Starting phenix.real_space_refine
on Sat Jun  7 14:18:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wiv_32537/06_2025/7wiv_32537.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wiv_32537/06_2025/7wiv_32537.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wiv_32537/06_2025/7wiv_32537.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wiv_32537/06_2025/7wiv_32537.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wiv_32537/06_2025/7wiv_32537.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wiv_32537/06_2025/7wiv_32537.cif"
  }
  resolution = 2.88
  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=  -0.001 sd=   0.049
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: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      14      5.16       5
     C    5511      2.51       5
     N    1553      2.21       5
     O    1565      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 63 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8646
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 571, 4344
          Classifications: {'peptide': 571}
          Link IDs: {'PTRANS': 25, 'TRANS': 545}
    Chain: "B"
      Number of atoms: 4271
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 576, 4271
          Classifications: {'peptide': 576}
          Link IDs: {'PTRANS': 25, 'TRANS': 550}
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ANP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.33, per 1000 atoms: 0.73
  Number of scatterers: 8646
  At special positions: 0
  Unit cell: (71.34, 95.94, 132.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P       3     15.00
     O    1565      8.00
     N    1553      7.00
     C    5511      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: 2.30
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2102

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 7 sheets defined
      63.7% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 280 through 286
    Processing helix  chain 'A' and resid 290 through 306
    Processing helix  chain 'A' and resid 309 through 323
      removed outlier: 3.559A  pdb=" N   VAL A 315 " --> pdb=" O   PHE A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 375
      removed outlier: 3.756A  pdb=" N   GLY A 334 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   HIS A 356 " --> pdb=" O   THR A 352 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ASP A 359 " --> pdb=" O   LEU A 355 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ARG A 361 " --> pdb=" O   VAL A 357 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   PHE A 362 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ARG A 369 " --> pdb=" O   ALA A 365 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   SER A 372 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   SER A 375 " --> pdb=" O   LEU A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 385
      removed outlier: 4.136A  pdb=" N   PHE A 382 " --> pdb=" O   PRO A 378 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   THR A 383 " --> pdb=" O   LEU A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 395
      removed outlier: 3.627A  pdb=" N   LYS A 391 " --> pdb=" O   SER A 387 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LEU A 393 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 407
      removed outlier: 3.564A  pdb=" N   LEU A 401 " --> pdb=" O   ASP A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 430
      removed outlier: 3.720A  pdb=" N   VAL A 416 " --> pdb=" O   ALA A 412 " (cutoff:3.500A)
      Proline residue:  A 419  - end of helix
    Processing helix  chain 'A' and resid 430 through 437
      removed outlier: 3.837A  pdb=" N   VAL A 436 " --> pdb=" O   ARG A 432 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LEU A 437 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 453
      removed outlier: 3.512A  pdb=" N   TYR A 444 " --> pdb=" O   PRO A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 479
      removed outlier: 4.076A  pdb=" N   GLN A 463 " --> pdb=" O   ILE A 459 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ASN A 470 " --> pdb=" O   ALA A 466 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLY A 471 " --> pdb=" O   GLU A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 486
    Processing helix  chain 'A' and resid 487 through 489
      No H-bonds generated for 'chain 'A' and resid 487 through 489'
    Processing helix  chain 'A' and resid 490 through 509
      removed outlier: 3.665A  pdb=" N   ASP A 498 " --> pdb=" O   ARG A 494 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   VAL A 505 " --> pdb=" O   ILE A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 513
      removed outlier: 4.139A  pdb=" N   GLY A 513 " --> pdb=" O   PRO A 510 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 510 through 513'
    Processing helix  chain 'A' and resid 516 through 521
    Processing helix  chain 'A' and resid 523 through 541
      removed outlier: 3.510A  pdb=" N   LEU A 537 " --> pdb=" O   ALA A 533 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   THR A 541 " --> pdb=" O   LEU A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 548
    Processing helix  chain 'A' and resid 549 through 556
    Processing helix  chain 'A' and resid 558 through 571
      removed outlier: 3.606A  pdb=" N   ARG A 562 " --> pdb=" O   THR A 558 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   ALA A 567 " --> pdb=" O   LEU A 563 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   TYR A 568 " --> pdb=" O   LEU A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 587
      removed outlier: 4.104A  pdb=" N   ALA A 579 " --> pdb=" O   THR A 575 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   THR A 586 " --> pdb=" O   HIS A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 655
    Processing helix  chain 'A' and resid 675 through 677
      No H-bonds generated for 'chain 'A' and resid 675 through 677'
    Processing helix  chain 'A' and resid 678 through 684
      removed outlier: 3.623A  pdb=" N   TYR A 683 " --> pdb=" O   ALA A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 705
      removed outlier: 3.632A  pdb=" N   ILE A 704 " --> pdb=" O   ALA A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 719
    Processing helix  chain 'A' and resid 725 through 731
    Processing helix  chain 'A' and resid 734 through 737
      removed outlier: 4.042A  pdb=" N   ASP A 737 " --> pdb=" O   ASP A 734 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 734 through 737'
    Processing helix  chain 'A' and resid 751 through 763
      removed outlier: 3.672A  pdb=" N   THR A 755 " --> pdb=" O   ARG A 751 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ASP A 763 " --> pdb=" O   ALA A 759 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 774
      No H-bonds generated for 'chain 'A' and resid 772 through 774'
    Processing helix  chain 'A' and resid 778 through 781
      removed outlier: 3.672A  pdb=" N   GLU A 781 " --> pdb=" O   PRO A 778 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 778 through 781'
    Processing helix  chain 'A' and resid 782 through 792
      removed outlier: 3.710A  pdb=" N   ARG A 790 " --> pdb=" O   GLN A 786 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 831
    Processing helix  chain 'A' and resid 836 through 842
    Processing helix  chain 'B' and resid 17 through 25
      removed outlier: 3.816A  pdb=" N   ALA B  21 " --> pdb=" O   LEU B  17 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU B  22 " --> pdb=" O   ILE B  18 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU B  23 " --> pdb=" O   GLY B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 37
      removed outlier: 3.773A  pdb=" N   ARG B  31 " --> pdb=" O   SER B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 46
      removed outlier: 3.821A  pdb=" N   LEU B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 53
    Processing helix  chain 'B' and resid 54 through 97
      removed outlier: 3.505A  pdb=" N   VAL B  69 " --> pdb=" O   VAL B  65 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLU B  80 " --> pdb=" O   ARG B  76 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   HIS B  91 " --> pdb=" O   ASN B  87 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ASP B  92 " --> pdb=" O   HIS B  88 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ALA B  94 " --> pdb=" O   GLN B  90 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ASP B  95 " --> pdb=" O   HIS B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 105
    Processing helix  chain 'B' and resid 106 through 119
      removed outlier: 3.642A  pdb=" N   ALA B 111 " --> pdb=" O   ALA B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 126
      removed outlier: 3.571A  pdb=" N   VAL B 125 " --> pdb=" O   GLY B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 150
      removed outlier: 3.543A  pdb=" N   LEU B 140 " --> pdb=" O   THR B 136 " (cutoff:3.500A)
      Proline residue:  B 142  - end of helix
      removed outlier: 3.889A  pdb=" N   LEU B 150 " --> pdb=" O   ALA B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 162
    Processing helix  chain 'B' and resid 162 through 193
      removed outlier: 4.057A  pdb=" N   LEU B 166 " --> pdb=" O   ALA B 162 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ASP B 182 " --> pdb=" O   ALA B 178 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ALA B 184 " --> pdb=" O   ARG B 180 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   THR B 190 " --> pdb=" O   ASP B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 202
    Processing helix  chain 'B' and resid 202 through 208
      removed outlier: 3.610A  pdb=" N   LEU B 206 " --> pdb=" O   THR B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 226
      removed outlier: 3.647A  pdb=" N   ALA B 215 " --> pdb=" O   ARG B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 265
      removed outlier: 3.991A  pdb=" N   LEU B 233 " --> pdb=" O   ALA B 229 " (cutoff:3.500A)
      Proline residue:  B 239  - end of helix
      removed outlier: 5.916A  pdb=" N   PHE B 244 " --> pdb=" O   GLY B 240 " (cutoff:3.500A)
      removed outlier: 4.867A  pdb=" N   SER B 245 " --> pdb=" O   GLN B 241 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ILE B 253 " --> pdb=" O   GLN B 249 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR B 263 " --> pdb=" O   THR B 259 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ILE B 264 " --> pdb=" O   ALA B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 284
    Processing helix  chain 'B' and resid 284 through 293
      removed outlier: 3.525A  pdb=" N   THR B 288 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU B 293 " --> pdb=" O   ALA B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 312
      removed outlier: 3.748A  pdb=" N   ARG B 306 " --> pdb=" O   ALA B 302 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   ILE B 307 " --> pdb=" O   THR B 303 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLY B 308 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   VAL B 310 " --> pdb=" O   ARG B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 381
    Processing helix  chain 'B' and resid 398 through 400
      No H-bonds generated for 'chain 'B' and resid 398 through 400'
    Processing helix  chain 'B' and resid 422 through 428
    Processing helix  chain 'B' and resid 439 through 444
      removed outlier: 3.842A  pdb=" N   VAL B 443 " --> pdb=" O   PHE B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 453
    Processing helix  chain 'B' and resid 457 through 461
      removed outlier: 3.648A  pdb=" N   ASN B 460 " --> pdb=" O   ASP B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 486
    Processing helix  chain 'B' and resid 503 through 514
    Processing helix  chain 'B' and resid 554 through 558
    Processing helix  chain 'B' and resid 559 through 571
      removed outlier: 3.867A  pdb=" N   PHE B 564 " --> pdb=" O   ARG B 560 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 610 through 613
      removed outlier: 3.811A  pdb=" N   GLN A 672 " --> pdb=" O   VAL A 669 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 615 through 617
      removed outlier: 5.112A  pdb=" N   VAL A 615 " --> pdb=" O   ASP A 628 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 687 through 689
      removed outlier: 6.527A  pdb=" N   THR A 639 " --> pdb=" O   VAL A 799 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   GLU A 823 " --> pdb=" O   VAL A 815 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 698 through 699
      removed outlier: 3.689A  pdb=" N   GLY A 698 " --> pdb=" O   LEU A 740 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 355 through 356
    Processing sheet with id=AA6, first strand: chain 'B' and resid 337 through 339
      removed outlier: 7.359A  pdb=" N   PHE B 339 " --> pdb=" O   ASP B 350 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   ASP B 350 " --> pdb=" O   PHE B 339 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 410 through 412
      removed outlier: 6.397A  pdb=" N   LEU B 491 " --> pdb=" O   VAL B 522 " (cutoff:3.500A)
      removed outlier: 7.702A  pdb=" N   VAL B 524 " --> pdb=" O   LEU B 491 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   VAL B 493 " --> pdb=" O   VAL B 524 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   THR B 362 " --> pdb=" O   ILE B 523 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   THR B 361 " --> pdb=" O   ARG B 536 " (cutoff:3.500A)
      removed outlier: 8.264A  pdb=" N   LEU B 538 " --> pdb=" O   THR B 361 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ALA B 363 " --> pdb=" O   LEU B 538 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   VAL B 540 " --> pdb=" O   ALA B 363 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   VAL B 365 " --> pdb=" O   VAL B 540 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   GLU B 547 " --> pdb=" O   PHE B 539 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ASP B 541 " --> pdb=" O   VAL B 545 " (cutoff:3.500A)
      removed outlier: 4.939A  pdb=" N   VAL B 545 " --> pdb=" O   ASP B 541 " (cutoff:3.500A)

    452 hydrogen bonds defined for protein.
    1305 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.63

  Time building geometry restraints manager: 2.75 seconds

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

  Histogram of bond lengths:
        1.14 -     1.27: 1405
        1.27 -     1.41: 2094
        1.41 -     1.54: 5206
        1.54 -     1.67: 81
        1.67 -     1.80: 25
  Bond restraints: 8811
  Sorted by residual:
  bond pdb=" O3A ANP A 901 "
       pdb=" PB  ANP A 901 "
    ideal  model  delta    sigma   weight residual
    1.700  1.550  0.150 2.00e-02 2.50e+03 5.61e+01
  bond pdb=" C   LYS B 486 "
       pdb=" O   LYS B 486 "
    ideal  model  delta    sigma   weight residual
    1.235  1.141  0.093 1.26e-02 6.30e+03 5.48e+01
  bond pdb=" C   VAL B 270 "
       pdb=" O   VAL B 270 "
    ideal  model  delta    sigma   weight residual
    1.240  1.171  0.068 1.26e-02 6.30e+03 2.95e+01
  bond pdb=" N3B ANP A 901 "
       pdb=" PG  ANP A 901 "
    ideal  model  delta    sigma   weight residual
    1.795  1.689  0.106 2.00e-02 2.50e+03 2.79e+01
  bond pdb=" C   THR B 269 "
       pdb=" O   THR B 269 "
    ideal  model  delta    sigma   weight residual
    1.233  1.164  0.069 1.32e-02 5.74e+03 2.71e+01
  ... (remaining 8806 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.58: 11889
        3.58 -     7.16: 139
        7.16 -    10.75: 11
       10.75 -    14.33: 3
       14.33 -    17.91: 1
  Bond angle restraints: 12043
  Sorted by residual:
  angle pdb=" N   GLY B 388 "
        pdb=" CA  GLY B 388 "
        pdb=" C   GLY B 388 "
      ideal   model   delta    sigma   weight residual
     110.21  119.62   -9.41 9.10e-01 1.21e+00 1.07e+02
  angle pdb=" C   THR B 267 "
        pdb=" CA  THR B 267 "
        pdb=" CB  THR B 267 "
      ideal   model   delta    sigma   weight residual
     110.96  123.88  -12.92 1.54e+00 4.22e-01 7.04e+01
  angle pdb=" N   ALA B 442 "
        pdb=" CA  ALA B 442 "
        pdb=" C   ALA B 442 "
      ideal   model   delta    sigma   weight residual
     114.64  102.34   12.30 1.52e+00 4.33e-01 6.55e+01
  angle pdb=" N   ILE B 531 "
        pdb=" CA  ILE B 531 "
        pdb=" C   ILE B 531 "
      ideal   model   delta    sigma   weight residual
     113.71  106.97    6.74 9.50e-01 1.11e+00 5.03e+01
  angle pdb=" N   GLN A 454 "
        pdb=" CA  GLN A 454 "
        pdb=" C   GLN A 454 "
      ideal   model   delta    sigma   weight residual
     114.16  104.32    9.84 1.48e+00 4.57e-01 4.42e+01
  ... (remaining 12038 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.31: 4716
       17.31 -    34.62: 414
       34.62 -    51.93: 71
       51.93 -    69.25: 19
       69.25 -    86.56: 13
  Dihedral angle restraints: 5233
    sinusoidal: 1972
      harmonic: 3261
  Sorted by residual:
  dihedral pdb=" C   THR B 267 "
           pdb=" N   THR B 267 "
           pdb=" CA  THR B 267 "
           pdb=" CB  THR B 267 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -139.89   17.89     0      2.50e+00 1.60e-01 5.12e+01
  dihedral pdb=" CA  ARG B 389 "
           pdb=" C   ARG B 389 "
           pdb=" N   VAL B 390 "
           pdb=" CA  VAL B 390 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.95   28.05     0      5.00e+00 4.00e-02 3.15e+01
  dihedral pdb=" CA  SER B 368 "
           pdb=" C   SER B 368 "
           pdb=" N   GLY B 369 "
           pdb=" CA  GLY B 369 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.37   27.63     0      5.00e+00 4.00e-02 3.05e+01
  ... (remaining 5230 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.115: 1422
       0.115 -    0.229: 37
       0.229 -    0.344: 5
       0.344 -    0.459: 1
       0.459 -    0.573: 1
  Chirality restraints: 1466
  Sorted by residual:
  chirality pdb=" CA  THR B 267 "
            pdb=" N   THR B 267 "
            pdb=" C   THR B 267 "
            pdb=" CB  THR B 267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.95    0.57 2.00e-01 2.50e+01 8.22e+00
  chirality pdb=" CA  LEU B 268 "
            pdb=" N   LEU B 268 "
            pdb=" C   LEU B 268 "
            pdb=" CB  LEU B 268 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.86   -0.35 2.00e-01 2.50e+01 3.14e+00
  chirality pdb=" CA  LYS B 486 "
            pdb=" N   LYS B 486 "
            pdb=" C   LYS B 486 "
            pdb=" CB  LYS B 486 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.81e+00
  ... (remaining 1463 not shown)

  Planarity restraints: 1537
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 836 "   -0.022 2.00e-02 2.50e+03   4.32e-02 1.87e+01
        pdb=" C   ARG A 836 "    0.075 2.00e-02 2.50e+03
        pdb=" O   ARG A 836 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   TYR A 837 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 342 "    0.019 2.00e-02 2.50e+03   3.84e-02 1.48e+01
        pdb=" C   ASP B 342 "   -0.066 2.00e-02 2.50e+03
        pdb=" O   ASP B 342 "    0.025 2.00e-02 2.50e+03
        pdb=" N   GLY B 343 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 545 "    0.047 5.00e-02 4.00e+02   7.17e-02 8.22e+00
        pdb=" N   PRO A 546 "   -0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO A 546 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 546 "    0.039 5.00e-02 4.00e+02
  ... (remaining 1534 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1210
        2.75 -     3.29: 8558
        3.29 -     3.82: 13573
        3.82 -     4.36: 17386
        4.36 -     4.90: 29541
  Nonbonded interactions: 70268
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 364 "
            pdb=" OG1 THR B 228 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" OG  SER B  27 "
            pdb=" OD1 ASP B  71 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" N3B ANP A 901 "
            pdb=" O2A ANP A 901 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" OD1 ASN B 221 "
            pdb=" N   ALA B 222 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" O   LEU B  70 "
            pdb=" OG1 THR B  74 "
     model   vdw
     2.285 3.040
  ... (remaining 70263 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             3.210
  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:             0.020
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.800
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
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      :  0.008   0.150   8811  Z= 0.403
  Angle     :  1.023  17.912  12043  Z= 0.626
  Chirality :  0.056   0.573   1466
  Planarity :  0.005   0.072   1537
  Dihedral  : 14.501  86.558   3131
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  9.36 %
    Favored  : 90.20 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  5.34 %
    Favored  : 93.98 %
  Cbeta Deviations :  0.38 %
  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: -5.21 (0.19), residues: 1143
  helix: -3.11 (0.15), residues: 698
  sheet: -3.96 (0.47), residues: 60
  loop : -3.68 (0.26), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 154 
 HIS   0.008   0.001   HIS A 818 
 PHE   0.016   0.002   PHE B 244 
 TYR   0.013   0.002   TYR A 837 
 ARG   0.006   0.001   ARG A 824 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25094 (  452)
  hydrogen bonds       : angle       8.60265 ( 1305)
  covalent geometry    : bond        0.00828 ( 8811)
  covalent geometry    : angle       1.02348 (12043)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 1.002 
Fit side-chains
REVERT: A  359 ASP cc_start: 0.8596 (t70) cc_final: 0.8379 (OUTLIER)
REVERT: A  392 LYS cc_start: 0.8734 (ttpp) cc_final: 0.8476 (tmmt)
REVERT: A  436 VAL cc_start: 0.9043 (t) cc_final: 0.8782 (m)
REVERT: A  515 LYS cc_start: 0.8946 (mttt) cc_final: 0.8728 (mttp)
REVERT: B   71 ASP cc_start: 0.7719 (m-30) cc_final: 0.7507 (m-30)
  outliers start: 6
  outliers final: 3
  residues processed: 76
  average time/residue: 1.5862
  time to fit residues: 127.6576
Evaluate side-chains
  45 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  329 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 86 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0270
   chunk 29 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0970
   chunk 89 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 103 optimal weight:    0.1980
   overall best weight:    0.3636

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

Flipped N/Q/H residues before XYZ refinement:
A 407 HIS
A 463 GLN
A 597 HIS
A 743 ASN
A 752 GLN
A 802 HIS
B  11 ASN
B 109 ASN
B 237 GLN
B 241 GLN
B 426 ASN
B 533 HIS
B 568 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.109074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.089471 restraints weight = 13663.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 2.18
r_work: 0.3033 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8716
moved from start:          0.1574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8811  Z= 0.129
  Angle     :  0.697   9.014  12043  Z= 0.358
  Chirality :  0.042   0.136   1466
  Planarity :  0.005   0.057   1537
  Dihedral  :  7.924  56.106   1281
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.79 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 10.23 %
    Favored  : 88.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -3.20 (0.22), residues: 1143
  helix: -1.44 (0.18), residues: 713
  sheet: -3.15 (0.48), residues: 75
  loop : -3.04 (0.28), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 529 
 HIS   0.004   0.001   HIS A 818 
 PHE   0.008   0.001   PHE A 559 
 TYR   0.018   0.001   TYR A 568 
 ARG   0.006   0.000   ARG B 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04182 (  452)
  hydrogen bonds       : angle       4.75024 ( 1305)
  covalent geometry    : bond        0.00273 ( 8811)
  covalent geometry    : angle       0.69746 (12043)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.996 
Fit side-chains
REVERT: A  392 LYS cc_start: 0.8839 (ttpp) cc_final: 0.8592 (tmtt)
REVERT: A  515 LYS cc_start: 0.9109 (mttt) cc_final: 0.8870 (mttp)
REVERT: A  517 LEU cc_start: 0.8904 (tp) cc_final: 0.8657 (mp)
REVERT: B   48 GLU cc_start: 0.7918 (pm20) cc_final: 0.7696 (pm20)
REVERT: B   71 ASP cc_start: 0.8697 (m-30) cc_final: 0.8437 (m-30)
REVERT: B  161 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8752 (mt)
REVERT: B  270 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.7989 (t)
REVERT: B  435 SER cc_start: 0.7094 (p) cc_final: 0.6765 (t)
REVERT: B  447 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7684 (mpt-90)
  outliers start: 13
  outliers final: 2
  residues processed: 77
  average time/residue: 1.1575
  time to fit residues: 96.2130
Evaluate side-chains
  58 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  447 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 111 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 57 optimal weight:    0.3980
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 463 GLN
A 743 ASN
B 130 ASN
B 357 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.107993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.088049 restraints weight = 13909.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 2.20
r_work: 0.3005 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8729
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8811  Z= 0.150
  Angle     :  0.661   7.909  12043  Z= 0.337
  Chirality :  0.043   0.145   1466
  Planarity :  0.005   0.058   1537
  Dihedral  :  6.514  55.742   1281
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.79 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 10.91 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.99 (0.24), residues: 1143
  helix: -0.49 (0.20), residues: 711
  sheet: -2.53 (0.52), residues: 75
  loop : -2.57 (0.29), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  56 
 HIS   0.005   0.001   HIS A 818 
 PHE   0.012   0.001   PHE B 244 
 TYR   0.012   0.001   TYR A 782 
 ARG   0.002   0.000   ARG B 560 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04233 (  452)
  hydrogen bonds       : angle       4.43225 ( 1305)
  covalent geometry    : bond        0.00343 ( 8811)
  covalent geometry    : angle       0.66077 (12043)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 59
  time to evaluate  : 0.947 
Fit side-chains
REVERT: A  392 LYS cc_start: 0.8875 (ttpp) cc_final: 0.8617 (tmtt)
REVERT: A  515 LYS cc_start: 0.9088 (mttt) cc_final: 0.8833 (mttp)
REVERT: A  517 LEU cc_start: 0.8921 (tp) cc_final: 0.8682 (mp)
REVERT: A  781 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7775 (tt0)
REVERT: B   71 ASP cc_start: 0.8663 (m-30) cc_final: 0.8355 (m-30)
REVERT: B  161 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8692 (mt)
REVERT: B  270 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.8197 (t)
REVERT: B  435 SER cc_start: 0.7134 (p) cc_final: 0.6807 (t)
REVERT: B  447 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7722 (mpt-90)
  outliers start: 26
  outliers final: 9
  residues processed: 77
  average time/residue: 0.9899
  time to fit residues: 83.0593
Evaluate side-chains
  62 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  708 VAL
Chi-restraints excluded: chain A residue  781 GLU
Chi-restraints excluded: chain B residue   13 HIS
Chi-restraints excluded: chain B residue  108 GLU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  447 ARG
Chi-restraints excluded: chain B residue  577 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 102 optimal weight:    7.9990
   chunk 53 optimal weight:    0.8980
   chunk 96 optimal weight:    2.9990
   chunk 69 optimal weight:    0.2980
   chunk 3 optimal weight:    0.0980
   chunk 50 optimal weight:    0.8980
   chunk 98 optimal weight:    2.9990
   chunk 89 optimal weight:    0.0970
   chunk 95 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
A 660 HIS
A 743 ASN
B 203 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.110713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.090854 restraints weight = 13649.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 2.17
r_work: 0.3042 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8811  Z= 0.114
  Angle     :  0.601   7.987  12043  Z= 0.306
  Chirality :  0.041   0.133   1466
  Planarity :  0.004   0.055   1537
  Dihedral  :  5.838  47.729   1281
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.00 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 12.39 %
    Favored  : 85.00 %
  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: -1.30 (0.25), residues: 1143
  helix:  0.04 (0.20), residues: 714
  sheet: -2.16 (0.56), residues: 75
  loop : -2.32 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  56 
 HIS   0.004   0.001   HIS A 818 
 PHE   0.009   0.001   PHE B 244 
 TYR   0.011   0.001   TYR A 782 
 ARG   0.006   0.000   ARG B 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03454 (  452)
  hydrogen bonds       : angle       4.18360 ( 1305)
  covalent geometry    : bond        0.00247 ( 8811)
  covalent geometry    : angle       0.60077 (12043)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 62
  time to evaluate  : 0.953 
Fit side-chains
REVERT: A  514 LYS cc_start: 0.8768 (mttp) cc_final: 0.8539 (mttt)
REVERT: A  515 LYS cc_start: 0.8987 (mttt) cc_final: 0.8737 (mttp)
REVERT: A  517 LEU cc_start: 0.8889 (tp) cc_final: 0.8688 (mp)
REVERT: A  519 ASP cc_start: 0.8818 (t0) cc_final: 0.8452 (t70)
REVERT: A  781 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7779 (tt0)
REVERT: B   71 ASP cc_start: 0.8631 (m-30) cc_final: 0.8354 (m-30)
REVERT: B  161 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8666 (mt)
  outliers start: 23
  outliers final: 5
  residues processed: 80
  average time/residue: 1.0557
  time to fit residues: 91.7370
Evaluate side-chains
  57 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  708 VAL
Chi-restraints excluded: chain A residue  781 GLU
Chi-restraints excluded: chain B residue   13 HIS
Chi-restraints excluded: chain B residue  108 GLU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  577 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 100 optimal weight:    0.0270
   chunk 74 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0670
   chunk 8 optimal weight:    0.9990
   chunk 102 optimal weight:    8.9990
   chunk 91 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0980
   overall best weight:    0.2976

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

Flipped N/Q/H residues before XYZ refinement:
A 627 GLN
A 743 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.111913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.091783 restraints weight = 13639.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.19
r_work: 0.3055 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8811  Z= 0.107
  Angle     :  0.601   8.579  12043  Z= 0.301
  Chirality :  0.040   0.164   1466
  Planarity :  0.004   0.052   1537
  Dihedral  :  5.373  41.475   1280
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.65 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 13.18 %
    Favored  : 84.43 %
  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: -0.85 (0.26), residues: 1143
  helix:  0.39 (0.21), residues: 714
  sheet: -1.84 (0.58), residues: 70
  loop : -2.15 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  56 
 HIS   0.004   0.000   HIS A 818 
 PHE   0.010   0.001   PHE B 244 
 TYR   0.011   0.001   TYR A 782 
 ARG   0.009   0.000   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03261 (  452)
  hydrogen bonds       : angle       4.06188 ( 1305)
  covalent geometry    : bond        0.00229 ( 8811)
  covalent geometry    : angle       0.60104 (12043)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 60
  time to evaluate  : 0.911 
Fit side-chains
REVERT: A  514 LYS cc_start: 0.8752 (mttp) cc_final: 0.8519 (mttt)
REVERT: A  515 LYS cc_start: 0.8938 (mttt) cc_final: 0.8686 (mttp)
REVERT: A  519 ASP cc_start: 0.8815 (t0) cc_final: 0.8460 (t70)
REVERT: A  595 ARG cc_start: 0.6824 (ptm-80) cc_final: 0.6429 (ptm-80)
REVERT: A  781 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7775 (tt0)
REVERT: B   71 ASP cc_start: 0.8635 (m-30) cc_final: 0.8395 (m-30)
REVERT: B  161 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8637 (mt)
REVERT: B  447 ARG cc_start: 0.8277 (mpt-90) cc_final: 0.7912 (mtt-85)
  outliers start: 21
  outliers final: 10
  residues processed: 79
  average time/residue: 1.0441
  time to fit residues: 89.3312
Evaluate side-chains
  63 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  708 VAL
Chi-restraints excluded: chain A residue  781 GLU
Chi-restraints excluded: chain B residue   13 HIS
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  108 GLU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  448 VAL
Chi-restraints excluded: chain B residue  577 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 70 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 110 optimal weight:    0.9980
   chunk 92 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 627 GLN
A 743 ASN
A 789 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.111156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.090818 restraints weight = 13579.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 2.20
r_work: 0.3037 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8678
moved from start:          0.2475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8811  Z= 0.119
  Angle     :  0.612   8.949  12043  Z= 0.304
  Chirality :  0.041   0.174   1466
  Planarity :  0.004   0.054   1537
  Dihedral  :  5.251  38.522   1280
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.17 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 14.55 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.65 (0.26), residues: 1143
  helix:  0.53 (0.20), residues: 719
  sheet: -1.65 (0.59), residues: 70
  loop : -2.11 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  56 
 HIS   0.004   0.000   HIS A 818 
 PHE   0.011   0.001   PHE B 244 
 TYR   0.012   0.001   TYR A 782 
 ARG   0.007   0.000   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03386 (  452)
  hydrogen bonds       : angle       4.05634 ( 1305)
  covalent geometry    : bond        0.00268 ( 8811)
  covalent geometry    : angle       0.61192 (12043)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 50
  time to evaluate  : 0.927 
Fit side-chains
REVERT: A  514 LYS cc_start: 0.8743 (mttp) cc_final: 0.8500 (mttt)
REVERT: A  519 ASP cc_start: 0.8810 (t0) cc_final: 0.8505 (t70)
REVERT: A  595 ARG cc_start: 0.6824 (ptm-80) cc_final: 0.6491 (ptm-80)
REVERT: A  781 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7783 (tt0)
REVERT: B   71 ASP cc_start: 0.8632 (m-30) cc_final: 0.8389 (m-30)
REVERT: B  161 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8671 (mt)
  outliers start: 20
  outliers final: 8
  residues processed: 69
  average time/residue: 1.1319
  time to fit residues: 84.3344
Evaluate side-chains
  58 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  708 VAL
Chi-restraints excluded: chain A residue  781 GLU
Chi-restraints excluded: chain B residue   13 HIS
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  108 GLU
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  329 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 627 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.110108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.089710 restraints weight = 13728.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 2.23
r_work: 0.3025 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8709
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8811  Z= 0.137
  Angle     :  0.626   9.197  12043  Z= 0.311
  Chirality :  0.042   0.174   1466
  Planarity :  0.004   0.056   1537
  Dihedral  :  5.256  38.003   1280
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.17 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 15.57 %
    Favored  : 82.50 %
  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: -0.59 (0.25), residues: 1143
  helix:  0.61 (0.20), residues: 714
  sheet: -1.61 (0.58), residues: 70
  loop : -2.13 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  56 
 HIS   0.005   0.001   HIS A 818 
 PHE   0.011   0.001   PHE B 244 
 TYR   0.013   0.001   TYR A 568 
 ARG   0.006   0.000   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03608 (  452)
  hydrogen bonds       : angle       4.10572 ( 1305)
  covalent geometry    : bond        0.00319 ( 8811)
  covalent geometry    : angle       0.62592 (12043)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 52
  time to evaluate  : 0.937 
Fit side-chains
REVERT: A  392 LYS cc_start: 0.8851 (ttpp) cc_final: 0.8631 (tmtt)
REVERT: A  519 ASP cc_start: 0.8805 (t0) cc_final: 0.8485 (t70)
REVERT: A  781 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7787 (tt0)
REVERT: B   71 ASP cc_start: 0.8627 (m-30) cc_final: 0.8360 (m-30)
REVERT: B  161 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8670 (mt)
  outliers start: 17
  outliers final: 7
  residues processed: 68
  average time/residue: 1.1337
  time to fit residues: 83.6056
Evaluate side-chains
  55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  708 VAL
Chi-restraints excluded: chain A residue  781 GLU
Chi-restraints excluded: chain B residue   13 HIS
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  329 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0770
   chunk 37 optimal weight:    4.9990
   chunk 64 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0980
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
A 463 GLN
A 627 GLN
A 743 ASN
A 789 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.111986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.091578 restraints weight = 13760.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.21
r_work: 0.3052 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8811  Z= 0.111
  Angle     :  0.610   9.394  12043  Z= 0.301
  Chirality :  0.041   0.172   1466
  Planarity :  0.004   0.054   1537
  Dihedral  :  5.136  38.504   1280
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.09 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 15.68 %
    Favored  : 82.05 %
  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: -0.39 (0.26), residues: 1143
  helix:  0.76 (0.20), residues: 715
  sheet: -1.55 (0.59), residues: 70
  loop : -2.04 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 323 
 HIS   0.004   0.000   HIS A 818 
 PHE   0.010   0.001   PHE B 244 
 TYR   0.011   0.001   TYR A 782 
 ARG   0.005   0.000   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03298 (  452)
  hydrogen bonds       : angle       3.99727 ( 1305)
  covalent geometry    : bond        0.00244 ( 8811)
  covalent geometry    : angle       0.61024 (12043)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 49
  time to evaluate  : 0.936 
Fit side-chains
REVERT: A  392 LYS cc_start: 0.8833 (ttpp) cc_final: 0.8627 (tmtt)
REVERT: A  519 ASP cc_start: 0.8809 (t0) cc_final: 0.8505 (t70)
REVERT: A  781 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7793 (tt0)
REVERT: B   71 ASP cc_start: 0.8609 (m-30) cc_final: 0.8364 (m-30)
REVERT: B  161 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8728 (mt)
REVERT: B  447 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7489 (mpt-90)
  outliers start: 20
  outliers final: 8
  residues processed: 67
  average time/residue: 1.0843
  time to fit residues: 78.7775
Evaluate side-chains
  58 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  708 VAL
Chi-restraints excluded: chain A residue  781 GLU
Chi-restraints excluded: chain B residue   13 HIS
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  447 ARG
Chi-restraints excluded: chain B residue  448 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 94 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 463 GLN
A 627 GLN
A 743 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.110836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.090384 restraints weight = 13770.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 2.22
r_work: 0.3036 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8811  Z= 0.132
  Angle     :  0.635   9.489  12043  Z= 0.314
  Chirality :  0.042   0.174   1466
  Planarity :  0.004   0.055   1537
  Dihedral  :  5.142  37.614   1280
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.17 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 16.25 %
    Favored  : 81.82 %
  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: -0.33 (0.26), residues: 1143
  helix:  0.81 (0.20), residues: 716
  sheet: -1.49 (0.59), residues: 70
  loop : -2.04 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 323 
 HIS   0.004   0.001   HIS A 818 
 PHE   0.011   0.001   PHE B 244 
 TYR   0.012   0.001   TYR A 568 
 ARG   0.005   0.000   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03475 (  452)
  hydrogen bonds       : angle       4.04152 ( 1305)
  covalent geometry    : bond        0.00304 ( 8811)
  covalent geometry    : angle       0.63506 (12043)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 45
  time to evaluate  : 1.009 
Fit side-chains
REVERT: A  519 ASP cc_start: 0.8799 (t0) cc_final: 0.8491 (t70)
REVERT: A  781 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7784 (tt0)
REVERT: B   71 ASP cc_start: 0.8634 (m-30) cc_final: 0.8368 (m-30)
REVERT: B  161 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8727 (mt)
REVERT: B  447 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7544 (mpt-90)
  outliers start: 17
  outliers final: 8
  residues processed: 61
  average time/residue: 1.2150
  time to fit residues: 80.4539
Evaluate side-chains
  55 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  708 VAL
Chi-restraints excluded: chain A residue  781 GLU
Chi-restraints excluded: chain B residue   13 HIS
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  447 ARG
Chi-restraints excluded: chain B residue  448 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 101 optimal weight:    0.0770
   chunk 74 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 55 optimal weight:    0.3980
   chunk 77 optimal weight:    1.9990
   chunk 99 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
A 463 GLN
A 627 GLN
A 743 ASN
A 789 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.111555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.091079 restraints weight = 13722.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 2.23
r_work: 0.3038 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8811  Z= 0.119
  Angle     :  0.623   9.431  12043  Z= 0.307
  Chirality :  0.042   0.173   1466
  Planarity :  0.004   0.055   1537
  Dihedral  :  5.091  37.923   1280
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.26 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 16.48 %
    Favored  : 81.82 %
  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: -0.19 (0.26), residues: 1143
  helix:  0.93 (0.20), residues: 715
  sheet: -1.42 (0.60), residues: 70
  loop : -1.98 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 323 
 HIS   0.004   0.001   HIS A 818 
 PHE   0.011   0.001   PHE B 244 
 TYR   0.011   0.001   TYR A 568 
 ARG   0.005   0.000   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03369 (  452)
  hydrogen bonds       : angle       4.00947 ( 1305)
  covalent geometry    : bond        0.00269 ( 8811)
  covalent geometry    : angle       0.62255 (12043)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.915 
Fit side-chains
REVERT: A  468 LYS cc_start: 0.8548 (ttpt) cc_final: 0.8331 (tttp)
REVERT: A  519 ASP cc_start: 0.8807 (t0) cc_final: 0.8496 (t70)
REVERT: A  781 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7820 (tt0)
REVERT: B   71 ASP cc_start: 0.8619 (m-30) cc_final: 0.8365 (m-30)
REVERT: B  161 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8735 (mt)
REVERT: B  231 MET cc_start: 0.7173 (pmm) cc_final: 0.6571 (mmm)
REVERT: B  447 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7527 (mpt-90)
  outliers start: 15
  outliers final: 8
  residues processed: 64
  average time/residue: 1.1163
  time to fit residues: 77.4936
Evaluate side-chains
  59 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  708 VAL
Chi-restraints excluded: chain A residue  781 GLU
Chi-restraints excluded: chain B residue   13 HIS
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  447 ARG
Chi-restraints excluded: chain B residue  448 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 23 optimal weight:    0.0970
   chunk 45 optimal weight:    0.2980
   chunk 49 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 112 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 101 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A 463 GLN
A 627 GLN
A 743 ASN
A 789 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.111655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.091019 restraints weight = 13712.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 2.24
r_work: 0.3044 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8811  Z= 0.123
  Angle     :  0.647  12.896  12043  Z= 0.321
  Chirality :  0.042   0.228   1466
  Planarity :  0.004   0.055   1537
  Dihedral  :  5.058  37.628   1280
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.09 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 16.48 %
    Favored  : 81.82 %
  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: -0.13 (0.26), residues: 1143
  helix:  0.98 (0.20), residues: 716
  sheet: -1.40 (0.60), residues: 70
  loop : -1.99 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 323 
 HIS   0.004   0.001   HIS A 818 
 PHE   0.011   0.001   PHE B 244 
 TYR   0.012   0.001   TYR A 568 
 ARG   0.005   0.000   ARG B 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03333 (  452)
  hydrogen bonds       : angle       3.99055 ( 1305)
  covalent geometry    : bond        0.00280 ( 8811)
  covalent geometry    : angle       0.64709 (12043)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5590.36 seconds
wall clock time: 97 minutes 27.60 seconds (5847.60 seconds total)