 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.25   22.75     0      5.00e+00 4.00e-02 2.07e+01
  ... (remaining 6371 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1209
       0.053 -    0.105: 321
       0.105 -    0.158: 62
       0.158 -    0.210: 16
       0.210 -    0.263: 8
  Chirality restraints: 1616
  Sorted by residual:
  chirality pdb=" CB  VAL B 248 "
            pdb=" CA  VAL B 248 "
            pdb=" CG1 VAL B 248 "
            pdb=" CG2 VAL B 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CB  VAL A 248 "
            pdb=" CA  VAL A 248 "
            pdb=" CG1 VAL A 248 "
            pdb=" CG2 VAL A 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CA  THR A 340 "
            pdb=" N   THR A 340 "
            pdb=" C   THR A 340 "
            pdb=" CB  THR A 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.27    0.26 2.00e-01 2.50e+01 1.65e+00
  ... (remaining 1613 not shown)

  Planarity restraints: 1870
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 455 "    0.047 5.00e-02 4.00e+02   7.01e-02 7.86e+00
        pdb=" N   PRO B 456 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO B 456 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 456 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 455 "    0.047 5.00e-02 4.00e+02   7.00e-02 7.83e+00
        pdb=" N   PRO A 456 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO A 456 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 456 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 401 "   -0.045 5.00e-02 4.00e+02   6.75e-02 7.29e+00
        pdb=" N   PRO A 402 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 402 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 402 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 1867 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2762
        2.77 -     3.30: 9675
        3.30 -     3.84: 17763
        3.84 -     4.37: 20103
        4.37 -     4.90: 34166
  Nonbonded interactions: 84469
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 439 "
            pdb=" OG1 THR A 443 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   TYR B 439 "
            pdb=" OG1 THR B 443 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   MET A 701 "
            pdb=" OG1 THR A 704 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   MET B 701 "
            pdb=" OG1 THR B 704 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OG  SER B 228 "
            pdb=" OG  SER B 569 "
     model   vdw
     2.305 3.040
  ... (remaining 84464 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.800
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     28.380
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.040
  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:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
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      :  0.007   0.070  10858  Z= 0.463
  Angle     :  0.991  10.261  14734  Z= 0.581
  Chirality :  0.053   0.263   1616
  Planarity :  0.007   0.070   1870
  Dihedral  : 15.633  89.167   3894
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  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: -5.94 (0.15), residues: 1284
  helix: -4.16 (0.08), residues: 880
  sheet: -2.98 (0.68), residues: 46
  loop : -2.65 (0.28), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 210 
 HIS   0.006   0.002   HIS B 611 
 PHE   0.028   0.002   PHE A 396 
 TYR   0.019   0.002   TYR A 279 
 ARG   0.004   0.001   ARG B 258 

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 1.150 
Fit side-chains
   revert: symmetry clash
REVERT: A  151 HIS cc_start: 0.7770 (t70) cc_final: 0.7353 (t-90)
REVERT: A  282 MET cc_start: 0.6936 (tpp) cc_final: 0.5147 (ptt)
REVERT: A  313 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7479 (tm-30)
REVERT: A  355 ASN cc_start: 0.9022 (t0) cc_final: 0.8720 (t0)
REVERT: A  491 GLU cc_start: 0.8030 (tp30) cc_final: 0.7777 (tp30)
REVERT: A  648 GLN cc_start: 0.6543 (mm110) cc_final: 0.5814 (pp30)
REVERT: B  151 HIS cc_start: 0.7776 (t70) cc_final: 0.7360 (t-90)
REVERT: B  282 MET cc_start: 0.6877 (tpp) cc_final: 0.5123 (ptt)
REVERT: B  291 GLN cc_start: 0.5455 (tm-30) cc_final: 0.5238 (tm-30)
REVERT: B  355 ASN cc_start: 0.9027 (t0) cc_final: 0.8666 (t0)
REVERT: B  359 ASN cc_start: 0.7573 (m-40) cc_final: 0.7168 (m-40)
REVERT: B  491 GLU cc_start: 0.8112 (tp30) cc_final: 0.7890 (tp30)
REVERT: B  527 CYS cc_start: 0.7724 (t) cc_final: 0.7308 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.2564
  time to fit residues: 80.2512
Evaluate side-chains
  138 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:    7.9990
   chunk 98 optimal weight:    5.9990
   chunk 54 optimal weight:    0.6980
   chunk 33 optimal weight:    6.9990
   chunk 66 optimal weight:    0.2980
   chunk 52 optimal weight:    0.8980
   chunk 101 optimal weight:    0.8980
   chunk 39 optimal weight:   10.0000
   chunk 61 optimal weight:    6.9990
   chunk 75 optimal weight:    0.8980
   chunk 118 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 355 ASN
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 401 HIS
A 510 GLN
** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 633 GLN
** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 355 ASN
B 374 GLN
B 401 HIS
B 510 GLN
B 633 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.146083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.112497 restraints weight = 17211.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.113289 restraints weight = 12119.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.113499 restraints weight = 10148.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10858  Z= 0.181
  Angle     :  0.629   7.822  14734  Z= 0.327
  Chirality :  0.041   0.163   1616
  Planarity :  0.005   0.051   1870
  Dihedral  :  4.964  18.702   1406
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 15.19 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.94 (0.20), residues: 1284
  helix: -1.82 (0.14), residues: 886
  sheet: -2.60 (0.69), residues: 46
  loop : -1.59 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 600 
 HIS   0.003   0.001   HIS B 479 
 PHE   0.014   0.001   PHE A 216 
 TYR   0.018   0.002   TYR A 439 
 ARG   0.005   0.000   ARG B 554 

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 176
  time to evaluate  : 1.274 
Fit side-chains
   revert: symmetry clash
REVERT: A  151 HIS cc_start: 0.7562 (t70) cc_final: 0.7175 (t-90)
REVERT: A  173 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7552 (t0)
REVERT: A  289 LEU cc_start: 0.7385 (tt) cc_final: 0.7111 (mm)
REVERT: A  539 ASP cc_start: 0.6997 (m-30) cc_final: 0.6747 (m-30)
REVERT: A  566 SER cc_start: 0.9040 (t) cc_final: 0.8817 (p)
REVERT: A  648 GLN cc_start: 0.6578 (mm110) cc_final: 0.5811 (pp30)
REVERT: B   49 THR cc_start: 0.8774 (p) cc_final: 0.8512 (m)
REVERT: B   87 ASP cc_start: 0.7799 (m-30) cc_final: 0.7432 (m-30)
REVERT: B  138 ASN cc_start: 0.6869 (t0) cc_final: 0.6551 (t0)
REVERT: B  151 HIS cc_start: 0.7505 (t70) cc_final: 0.7119 (t-90)
REVERT: B  173 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7576 (t0)
REVERT: B  355 ASN cc_start: 0.9176 (t0) cc_final: 0.8720 (t0)
REVERT: B  387 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.8067 (m-80)
  outliers start: 15
  outliers final: 7
  residues processed: 187
  average time/residue: 0.2418
  time to fit residues: 64.1028
Evaluate side-chains
  147 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 137
  time to evaluate  : 1.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  666 HIS
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  387 PHE
Chi-restraints excluded: chain B residue  666 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 40 optimal weight:   20.0000
   chunk 30 optimal weight:   10.0000
   chunk 51 optimal weight:    0.8980
   chunk 28 optimal weight:    9.9990
   chunk 97 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 57 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 91 optimal weight:   30.0000
   chunk 7 optimal weight:    4.9990
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 374 GLN
A 510 GLN
** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 ASN
** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 510 GLN
** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.139661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.108722 restraints weight = 18106.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.107594 restraints weight = 15261.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.108469 restraints weight = 15595.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.3036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055  10858  Z= 0.390
  Angle     :  0.716   8.866  14734  Z= 0.370
  Chirality :  0.045   0.172   1616
  Planarity :  0.005   0.046   1870
  Dihedral  :  4.945  17.132   1406
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 17.94 %
    Favored  : 78.33 %
  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: -1.90 (0.22), residues: 1284
  helix: -0.89 (0.16), residues: 900
  sheet: -2.39 (0.75), residues: 42
  loop : -1.68 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 141 
 HIS   0.004   0.001   HIS A 611 
 PHE   0.030   0.002   PHE A 315 
 TYR   0.020   0.002   TYR A 279 
 ARG   0.005   0.001   ARG B 639 

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 138
  time to evaluate  : 1.244 
Fit side-chains
   revert: symmetry clash
REVERT: A  305 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8333 (tt)
REVERT: A  648 GLN cc_start: 0.6798 (mm110) cc_final: 0.5844 (pp30)
REVERT: B   87 ASP cc_start: 0.7910 (m-30) cc_final: 0.7689 (m-30)
REVERT: B  138 ASN cc_start: 0.7315 (t0) cc_final: 0.6964 (t0)
REVERT: B  400 LEU cc_start: 0.7991 (pp) cc_final: 0.7776 (pp)
REVERT: B  437 MET cc_start: 0.8884 (tpt) cc_final: 0.8590 (tpp)
  outliers start: 42
  outliers final: 30
  residues processed: 177
  average time/residue: 0.2233
  time to fit residues: 56.9080
Evaluate side-chains
  158 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 127
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  503 ASP
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  666 HIS
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  440 PHE
Chi-restraints excluded: chain B residue  503 ASP
Chi-restraints excluded: chain B residue  566 SER
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain B residue  666 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 128 optimal weight:    7.9990
   chunk 70 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 76 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 80 optimal weight:    6.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 479 HIS
** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.141497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.110416 restraints weight = 17692.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.108947 restraints weight = 14922.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.109912 restraints weight = 15332.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.3410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10858  Z= 0.276
  Angle     :  0.648   7.128  14734  Z= 0.329
  Chirality :  0.042   0.161   1616
  Planarity :  0.004   0.045   1870
  Dihedral  :  4.657  16.778   1406
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 20.78 %
    Favored  : 75.22 %
  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: -1.30 (0.23), residues: 1284
  helix: -0.43 (0.17), residues: 898
  sheet: -2.50 (0.73), residues: 42
  loop : -1.42 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 141 
 HIS   0.003   0.001   HIS A 611 
 PHE   0.037   0.002   PHE A 315 
 TYR   0.015   0.002   TYR A 279 
 ARG   0.003   0.000   ARG B 639 

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 139
  time to evaluate  : 1.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7610 (mt0)
REVERT: A  440 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7570 (t80)
REVERT: B   87 ASP cc_start: 0.7928 (m-30) cc_final: 0.7697 (m-30)
REVERT: B  312 LEU cc_start: 0.8849 (mt) cc_final: 0.8641 (mt)
REVERT: B  384 MET cc_start: 0.7490 (mtt) cc_final: 0.7284 (mtt)
REVERT: B  437 MET cc_start: 0.8838 (tpt) cc_final: 0.8485 (tpp)
  outliers start: 45
  outliers final: 31
  residues processed: 179
  average time/residue: 0.2359
  time to fit residues: 60.8193
Evaluate side-chains
  159 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 127
  time to evaluate  : 1.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  503 ASP
Chi-restraints excluded: chain A residue  566 SER
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  666 HIS
Chi-restraints excluded: chain A residue  707 ILE
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  440 PHE
Chi-restraints excluded: chain B residue  503 ASP
Chi-restraints excluded: chain B residue  566 SER
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain B residue  666 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 89 optimal weight:    7.9990
   chunk 93 optimal weight:    9.9990
   chunk 66 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 97 optimal weight:   10.0000
   chunk 106 optimal weight:    0.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
A 138 ASN
** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  42 GLN
** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.144158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.112603 restraints weight = 17342.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.111736 restraints weight = 15099.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.112372 restraints weight = 14020.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.3639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10858  Z= 0.196
  Angle     :  0.606   7.706  14734  Z= 0.305
  Chirality :  0.040   0.156   1616
  Planarity :  0.004   0.041   1870
  Dihedral  :  4.345  15.814   1406
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 20.52 %
    Favored  : 74.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.23), residues: 1284
  helix:  0.06 (0.17), residues: 894
  sheet: -2.45 (0.75), residues: 42
  loop : -1.27 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 141 
 HIS   0.003   0.001   HIS A 611 
 PHE   0.038   0.001   PHE A 315 
 TYR   0.012   0.001   TYR A 279 
 ARG   0.004   0.000   ARG A 249 

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 140
  time to evaluate  : 1.208 
Fit side-chains
   revert: symmetry clash
REVERT: A  305 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8221 (tt)
REVERT: A  440 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7520 (t80)
REVERT: B  384 MET cc_start: 0.7481 (mtt) cc_final: 0.7146 (mmt)
REVERT: B  437 MET cc_start: 0.8913 (tpt) cc_final: 0.8175 (tpt)
REVERT: B  443 THR cc_start: 0.7857 (p) cc_final: 0.7418 (t)
  outliers start: 51
  outliers final: 38
  residues processed: 185
  average time/residue: 0.2097
  time to fit residues: 56.5883
Evaluate side-chains
  163 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 123
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  187 PHE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  503 ASP
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  666 HIS
Chi-restraints excluded: chain A residue  707 ILE
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  187 PHE
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  398 HIS
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  440 PHE
Chi-restraints excluded: chain B residue  503 ASP
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain B residue  666 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 120 optimal weight:    0.5980
   chunk 6 optimal weight:    5.9990
   chunk 117 optimal weight:    0.6980
   chunk 98 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 60 optimal weight:    6.9990
   chunk 88 optimal weight:    1.9990
   chunk 96 optimal weight:    9.9990
   chunk 57 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
A 138 ASN
A 156 ASN
** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  42 GLN
B 156 ASN
** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.142982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.112050 restraints weight = 17607.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.111145 restraints weight = 16430.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.112421 restraints weight = 14548.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.3787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10858  Z= 0.233
  Angle     :  0.613   8.721  14734  Z= 0.312
  Chirality :  0.041   0.179   1616
  Planarity :  0.004   0.038   1870
  Dihedral  :  4.287  15.207   1406
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 21.58 %
    Favored  : 73.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.24), residues: 1284
  helix:  0.27 (0.17), residues: 892
  sheet: -2.46 (0.76), residues: 42
  loop : -1.09 (0.36), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 141 
 HIS   0.003   0.001   HIS A 611 
 PHE   0.037   0.002   PHE A 315 
 TYR   0.015   0.002   TYR A 393 
 ARG   0.006   0.000   ARG B 249 

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 133
  time to evaluate  : 1.139 
Fit side-chains
   revert: symmetry clash
REVERT: A  305 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8205 (tt)
REVERT: A  440 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7566 (t80)
REVERT: B  437 MET cc_start: 0.8879 (tpt) cc_final: 0.8536 (tpp)
REVERT: B  443 THR cc_start: 0.7541 (p) cc_final: 0.7197 (t)
  outliers start: 56
  outliers final: 42
  residues processed: 182
  average time/residue: 0.2097
  time to fit residues: 55.5853
Evaluate side-chains
  171 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 127
  time to evaluate  : 1.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 HIS
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  503 ASP
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  666 HIS
Chi-restraints excluded: chain A residue  707 ILE
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  187 PHE
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  398 HIS
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  440 PHE
Chi-restraints excluded: chain B residue  503 ASP
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain B residue  666 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 95 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0270
   chunk 58 optimal weight:    0.9990
   chunk 108 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.8044

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 ASN
B  42 GLN
** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.145857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.114386 restraints weight = 17605.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.113311 restraints weight = 15650.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.114134 restraints weight = 13638.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.3950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10858  Z= 0.173
  Angle     :  0.598   9.448  14734  Z= 0.299
  Chirality :  0.040   0.181   1616
  Planarity :  0.004   0.038   1870
  Dihedral  :  4.104  14.382   1406
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 22.47 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.24), residues: 1284
  helix:  0.55 (0.17), residues: 890
  sheet: -2.44 (0.75), residues: 42
  loop : -0.90 (0.36), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 141 
 HIS   0.002   0.000   HIS A 611 
 PHE   0.038   0.001   PHE A 315 
 TYR   0.015   0.001   TYR B 188 
 ARG   0.004   0.000   ARG B 249 

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 139
  time to evaluate  : 1.264 
Fit side-chains
   revert: symmetry clash
REVERT: A  305 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8191 (tt)
REVERT: A  437 MET cc_start: 0.8796 (tpt) cc_final: 0.8027 (tpt)
REVERT: A  440 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7543 (t80)
REVERT: B  223 LEU cc_start: 0.7745 (tt) cc_final: 0.7534 (mt)
REVERT: B  305 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8310 (tt)
REVERT: B  437 MET cc_start: 0.8840 (tpt) cc_final: 0.8554 (tpp)
REVERT: B  443 THR cc_start: 0.7581 (p) cc_final: 0.7256 (t)
  outliers start: 48
  outliers final: 36
  residues processed: 180
  average time/residue: 0.2113
  time to fit residues: 55.5654
Evaluate side-chains
  168 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 129
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  187 PHE
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 HIS
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  503 ASP
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  666 HIS
Chi-restraints excluded: chain A residue  707 ILE
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  187 PHE
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  398 HIS
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  440 PHE
Chi-restraints excluded: chain B residue  503 ASP
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain B residue  646 LEU
Chi-restraints excluded: chain B residue  666 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 106 optimal weight:    0.2980
   chunk 76 optimal weight:    7.9990
   chunk 98 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 126 optimal weight:   10.0000
   chunk 80 optimal weight:    0.0470
   chunk 70 optimal weight:    2.9990
   chunk 72 optimal weight:    8.9990
   overall best weight:    1.4482

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 510 GLN
B  42 GLN
** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.144438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.113141 restraints weight = 17406.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.111872 restraints weight = 15766.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.112651 restraints weight = 14245.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.4015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10858  Z= 0.216
  Angle     :  0.626  10.398  14734  Z= 0.315
  Chirality :  0.041   0.195   1616
  Planarity :  0.004   0.037   1870
  Dihedral  :  4.096  14.345   1406
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 22.65 %
    Favored  : 73.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.24), residues: 1284
  helix:  0.62 (0.17), residues: 888
  sheet: -2.92 (0.65), residues: 44
  loop : -1.09 (0.36), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 141 
 HIS   0.003   0.001   HIS A 611 
 PHE   0.038   0.001   PHE A 315 
 TYR   0.014   0.002   TYR A 188 
 ARG   0.004   0.000   ARG B 249 

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 130
  time to evaluate  : 1.204 
Fit side-chains
   revert: symmetry clash
REVERT: A  305 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8175 (tt)
REVERT: A  440 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.7509 (t80)
REVERT: B  173 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7434 (t0)
REVERT: B  262 GLU cc_start: 0.7018 (pm20) cc_final: 0.6815 (pm20)
REVERT: B  305 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8279 (tt)
REVERT: B  437 MET cc_start: 0.8807 (tpt) cc_final: 0.8544 (tpp)
REVERT: B  701 MET cc_start: 0.8310 (tmm) cc_final: 0.8109 (tmm)
  outliers start: 49
  outliers final: 38
  residues processed: 173
  average time/residue: 0.2047
  time to fit residues: 52.9044
Evaluate side-chains
  164 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 122
  time to evaluate  : 1.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  187 PHE
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 HIS
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  503 ASP
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  666 HIS
Chi-restraints excluded: chain A residue  707 ILE
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  187 PHE
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  398 HIS
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  440 PHE
Chi-restraints excluded: chain B residue  503 ASP
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain B residue  646 LEU
Chi-restraints excluded: chain B residue  666 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 96 optimal weight:   10.0000
   chunk 80 optimal weight:    4.9990
   chunk 127 optimal weight:    8.9990
   chunk 129 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 110 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 118 optimal weight:    0.5980
   chunk 113 optimal weight:    0.6980
   chunk 58 optimal weight:    5.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  42 GLN
B 510 GLN
** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.144591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.112302 restraints weight = 17527.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.111898 restraints weight = 15071.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.113140 restraints weight = 12938.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.4063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10858  Z= 0.220
  Angle     :  0.637  10.868  14734  Z= 0.319
  Chirality :  0.041   0.198   1616
  Planarity :  0.004   0.037   1870
  Dihedral  :  4.104  14.734   1406
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 22.47 %
    Favored  : 73.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.24), residues: 1284
  helix:  0.67 (0.17), residues: 888
  sheet: -2.88 (0.65), residues: 44
  loop : -1.05 (0.36), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 141 
 HIS   0.003   0.001   HIS A 611 
 PHE   0.040   0.001   PHE A 315 
 TYR   0.014   0.001   TYR B 188 
 ARG   0.004   0.000   ARG B 249 

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 129
  time to evaluate  : 1.173 
Fit side-chains
   revert: symmetry clash
REVERT: A  305 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8106 (tt)
REVERT: A  440 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7569 (t80)
REVERT: A  510 GLN cc_start: 0.8502 (tt0) cc_final: 0.8296 (tt0)
REVERT: B   67 PHE cc_start: 0.8575 (m-10) cc_final: 0.8366 (m-10)
REVERT: B  173 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7405 (t0)
REVERT: B  305 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8204 (tt)
REVERT: B  437 MET cc_start: 0.8836 (tpt) cc_final: 0.8570 (tpp)
  outliers start: 50
  outliers final: 44
  residues processed: 175
  average time/residue: 0.1970
  time to fit residues: 51.1446
Evaluate side-chains
  169 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 121
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  187 PHE
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 HIS
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  503 ASP
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  616 VAL
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  666 HIS
Chi-restraints excluded: chain A residue  707 ILE
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  187 PHE
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  381 THR
Chi-restraints excluded: chain B residue  398 HIS
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  440 PHE
Chi-restraints excluded: chain B residue  503 ASP
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain B residue  616 VAL
Chi-restraints excluded: chain B residue  646 LEU
Chi-restraints excluded: chain B residue  666 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 129 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0970
   chunk 94 optimal weight:    5.9990
   chunk 101 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0270
   chunk 58 optimal weight:    8.9990
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  42 GLN
B 510 GLN
** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 611 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.147805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.116019 restraints weight = 17139.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.115851 restraints weight = 14050.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.117103 restraints weight = 12221.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.4290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10858  Z= 0.167
  Angle     :  0.614  11.570  14734  Z= 0.305
  Chirality :  0.040   0.177   1616
  Planarity :  0.004   0.038   1870
  Dihedral  :  3.969  15.094   1406
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 24.16 %
    Favored  : 72.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.24), residues: 1284
  helix:  0.86 (0.17), residues: 890
  sheet: -2.69 (0.67), residues: 44
  loop : -0.77 (0.36), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 141 
 HIS   0.002   0.000   HIS A 611 
 PHE   0.043   0.001   PHE A 315 
 TYR   0.015   0.001   TYR B 188 
 ARG   0.002   0.000   ARG B 249 

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 141
  time to evaluate  : 1.270 
Fit side-chains
   revert: symmetry clash
REVERT: A  305 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8066 (tt)
REVERT: A  437 MET cc_start: 0.8756 (tpt) cc_final: 0.7967 (tpt)
REVERT: A  440 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7567 (t80)
REVERT: A  510 GLN cc_start: 0.8420 (tt0) cc_final: 0.8044 (tt0)
REVERT: A  622 PHE cc_start: 0.8619 (t80) cc_final: 0.8266 (t80)
REVERT: B  173 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7341 (t0)
REVERT: B  305 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8190 (tt)
REVERT: B  440 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7405 (t80)
REVERT: B  510 GLN cc_start: 0.8493 (tt0) cc_final: 0.8253 (tt0)
REVERT: B  622 PHE cc_start: 0.8642 (t80) cc_final: 0.8312 (t80)
  outliers start: 37
  outliers final: 26
  residues processed: 173
  average time/residue: 0.2091
  time to fit residues: 53.1757
Evaluate side-chains
  156 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 125
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  187 PHE
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  398 HIS
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  503 ASP
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  666 HIS
Chi-restraints excluded: chain A residue  707 ILE
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  173 ASP
Chi-restraints excluded: chain B residue  187 PHE
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  398 HIS
Chi-restraints excluded: chain B residue  415 THR
Chi-restraints excluded: chain B residue  440 PHE
Chi-restraints excluded: chain B residue  503 ASP
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain B residue  666 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 82 optimal weight:    0.5980
   chunk 88 optimal weight:    3.9990
   chunk 108 optimal weight:    0.6980
   chunk 73 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 71 optimal weight:    5.9990
   chunk 125 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
A 156 ASN
** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  42 GLN
** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.145732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.113924 restraints weight = 17118.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.114383 restraints weight = 14754.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.115617 restraints weight = 11869.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.4283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10858  Z= 0.207
  Angle     :  0.643  11.328  14734  Z= 0.320
  Chirality :  0.041   0.167   1616
  Planarity :  0.004   0.037   1870
  Dihedral  :  3.970  14.349   1406
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 24.33 %
    Favored  : 72.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.24), residues: 1284
  helix:  0.85 (0.17), residues: 898
  sheet: -2.68 (0.65), residues: 44
  loop : -0.67 (0.37), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 141 
 HIS   0.003   0.001   HIS A 611 
 PHE   0.043   0.001   PHE A 315 
 TYR   0.014   0.001   TYR A 393 
 ARG   0.010   0.000   ARG A 639 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2846.99 seconds
wall clock time: 52 minutes 8.82 seconds (3128.82 seconds total)