Starting phenix.real_space_refine
on Tue Mar  3 19:45:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7aa3_11689/03_2026/7aa3_11689.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7aa3_11689/03_2026/7aa3_11689.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7aa3_11689/03_2026/7aa3_11689.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7aa3_11689/03_2026/7aa3_11689.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7aa3_11689/03_2026/7aa3_11689.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7aa3_11689/03_2026/7aa3_11689.map"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.031
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      29      5.16       5
     C    5336      2.51       5
     N    1438      2.21       5
     O    1586      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8389
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4211
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 550, 4211
          Classifications: {'peptide': 550}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 29, 'TRANS': 520}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 66
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 62
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 27
    Chain: "B"
      Number of atoms: 4178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 544, 4178
          Classifications: {'peptide': 544}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 27, 'TRANS': 516}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 2.15, per 1000 atoms: 0.26
  Number of scatterers: 8389
  At special positions: 0
  Unit cell: (101.85, 122.85, 81.9, 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      29     16.00
     O    1586      8.00
     N    1438      7.00
     C    5336      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.46
  Conformation dependent library (CDL) restraints added in 324.1 milliseconds
  

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1990

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 2 sheets defined
      48.5% alpha, 0.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 48
    Processing helix  chain 'A' and resid 52 through 56
    Processing helix  chain 'A' and resid 72 through 85
      removed outlier: 3.771A  pdb=" N   THR A  77 " --> pdb=" O   VAL A  73 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   ARG A  78 " --> pdb=" O   ASP A  74 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   GLU A  82 " --> pdb=" O   ARG A  78 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   THR A  85 " --> pdb=" O   GLU A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 97
      removed outlier: 3.527A  pdb=" N   HIS A  97 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 111
      removed outlier: 3.595A  pdb=" N   ILE A 103 " --> pdb=" O   GLY A  99 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   HIS A 108 " --> pdb=" O   ARG A 104 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ALA A 109 " --> pdb=" O   MET A 105 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA A 110 " --> pdb=" O   ALA A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 146
      removed outlier: 4.115A  pdb=" N   ARG A 146 " --> pdb=" O   ASP A 142 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 142 through 146'
    Processing helix  chain 'A' and resid 148 through 156
      removed outlier: 5.028A  pdb=" N   LYS A 154 " --> pdb=" O   PRO A 150 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   TYR A 155 " --> pdb=" O   VAL A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 176
      removed outlier: 3.535A  pdb=" N   MET A 176 " --> pdb=" O   ALA A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 252
    Processing helix  chain 'A' and resid 331 through 337
    Processing helix  chain 'A' and resid 382 through 387
      removed outlier: 3.539A  pdb=" N   VAL A 386 " --> pdb=" O   LEU A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 395
      removed outlier: 4.132A  pdb=" N   ILE A 393 " --> pdb=" O   ILE A 389 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ARG A 395 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 399
      removed outlier: 3.517A  pdb=" N   GLU A 399 " --> pdb=" O   ARG A 396 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 396 through 399'
    Processing helix  chain 'A' and resid 402 through 417
      removed outlier: 3.895A  pdb=" N   ASP A 406 " --> pdb=" O   GLU A 402 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLU A 407 " --> pdb=" O   GLU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 440
    Processing helix  chain 'A' and resid 451 through 460
      removed outlier: 3.667A  pdb=" N   ALA A 456 " --> pdb=" O   GLU A 452 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   SER A 457 " --> pdb=" O   ALA A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 465
      removed outlier: 3.560A  pdb=" N   SER A 465 " --> pdb=" O   ILE A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 481
      removed outlier: 3.940A  pdb=" N   LEU A 472 " --> pdb=" O   THR A 468 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL A 473 " --> pdb=" O   VAL A 469 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   SER A 474 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 498
      removed outlier: 4.124A  pdb=" N   ARG A 498 " --> pdb=" O   GLY A 495 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 495 through 498'
    Processing helix  chain 'A' and resid 499 through 504
      removed outlier: 3.593A  pdb=" N   GLY A 504 " --> pdb=" O   GLN A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 531
      removed outlier: 3.791A  pdb=" N   LYS A 516 " --> pdb=" O   GLY A 512 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   ILE A 518 " --> pdb=" O   LEU A 514 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   THR A 520 " --> pdb=" O   LYS A 516 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ALA A 531 " --> pdb=" O   SER A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 544
      removed outlier: 4.435A  pdb=" N   LEU A 543 " --> pdb=" O   SER A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 556
      removed outlier: 3.710A  pdb=" N   GLY A 548 " --> pdb=" O   VAL A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 579
      removed outlier: 3.675A  pdb=" N   GLN A 578 " --> pdb=" O   SER A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 617
      removed outlier: 3.799A  pdb=" N   LEU A 610 " --> pdb=" O   ALA A 606 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   LEU A 611 " --> pdb=" O   GLU A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 635
    Processing helix  chain 'A' and resid 637 through 641
    Processing helix  chain 'A' and resid 655 through 663
      removed outlier: 4.020A  pdb=" N   LEU A 662 " --> pdb=" O   PHE A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 712
      removed outlier: 4.052A  pdb=" N   TYR A 711 " --> pdb=" O   LEU A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 716 through 733
      removed outlier: 3.575A  pdb=" N   PHE A 720 " --> pdb=" O   ALA A 716 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 733 through 738
      removed outlier: 3.817A  pdb=" N   PHE A 737 " --> pdb=" O   ASN A 733 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   ASP A 738 " --> pdb=" O   LEU A 734 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 733 through 738'
    Processing helix  chain 'B' and resid 44 through 48
    Processing helix  chain 'B' and resid 63 through 67
    Processing helix  chain 'B' and resid 72 through 77
    Processing helix  chain 'B' and resid 79 through 84
      removed outlier: 3.512A  pdb=" N   MET B  84 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 107
      removed outlier: 3.623A  pdb=" N   PHE B 102 " --> pdb=" O   TYR B  98 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   ARG B 104 " --> pdb=" O   PRO B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 153
    Processing helix  chain 'B' and resid 155 through 159
      removed outlier: 3.900A  pdb=" N   LYS B 158 " --> pdb=" O   TYR B 155 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   LEU B 159 " --> pdb=" O   GLY B 156 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 155 through 159'
    Processing helix  chain 'B' and resid 160 through 176
    Processing helix  chain 'B' and resid 242 through 252
    Processing helix  chain 'B' and resid 382 through 387
      removed outlier: 3.787A  pdb=" N   VAL B 386 " --> pdb=" O   LEU B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 392
      removed outlier: 3.713A  pdb=" N   ARG B 392 " --> pdb=" O   PRO B 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 400
      removed outlier: 4.311A  pdb=" N   GLU B 399 " --> pdb=" O   ARG B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 401 through 413
      removed outlier: 4.054A  pdb=" N   ASP B 406 " --> pdb=" O   GLU B 402 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   GLU B 407 " --> pdb=" O   GLU B 403 " (cutoff:3.500A)
      removed outlier: 5.169A  pdb=" N   LYS B 410 " --> pdb=" O   ASP B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 440
    Processing helix  chain 'B' and resid 454 through 462
    Processing helix  chain 'B' and resid 468 through 479
      removed outlier: 3.989A  pdb=" N   LEU B 472 " --> pdb=" O   THR B 468 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL B 473 " --> pdb=" O   VAL B 469 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   SER B 474 " --> pdb=" O   SER B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 495 through 498
      removed outlier: 4.078A  pdb=" N   ARG B 498 " --> pdb=" O   GLY B 495 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 495 through 498'
    Processing helix  chain 'B' and resid 499 through 504
      removed outlier: 3.580A  pdb=" N   GLY B 504 " --> pdb=" O   GLN B 500 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 529
      removed outlier: 3.508A  pdb=" N   VAL B 517 " --> pdb=" O   ASP B 513 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ARG B 519 " --> pdb=" O   ARG B 515 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   THR B 520 " --> pdb=" O   LYS B 516 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 560
      removed outlier: 3.981A  pdb=" N   LEU B 543 " --> pdb=" O   SER B 539 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   VAL B 545 " --> pdb=" O   ALA B 541 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   GLY B 548 " --> pdb=" O   VAL B 544 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LYS B 557 " --> pdb=" O   GLU B 553 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ALA B 558 " --> pdb=" O   LYS B 554 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   GLY B 560 " --> pdb=" O   ALA B 556 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 607 through 617
    Processing helix  chain 'B' and resid 620 through 635
    Processing helix  chain 'B' and resid 637 through 641
      removed outlier: 3.592A  pdb=" N   LEU B 641 " --> pdb=" O   TYR B 638 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 655 through 661
    Processing helix  chain 'B' and resid 695 through 700
    Processing helix  chain 'B' and resid 701 through 706
      removed outlier: 3.741A  pdb=" N   ALA B 706 " --> pdb=" O   SER B 702 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 716 through 733
      removed outlier: 3.579A  pdb=" N   PHE B 720 " --> pdb=" O   ALA B 716 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 667 through 670
      removed outlier: 6.870A  pdb=" N   GLY A 680 " --> pdb=" O   LYS A 688 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 667 through 668

    253 hydrogen bonds defined for protein.
    690 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.00

  Time building geometry restraints manager: 0.65 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2807
        1.34 -     1.46: 1865
        1.46 -     1.58: 3863
        1.58 -     1.69: 0
        1.69 -     1.81: 54
  Bond restraints: 8589
  Sorted by residual:
  bond pdb=" CB  VAL B 166 "
       pdb=" CG1 VAL B 166 "
    ideal  model  delta    sigma   weight residual
    1.521  1.468  0.053 3.30e-02 9.18e+02 2.61e+00
  bond pdb=" CA  ARG B 104 "
       pdb=" C   ARG B 104 "
    ideal  model  delta    sigma   weight residual
    1.522  1.495  0.027 1.72e-02 3.38e+03 2.49e+00
  bond pdb=" N   VAL A 423 "
       pdb=" CA  VAL A 423 "
    ideal  model  delta    sigma   weight residual
    1.474  1.455  0.020 1.57e-02 4.06e+03 1.57e+00
  bond pdb=" CB  ILE B 416 "
       pdb=" CG2 ILE B 416 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.18e+00
  bond pdb=" C   ASN A 238 "
       pdb=" N   PRO A 239 "
    ideal  model  delta    sigma   weight residual
    1.334  1.359 -0.025 2.34e-02 1.83e+03 1.13e+00
  ... (remaining 8584 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 11199
        1.46 -     2.91: 398
        2.91 -     4.37: 71
        4.37 -     5.83: 17
        5.83 -     7.29: 4
  Bond angle restraints: 11689
  Sorted by residual:
  angle pdb=" N   LEU A 382 "
        pdb=" CA  LEU A 382 "
        pdb=" C   LEU A 382 "
      ideal   model   delta    sigma   weight residual
     113.72  108.77    4.95 1.52e+00 4.33e-01 1.06e+01
  angle pdb=" CB  LYS A 433 "
        pdb=" CG  LYS A 433 "
        pdb=" CD  LYS A 433 "
      ideal   model   delta    sigma   weight residual
     111.30  118.21   -6.91 2.30e+00 1.89e-01 9.03e+00
  angle pdb=" N   VAL A 423 "
        pdb=" CA  VAL A 423 "
        pdb=" C   VAL A 423 "
      ideal   model   delta    sigma   weight residual
     106.21  109.13   -2.92 1.07e+00 8.73e-01 7.42e+00
  angle pdb=" C   PRO A 422 "
        pdb=" N   VAL A 423 "
        pdb=" CA  VAL A 423 "
      ideal   model   delta    sigma   weight residual
     121.65  119.13    2.52 9.40e-01 1.13e+00 7.18e+00
  angle pdb=" N   VAL A 267 "
        pdb=" CA  VAL A 267 "
        pdb=" C   VAL A 267 "
      ideal   model   delta    sigma   weight residual
     109.34  104.26    5.08 2.08e+00 2.31e-01 5.96e+00
  ... (remaining 11684 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 4515
       17.74 -    35.49: 424
       35.49 -    53.23: 73
       53.23 -    70.98: 9
       70.98 -    88.72: 8
  Dihedral angle restraints: 5029
    sinusoidal: 1925
      harmonic: 3104
  Sorted by residual:
  dihedral pdb=" CA  HIS B  97 "
           pdb=" C   HIS B  97 "
           pdb=" N   TYR B  98 "
           pdb=" CA  TYR B  98 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.01   27.99     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  ASP B 406 "
           pdb=" C   ASP B 406 "
           pdb=" N   GLU B 407 "
           pdb=" CA  GLU B 407 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.64   23.36     0      5.00e+00 4.00e-02 2.18e+01
  dihedral pdb=" CA  VAL A 423 "
           pdb=" C   VAL A 423 "
           pdb=" N   ALA A 424 "
           pdb=" CA  ALA A 424 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.51   21.49     0      5.00e+00 4.00e-02 1.85e+01
  ... (remaining 5026 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 658
       0.030 -    0.059: 422
       0.059 -    0.089: 136
       0.089 -    0.118: 54
       0.118 -    0.147: 7
  Chirality restraints: 1277
  Sorted by residual:
  chirality pdb=" CA  VAL A 267 "
            pdb=" N   VAL A 267 "
            pdb=" C   VAL A 267 "
            pdb=" CB  VAL A 267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.44e-01
  chirality pdb=" CB  VAL B 151 "
            pdb=" CA  VAL B 151 "
            pdb=" CG1 VAL B 151 "
            pdb=" CG2 VAL B 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 5.15e-01
  chirality pdb=" CB  ILE B 416 "
            pdb=" CA  ILE B 416 "
            pdb=" CG1 ILE B 416 "
            pdb=" CG2 ILE B 416 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.69e-01
  ... (remaining 1274 not shown)

  Planarity restraints: 1533
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B  99 "    0.035 5.00e-02 4.00e+02   5.20e-02 4.33e+00
        pdb=" N   PRO B 100 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO B 100 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 100 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B 149 "   -0.029 5.00e-02 4.00e+02   4.42e-02 3.13e+00
        pdb=" N   PRO B 150 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO B 150 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 150 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 149 "    0.024 5.00e-02 4.00e+02   3.65e-02 2.13e+00
        pdb=" N   PRO A 150 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 150 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 150 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1530 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 103
        2.62 -     3.19: 7649
        3.19 -     3.76: 11793
        3.76 -     4.33: 16797
        4.33 -     4.90: 27958
  Nonbonded interactions: 64300
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 337 "
            pdb=" O   THR B 394 "
     model   vdw
     2.046 3.040
  nonbonded pdb=" O   TRP A  91 "
            pdb=" OH  TYR A  98 "
     model   vdw
     2.155 3.040
  nonbonded pdb=" OG  SER B 539 "
            pdb=" O   ARG B 571 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" OH  TYR A 113 "
            pdb=" OD2 ASP A 487 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OD2 ASP A  79 "
            pdb=" NZ  LYS A 154 "
     model   vdw
     2.227 3.120
  ... (remaining 64295 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 43 through 124 or resid 141 through 142 or (resid 143 thro \ 
ugh 144 and (name N or name CA or name C or name O or name CB )) or resid 145 th \ 
rough 189 or (resid 190 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 191 through 193 or resid 242 through 341 or (resid 342 through 379 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 380 through 432 o \ 
r (resid 433 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 
34 through 680 or (resid 681 and (name N or name CA or name C or name O or name  \ 
CB )) or resid 682 through 739))
  selection = (chain 'B' and (resid 43 through 271 or (resid 272 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 329 through 343 or resid 379 through 391 or \ 
 (resid 392 and (name N or name CA or name C or name O or name CB )) or resid 39 \ 
3 through 502 or (resid 503 and (name N or name CA or name C or name O or name C \ 
B )) or resid 504 through 514 or (resid 515 through 516 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 517 through 687 or (resid 688 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 689 through 736 or (re \ 
sid 737 and (name N or name CA or name C or name O or name CB )) or resid 738 th \ 
rough 739))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             2.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.460
  Find NCS groups from input model:        0.170
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
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      :  0.004   0.053   8589  Z= 0.194
  Angle     :  0.659   7.285  11689  Z= 0.365
  Chirality :  0.043   0.147   1277
  Planarity :  0.004   0.052   1533
  Dihedral  : 14.112  88.722   3039
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.15 %
    Favored  : 89.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.38 (0.24), residues: 1074
  helix: -1.92 (0.24), residues: 454
  sheet: -4.27 (0.99), residues: 20
  loop : -2.49 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 418 
 TYR   0.010   0.001   TYR A 638 
 PHE   0.012   0.001   PHE A 332 
 TRP   0.017   0.001   TRP A 191 
 HIS   0.003   0.001   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 8589)
  covalent geometry    : angle       0.65914 (11689)
  hydrogen bonds       : bond        0.21458 (  253)
  hydrogen bonds       : angle       7.45653 (  690)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 TRP cc_start: 0.8144 (t60) cc_final: 0.7710 (t-100)
REVERT: A  535 ASN cc_start: 0.8543 (t0) cc_final: 0.8251 (t0)
REVERT: A  664 MET cc_start: 0.8612 (mmm) cc_final: 0.8306 (tpp)
REVERT: B  416 ILE cc_start: 0.8497 (mm) cc_final: 0.8217 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0800
  time to fit residues: 8.4834
Evaluate side-chains
  59 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 615 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.126456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.101548 restraints weight = 13727.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.105739 restraints weight = 7717.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.108595 restraints weight = 5284.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.110486 restraints weight = 4072.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.111941 restraints weight = 3401.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.0983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8589  Z= 0.128
  Angle     :  0.591   7.006  11689  Z= 0.301
  Chirality :  0.040   0.142   1277
  Planarity :  0.004   0.047   1533
  Dihedral  :  5.208  23.811   1174
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.22 %
    Favored  : 90.78 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  7.30 %
    Favored  : 92.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.84 (0.25), residues: 1074
  helix: -1.57 (0.25), residues: 463
  sheet: -4.13 (0.97), residues: 20
  loop : -2.08 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 114 
 TYR   0.016   0.001   TYR A 638 
 PHE   0.010   0.001   PHE A 332 
 TRP   0.012   0.001   TRP A 191 
 HIS   0.002   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 8589)
  covalent geometry    : angle       0.59142 (11689)
  hydrogen bonds       : bond        0.03732 (  253)
  hydrogen bonds       : angle       4.54492 (  690)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A  107 TRP cc_start: 0.8326 (t60) cc_final: 0.7757 (t-100)
REVERT: A  535 ASN cc_start: 0.8519 (t0) cc_final: 0.8310 (t0)
REVERT: A  623 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7262 (mt-10)
REVERT: B  416 ILE cc_start: 0.8404 (mm) cc_final: 0.8118 (mt)
  outliers start: 2
  outliers final: 1
  residues processed: 76
  average time/residue: 0.0769
  time to fit residues: 8.6899
Evaluate side-chains
  61 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain B residue  544 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0980
   chunk 41 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9980
   chunk 99 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  49 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.126934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.101706 restraints weight = 13618.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.105819 restraints weight = 7744.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.108680 restraints weight = 5357.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.110652 restraints weight = 4138.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.112049 restraints weight = 3442.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.1240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8589  Z= 0.126
  Angle     :  0.570   7.083  11689  Z= 0.287
  Chirality :  0.040   0.132   1277
  Planarity :  0.004   0.042   1533
  Dihedral  :  4.917  23.308   1174
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.66 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.37 %
    Favored  : 88.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.25), residues: 1074
  helix: -1.38 (0.25), residues: 470
  sheet: -4.08 (0.90), residues: 20
  loop : -2.03 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 114 
 TYR   0.016   0.001   TYR B 638 
 PHE   0.012   0.001   PHE A 332 
 TRP   0.010   0.001   TRP A 191 
 HIS   0.006   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8589)
  covalent geometry    : angle       0.56961 (11689)
  hydrogen bonds       : bond        0.03375 (  253)
  hydrogen bonds       : angle       4.18205 (  690)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A  107 TRP cc_start: 0.8397 (t60) cc_final: 0.8121 (t60)
REVERT: A  420 MET cc_start: 0.8594 (mtp) cc_final: 0.8387 (mtp)
REVERT: A  487 ASP cc_start: 0.8889 (t0) cc_final: 0.8485 (t0)
REVERT: A  535 ASN cc_start: 0.8562 (t0) cc_final: 0.8280 (t0)
REVERT: A  608 TYR cc_start: 0.8404 (m-80) cc_final: 0.8043 (m-80)
REVERT: A  623 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7258 (mt-10)
REVERT: B  416 ILE cc_start: 0.8403 (mm) cc_final: 0.8100 (mt)
REVERT: B  419 ASP cc_start: 0.7816 (p0) cc_final: 0.7555 (p0)
REVERT: B  562 ASN cc_start: 0.8272 (p0) cc_final: 0.7985 (t0)
REVERT: B  735 ASP cc_start: 0.8531 (t0) cc_final: 0.8303 (t0)
  outliers start: 6
  outliers final: 5
  residues processed: 76
  average time/residue: 0.0740
  time to fit residues: 8.4745
Evaluate side-chains
  72 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  544 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 45 optimal weight:    0.2980
   chunk 49 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0020
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
B 561 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.126996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.102576 restraints weight = 13920.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.106607 restraints weight = 7988.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.109449 restraints weight = 5539.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.111409 restraints weight = 4278.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.112682 restraints weight = 3547.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.1545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8589  Z= 0.110
  Angle     :  0.538   7.043  11689  Z= 0.271
  Chirality :  0.039   0.125   1277
  Planarity :  0.004   0.037   1533
  Dihedral  :  4.643  23.616   1174
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 11.19 %
    Favored  : 87.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.45 (0.25), residues: 1074
  helix: -1.13 (0.25), residues: 464
  sheet: -4.09 (0.91), residues: 20
  loop : -1.97 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 114 
 TYR   0.016   0.001   TYR B 638 
 PHE   0.010   0.001   PHE A 332 
 TRP   0.009   0.001   TRP A 191 
 HIS   0.003   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8589)
  covalent geometry    : angle       0.53785 (11689)
  hydrogen bonds       : bond        0.02988 (  253)
  hydrogen bonds       : angle       3.94676 (  690)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A  420 MET cc_start: 0.8519 (mtp) cc_final: 0.8314 (mtp)
REVERT: A  487 ASP cc_start: 0.8792 (t0) cc_final: 0.8414 (t0)
REVERT: A  535 ASN cc_start: 0.8549 (t0) cc_final: 0.8310 (t0)
REVERT: A  608 TYR cc_start: 0.8402 (m-80) cc_final: 0.7994 (m-80)
REVERT: A  623 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7218 (mt-10)
REVERT: B  416 ILE cc_start: 0.8388 (mm) cc_final: 0.8084 (mt)
REVERT: B  623 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7176 (mt-10)
  outliers start: 10
  outliers final: 7
  residues processed: 81
  average time/residue: 0.0571
  time to fit residues: 7.1099
Evaluate side-chains
  73 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  544 VAL
Chi-restraints excluded: chain B residue  623 GLU
Chi-restraints excluded: chain B residue  687 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 97 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 103 optimal weight:    4.9990
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.124398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.100141 restraints weight = 13633.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.104112 restraints weight = 7846.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.106852 restraints weight = 5442.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.108765 restraints weight = 4212.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.110122 restraints weight = 3499.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8589  Z= 0.141
  Angle     :  0.558   7.614  11689  Z= 0.281
  Chirality :  0.040   0.119   1277
  Planarity :  0.004   0.038   1533
  Dihedral  :  4.677  23.731   1174
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.66 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 12.60 %
    Favored  : 85.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.40 (0.25), residues: 1074
  helix: -1.10 (0.25), residues: 460
  sheet: -4.11 (0.90), residues: 20
  loop : -1.92 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 146 
 TYR   0.014   0.001   TYR B 638 
 PHE   0.013   0.001   PHE A 332 
 TRP   0.010   0.001   TRP A 191 
 HIS   0.003   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8589)
  covalent geometry    : angle       0.55822 (11689)
  hydrogen bonds       : bond        0.03226 (  253)
  hydrogen bonds       : angle       3.94648 (  690)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A  487 ASP cc_start: 0.8828 (t0) cc_final: 0.8432 (t0)
REVERT: A  535 ASN cc_start: 0.8537 (t0) cc_final: 0.8306 (t0)
REVERT: A  608 TYR cc_start: 0.8429 (m-80) cc_final: 0.8060 (m-80)
REVERT: A  623 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7241 (mt-10)
REVERT: B  416 ILE cc_start: 0.8444 (mm) cc_final: 0.8132 (mt)
REVERT: B  542 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7861 (t0)
REVERT: B  623 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7234 (mt-10)
REVERT: B  668 TRP cc_start: 0.8475 (m100) cc_final: 0.8110 (m100)
  outliers start: 13
  outliers final: 9
  residues processed: 76
  average time/residue: 0.0709
  time to fit residues: 8.3383
Evaluate side-chains
  74 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  176 MET
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  542 ASP
Chi-restraints excluded: chain B residue  544 VAL
Chi-restraints excluded: chain B residue  623 GLU
Chi-restraints excluded: chain B residue  687 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 73 optimal weight:    0.5980
   chunk 105 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 99 optimal weight:    2.9990
   chunk 93 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B 602 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.126737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.101371 restraints weight = 13761.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.105379 restraints weight = 8089.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.108178 restraints weight = 5680.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.110167 restraints weight = 4438.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.111525 restraints weight = 3705.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8589  Z= 0.143
  Angle     :  0.566   8.806  11689  Z= 0.284
  Chirality :  0.041   0.135   1277
  Planarity :  0.004   0.038   1533
  Dihedral  :  4.679  23.661   1174
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.94 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 14.25 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.39 (0.25), residues: 1074
  helix: -1.13 (0.25), residues: 467
  sheet: -4.03 (0.90), residues: 20
  loop : -1.88 (0.25), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 632 
 TYR   0.018   0.001   TYR B 638 
 PHE   0.012   0.001   PHE A 332 
 TRP   0.010   0.001   TRP A 191 
 HIS   0.003   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8589)
  covalent geometry    : angle       0.56595 (11689)
  hydrogen bonds       : bond        0.03189 (  253)
  hydrogen bonds       : angle       3.93018 (  690)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A  487 ASP cc_start: 0.8824 (t0) cc_final: 0.8435 (t0)
REVERT: A  535 ASN cc_start: 0.8519 (t0) cc_final: 0.8292 (t0)
REVERT: A  608 TYR cc_start: 0.8425 (m-80) cc_final: 0.8073 (m-80)
REVERT: A  623 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7288 (mt-10)
REVERT: B  416 ILE cc_start: 0.8480 (mm) cc_final: 0.8169 (mt)
REVERT: B  542 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7783 (t0)
REVERT: B  623 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7254 (mt-10)
REVERT: B  668 TRP cc_start: 0.8496 (m100) cc_final: 0.8210 (m100)
  outliers start: 12
  outliers final: 8
  residues processed: 76
  average time/residue: 0.0628
  time to fit residues: 7.7587
Evaluate side-chains
  72 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  176 MET
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  542 ASP
Chi-restraints excluded: chain B residue  544 VAL
Chi-restraints excluded: chain B residue  623 GLU
Chi-restraints excluded: chain B residue  687 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0570
   chunk 36 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0370
   chunk 7 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0060
   chunk 37 optimal weight:    0.2980
   overall best weight:    0.2192

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

Flipped N/Q/H residues before XYZ refinement:
B 602 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.129131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.104885 restraints weight = 13667.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.109064 restraints weight = 7727.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.111961 restraints weight = 5283.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.113982 restraints weight = 4040.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.115437 restraints weight = 3317.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8589  Z= 0.093
  Angle     :  0.537  10.557  11689  Z= 0.269
  Chirality :  0.038   0.122   1277
  Planarity :  0.004   0.036   1533
  Dihedral  :  4.300  23.657   1174
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 15.78 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.12 (0.25), residues: 1074
  helix: -0.87 (0.25), residues: 469
  sheet: -4.05 (0.84), residues: 20
  loop : -1.76 (0.25), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 418 
 TYR   0.016   0.001   TYR B 638 
 PHE   0.007   0.001   PHE A 657 
 TRP   0.010   0.001   TRP A 191 
 HIS   0.003   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 8589)
  covalent geometry    : angle       0.53739 (11689)
  hydrogen bonds       : bond        0.02501 (  253)
  hydrogen bonds       : angle       3.70030 (  690)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A  420 MET cc_start: 0.8607 (mtp) cc_final: 0.8311 (mtm)
REVERT: A  487 ASP cc_start: 0.8643 (t0) cc_final: 0.8364 (t0)
REVERT: A  535 ASN cc_start: 0.8472 (t0) cc_final: 0.8254 (t0)
REVERT: A  608 TYR cc_start: 0.8419 (m-80) cc_final: 0.8037 (m-80)
REVERT: A  623 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7161 (mt-10)
REVERT: B  416 ILE cc_start: 0.8359 (mm) cc_final: 0.8065 (mt)
REVERT: B  419 ASP cc_start: 0.7822 (p0) cc_final: 0.7578 (p0)
REVERT: B  668 TRP cc_start: 0.8424 (m100) cc_final: 0.8055 (m100)
  outliers start: 7
  outliers final: 4
  residues processed: 77
  average time/residue: 0.0639
  time to fit residues: 7.9138
Evaluate side-chains
  70 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain B residue  544 VAL
Chi-restraints excluded: chain B residue  602 ASN
Chi-restraints excluded: chain B residue  687 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 56 optimal weight:    0.0270
   chunk 89 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 77 optimal weight:    0.0970
   chunk 19 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   overall best weight:    0.4436

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.130342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.104988 restraints weight = 13666.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.109303 restraints weight = 7756.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.112282 restraints weight = 5314.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.114352 restraints weight = 4074.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.115736 restraints weight = 3361.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8589  Z= 0.103
  Angle     :  0.548  10.643  11689  Z= 0.272
  Chirality :  0.039   0.118   1277
  Planarity :  0.004   0.039   1533
  Dihedral  :  4.263  23.947   1174
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 16.02 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.00 (0.25), residues: 1074
  helix: -0.77 (0.25), residues: 465
  sheet: -3.86 (0.88), residues: 20
  loop : -1.71 (0.25), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 114 
 TYR   0.024   0.001   TYR B 638 
 PHE   0.009   0.001   PHE A 332 
 TRP   0.008   0.001   TRP A 191 
 HIS   0.003   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 8589)
  covalent geometry    : angle       0.54815 (11689)
  hydrogen bonds       : bond        0.02696 (  253)
  hydrogen bonds       : angle       3.70686 (  690)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A  487 ASP cc_start: 0.8737 (t0) cc_final: 0.8398 (t0)
REVERT: A  535 ASN cc_start: 0.8520 (t0) cc_final: 0.8282 (t0)
REVERT: A  608 TYR cc_start: 0.8399 (m-80) cc_final: 0.8015 (m-80)
REVERT: A  623 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7216 (mt-10)
REVERT: B  416 ILE cc_start: 0.8360 (mm) cc_final: 0.8034 (mt)
REVERT: B  419 ASP cc_start: 0.7848 (p0) cc_final: 0.7538 (p0)
REVERT: B  668 TRP cc_start: 0.8497 (m100) cc_final: 0.8191 (m100)
  outliers start: 7
  outliers final: 4
  residues processed: 73
  average time/residue: 0.0633
  time to fit residues: 7.4598
Evaluate side-chains
  69 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  544 VAL
Chi-restraints excluded: chain B residue  687 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 15 optimal weight:    0.0970
   chunk 3 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 90 optimal weight:    0.5980
   chunk 60 optimal weight:    0.0470
   chunk 66 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.4276

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.129431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.104817 restraints weight = 13511.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.109057 restraints weight = 7563.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.112038 restraints weight = 5134.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.114082 restraints weight = 3907.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.115572 restraints weight = 3209.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8589  Z= 0.102
  Angle     :  0.546  10.980  11689  Z= 0.270
  Chirality :  0.039   0.123   1277
  Planarity :  0.004   0.038   1533
  Dihedral  :  4.199  23.992   1174
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 16.25 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.85 (0.25), residues: 1074
  helix: -0.60 (0.25), residues: 465
  sheet: -3.62 (0.92), residues: 20
  loop : -1.67 (0.25), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 632 
 TYR   0.024   0.001   TYR B 638 
 PHE   0.009   0.001   PHE A 332 
 TRP   0.009   0.001   TRP A 191 
 HIS   0.003   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 8589)
  covalent geometry    : angle       0.54603 (11689)
  hydrogen bonds       : bond        0.02648 (  253)
  hydrogen bonds       : angle       3.64164 (  690)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A  487 ASP cc_start: 0.8732 (t0) cc_final: 0.8380 (t0)
REVERT: A  608 TYR cc_start: 0.8394 (m-80) cc_final: 0.8013 (m-80)
REVERT: A  623 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7189 (mt-10)
REVERT: B  416 ILE cc_start: 0.8332 (mm) cc_final: 0.7999 (mt)
REVERT: B  419 ASP cc_start: 0.7869 (p0) cc_final: 0.7510 (p0)
REVERT: B  668 TRP cc_start: 0.8477 (m100) cc_final: 0.8175 (m100)
  outliers start: 7
  outliers final: 6
  residues processed: 73
  average time/residue: 0.0584
  time to fit residues: 6.8748
Evaluate side-chains
  73 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  544 VAL
Chi-restraints excluded: chain B residue  687 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0570
   chunk 69 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 103 optimal weight:    3.9990
   chunk 85 optimal weight:    0.4980
   chunk 1 optimal weight:    0.9990
   chunk 104 optimal weight:    3.9990
   chunk 84 optimal weight:    6.9990
   chunk 105 optimal weight:    0.7980
   overall best weight:    0.6098

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.129133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.104093 restraints weight = 13604.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.108335 restraints weight = 7671.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.111292 restraints weight = 5239.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.113338 restraints weight = 4014.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.114835 restraints weight = 3309.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8589  Z= 0.119
  Angle     :  0.572  11.997  11689  Z= 0.283
  Chirality :  0.040   0.124   1277
  Planarity :  0.004   0.040   1533
  Dihedral  :  4.271  24.015   1174
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 16.84 %
    Favored  : 82.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.87 (0.25), residues: 1074
  helix: -0.59 (0.25), residues: 472
  sheet: -3.60 (0.93), residues: 20
  loop : -1.72 (0.25), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 463 
 TYR   0.024   0.001   TYR B 638 
 PHE   0.010   0.001   PHE A 332 
 TRP   0.008   0.001   TRP A 191 
 HIS   0.003   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8589)
  covalent geometry    : angle       0.57151 (11689)
  hydrogen bonds       : bond        0.02841 (  253)
  hydrogen bonds       : angle       3.63648 (  690)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A  487 ASP cc_start: 0.8814 (t0) cc_final: 0.8431 (t0)
REVERT: A  608 TYR cc_start: 0.8403 (m-80) cc_final: 0.8032 (m-80)
REVERT: A  623 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7174 (mt-10)
REVERT: B  416 ILE cc_start: 0.8381 (mm) cc_final: 0.8053 (mt)
REVERT: B  419 ASP cc_start: 0.7914 (p0) cc_final: 0.7619 (p0)
REVERT: B  668 TRP cc_start: 0.8465 (m100) cc_final: 0.8161 (m100)
  outliers start: 7
  outliers final: 6
  residues processed: 75
  average time/residue: 0.0663
  time to fit residues: 7.6560
Evaluate side-chains
  72 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  544 VAL
Chi-restraints excluded: chain B residue  687 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 62 optimal weight:    0.0060
   chunk 21 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 85 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.6396

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.128907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.103928 restraints weight = 13556.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.108107 restraints weight = 7654.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.111122 restraints weight = 5243.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.113190 restraints weight = 3998.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.114553 restraints weight = 3286.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.2195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8589  Z= 0.122
  Angle     :  0.571  11.790  11689  Z= 0.282
  Chirality :  0.040   0.123   1277
  Planarity :  0.004   0.039   1533
  Dihedral  :  4.308  23.976   1174
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.01 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 16.96 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.85 (0.25), residues: 1074
  helix: -0.56 (0.25), residues: 472
  sheet: -3.58 (0.94), residues: 20
  loop : -1.73 (0.25), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 463 
 TYR   0.023   0.001   TYR B 638 
 PHE   0.010   0.001   PHE A 332 
 TRP   0.009   0.001   TRP A 191 
 HIS   0.003   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8589)
  covalent geometry    : angle       0.57126 (11689)
  hydrogen bonds       : bond        0.02862 (  253)
  hydrogen bonds       : angle       3.70482 (  690)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1275.34 seconds
wall clock time: 22 minutes 37.51 seconds (1357.51 seconds total)