Starting phenix.real_space_refine
on Wed Feb 12 22:18:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7aa3_11689/02_2025/7aa3_11689.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7aa3_11689/02_2025/7aa3_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7aa3_11689/02_2025/7aa3_11689.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7aa3_11689/02_2025/7aa3_11689.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7aa3_11689/02_2025/7aa3_11689.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7aa3_11689/02_2025/7aa3_11689.cif"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.031
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'PHE:plan': 2, 'ARG:plan': 3}
          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: 5.80, per 1000 atoms: 0.69
  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: 2.36
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.88
  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: 2.03

  Time building geometry restraints manager: 2.69 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:             1.590
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.690
  Find NCS groups from input model:        0.370
  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:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.180
-------------------------------------------------------------------------------
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= 0.289
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.38 (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
 TRP   0.017   0.001   TRP A 191 
 HIS   0.003   0.001   HIS B 561 
 PHE   0.012   0.001   PHE A 332 
 TYR   0.010   0.001   TYR A 638 
 ARG   0.006   0.000   ARG B 418 

*********************** 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  : 0.966 
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: 0.1947
  time to fit residues: 20.7394
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  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:   10.0000
   chunk 82 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 85 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3604 r_free = 0.3604 target = 0.123856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.099494 restraints weight = 13662.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.103488 restraints weight = 7873.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.106231 restraints weight = 5474.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.0912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8589  Z= 0.233
  Angle     :  0.607   6.851  11689  Z= 0.310
  Chirality :  0.041   0.142   1277
  Planarity :  0.004   0.048   1533
  Dihedral  :  5.323  23.968   1174
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.15 %
    Favored  : 89.85 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  7.54 %
    Favored  : 92.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.90 (0.25), residues: 1074
  helix: -1.62 (0.24), residues: 463
  sheet: -4.10 (0.99), residues: 20
  loop : -2.11 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 191 
 HIS   0.002   0.001   HIS B 116 
 PHE   0.012   0.001   PHE A 332 
 TYR   0.017   0.001   TYR A 638 
 ARG   0.003   0.000   ARG B 114 

*********************** 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
  77 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 74
  time to evaluate  : 0.920 
Fit side-chains
REVERT: A  107 TRP cc_start: 0.8273 (t60) cc_final: 0.7782 (t-100)
REVERT: A  535 ASN cc_start: 0.8575 (t0) cc_final: 0.8289 (t0)
REVERT: A  623 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7326 (mt-10)
REVERT: B  416 ILE cc_start: 0.8358 (mm) cc_final: 0.8158 (mt)
  outliers start: 3
  outliers final: 2
  residues processed: 77
  average time/residue: 0.1790
  time to fit residues: 20.6381
Evaluate side-chains
  62 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain B residue  160 SER
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 53 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 42 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 88 optimal weight:    0.0970
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.3614 r_free = 0.3614 target = 0.123898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.099381 restraints weight = 13905.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.103348 restraints weight = 8056.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.106072 restraints weight = 5614.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.1149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8589  Z= 0.235
  Angle     :  0.590   7.158  11689  Z= 0.298
  Chirality :  0.041   0.128   1277
  Planarity :  0.004   0.044   1533
  Dihedral  :  5.077  23.316   1174
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.94 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 10.25 %
    Favored  : 88.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.75 (0.25), residues: 1074
  helix: -1.47 (0.24), residues: 470
  sheet: -4.06 (0.93), residues: 20
  loop : -2.06 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 191 
 HIS   0.006   0.001   HIS A  49 
 PHE   0.013   0.001   PHE A 332 
 TYR   0.016   0.001   TYR B 638 
 ARG   0.002   0.000   ARG A 498 

*********************** 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: 8
    poor density    : 68
  time to evaluate  : 0.875 
Fit side-chains
REVERT: A  107 TRP cc_start: 0.8366 (t60) cc_final: 0.8147 (t60)
REVERT: A  420 MET cc_start: 0.8609 (mtp) cc_final: 0.8401 (mtp)
REVERT: A  487 ASP cc_start: 0.8938 (t0) cc_final: 0.8473 (t0)
REVERT: A  535 ASN cc_start: 0.8556 (t0) cc_final: 0.8200 (t0)
REVERT: A  608 TYR cc_start: 0.8422 (m-80) cc_final: 0.8101 (m-80)
REVERT: A  623 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7286 (mt-10)
REVERT: B  416 ILE cc_start: 0.8516 (mm) cc_final: 0.8221 (mt)
REVERT: B  735 ASP cc_start: 0.8513 (t0) cc_final: 0.8309 (t0)
  outliers start: 8
  outliers final: 6
  residues processed: 76
  average time/residue: 0.1655
  time to fit residues: 19.3281
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  : 0.971 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain B residue  687 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 108 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0770
   chunk 99 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0370
   chunk 16 optimal weight:    0.0170
   overall best weight:    0.3454

-------------------------------------------------------------------------------
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 = 0.3659 r_free = 0.3659 target = 0.127216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.103234 restraints weight = 13520.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.107332 restraints weight = 7687.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.110162 restraints weight = 5272.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.1620

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= 0.145
  Angle     :  0.533   7.260  11689  Z= 0.268
  Chirality :  0.039   0.131   1277
  Planarity :  0.004   0.038   1533
  Dihedral  :  4.595  23.638   1174
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.10 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 12.13 %
    Favored  : 87.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.45 (0.25), residues: 1074
  helix: -1.11 (0.25), residues: 463
  sheet: -4.14 (0.88), residues: 20
  loop : -1.98 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 191 
 HIS   0.003   0.001   HIS B 116 
 PHE   0.007   0.001   PHE A 332 
 TYR   0.012   0.001   TYR B 638 
 ARG   0.002   0.000   ARG B 632 

*********************** 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
  75 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.816 
Fit side-chains
REVERT: A  420 MET cc_start: 0.8516 (mtp) cc_final: 0.8314 (mtp)
REVERT: A  487 ASP cc_start: 0.8758 (t0) cc_final: 0.8373 (t0)
REVERT: A  535 ASN cc_start: 0.8573 (t0) cc_final: 0.8334 (t0)
REVERT: A  623 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7206 (mt-10)
REVERT: B  416 ILE cc_start: 0.8388 (mm) cc_final: 0.8100 (mt)
REVERT: B  562 ASN cc_start: 0.8214 (p0) cc_final: 0.7926 (t0)
REVERT: B  623 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7143 (mt-10)
  outliers start: 4
  outliers final: 2
  residues processed: 75
  average time/residue: 0.1694
  time to fit residues: 19.2557
Evaluate side-chains
  65 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  623 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 97 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 78 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 80 optimal weight:    8.9990
   chunk 85 optimal weight:    1.9990
   chunk 105 optimal weight:    0.5980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3629 r_free = 0.3629 target = 0.126297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.101219 restraints weight = 13609.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.105165 restraints weight = 8015.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.107997 restraints weight = 5655.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.1537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8589  Z= 0.243
  Angle     :  0.568   7.944  11689  Z= 0.285
  Chirality :  0.041   0.119   1277
  Planarity :  0.004   0.038   1533
  Dihedral  :  4.712  23.619   1174
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 13.55 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.41 (0.25), residues: 1074
  helix: -1.11 (0.25), residues: 459
  sheet: -4.04 (0.90), residues: 20
  loop : -1.93 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 191 
 HIS   0.003   0.001   HIS B 116 
 PHE   0.014   0.001   PHE A 332 
 TYR   0.008   0.001   TYR B 337 
 ARG   0.002   0.000   ARG B 632 

*********************** 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
  76 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.982 
Fit side-chains
REVERT: A  487 ASP cc_start: 0.8853 (t0) cc_final: 0.8442 (t0)
REVERT: A  535 ASN cc_start: 0.8645 (t0) cc_final: 0.8331 (t0)
REVERT: A  608 TYR cc_start: 0.8418 (m-80) cc_final: 0.8053 (m-80)
REVERT: A  623 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7273 (mt-10)
REVERT: B  416 ILE cc_start: 0.8483 (mm) cc_final: 0.8162 (mt)
REVERT: B  542 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7940 (t0)
REVERT: B  562 ASN cc_start: 0.8266 (p0) cc_final: 0.8032 (t0)
REVERT: B  623 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7254 (mt-10)
REVERT: B  668 TRP cc_start: 0.8483 (m100) cc_final: 0.8195 (m100)
  outliers start: 11
  outliers final: 7
  residues processed: 75
  average time/residue: 0.1596
  time to fit residues: 18.3314
Evaluate side-chains
  72 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
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  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 31 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0870
   chunk 89 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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 = 0.3653 r_free = 0.3653 target = 0.128244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.102747 restraints weight = 13623.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.106992 restraints weight = 7804.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.109910 restraints weight = 5385.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.1734

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= 0.173
  Angle     :  0.532   6.313  11689  Z= 0.269
  Chirality :  0.039   0.137   1277
  Planarity :  0.004   0.038   1533
  Dihedral  :  4.529  23.479   1174
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.66 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 14.72 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.29 (0.25), residues: 1074
  helix: -1.02 (0.25), residues: 465
  sheet: -4.04 (0.89), residues: 20
  loop : -1.86 (0.25), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 191 
 HIS   0.003   0.001   HIS B 116 
 PHE   0.010   0.001   PHE A 332 
 TYR   0.006   0.001   TYR B 337 
 ARG   0.002   0.000   ARG B 632 

*********************** 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
  74 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.896 
Fit side-chains
REVERT: A  420 MET cc_start: 0.8533 (mtp) cc_final: 0.8326 (mtm)
REVERT: A  487 ASP cc_start: 0.8798 (t0) cc_final: 0.8424 (t0)
REVERT: A  535 ASN cc_start: 0.8605 (t0) cc_final: 0.8360 (t0)
REVERT: A  608 TYR cc_start: 0.8371 (m-80) cc_final: 0.7999 (m-80)
REVERT: A  623 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7228 (mt-10)
REVERT: B  416 ILE cc_start: 0.8410 (mm) cc_final: 0.8109 (mt)
REVERT: B  623 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7278 (mt-10)
REVERT: B  668 TRP cc_start: 0.8469 (m100) cc_final: 0.8158 (m100)
REVERT: B  735 ASP cc_start: 0.8513 (t0) cc_final: 0.8305 (t0)
  outliers start: 7
  outliers final: 4
  residues processed: 74
  average time/residue: 0.1574
  time to fit residues: 18.2255
Evaluate side-chains
  70 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
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  602 ASN
Chi-restraints excluded: chain B residue  623 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 108 optimal weight:    0.0970
   chunk 1 optimal weight:    0.3980
   chunk 62 optimal weight:    0.0470
   chunk 12 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 94 optimal weight:    3.9990
   overall best weight:    0.4076

-------------------------------------------------------------------------------
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 = 0.129479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.103730 restraints weight = 13760.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.108087 restraints weight = 7751.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.111077 restraints weight = 5293.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.1925

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= 0.155
  Angle     :  0.534   9.337  11689  Z= 0.267
  Chirality :  0.039   0.120   1277
  Planarity :  0.004   0.038   1533
  Dihedral  :  4.376  23.670   1174
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 15.43 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.25), residues: 1074
  helix: -0.89 (0.25), residues: 464
  sheet: -3.98 (0.90), residues: 20
  loop : -1.79 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 191 
 HIS   0.003   0.001   HIS B 116 
 PHE   0.009   0.001   PHE A 332 
 TYR   0.006   0.001   TYR B 337 
 ARG   0.002   0.000   ARG B 632 

*********************** 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
  74 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.909 
Fit side-chains
REVERT: A  420 MET cc_start: 0.8586 (mtp) cc_final: 0.8319 (mtm)
REVERT: A  487 ASP cc_start: 0.8798 (t0) cc_final: 0.8408 (t0)
REVERT: A  535 ASN cc_start: 0.8634 (t0) cc_final: 0.8337 (t0)
REVERT: A  608 TYR cc_start: 0.8274 (m-80) cc_final: 0.7871 (m-80)
REVERT: A  623 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7178 (mt-10)
REVERT: B  416 ILE cc_start: 0.8312 (mm) cc_final: 0.7999 (mt)
REVERT: B  623 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7240 (mt-10)
REVERT: B  668 TRP cc_start: 0.8457 (m100) cc_final: 0.8099 (m100)
  outliers start: 6
  outliers final: 3
  residues processed: 74
  average time/residue: 0.1493
  time to fit residues: 17.5094
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  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
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  623 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 93 optimal weight:    4.9990
   chunk 63 optimal weight:    0.0070
   chunk 36 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 50 optimal weight:    0.7980
   chunk 7 optimal weight:    0.1980
   chunk 65 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 71 optimal weight:    0.3980
   chunk 57 optimal weight:    0.5980
   chunk 91 optimal weight:    5.9990
   overall best weight:    0.3998

-------------------------------------------------------------------------------
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 = 0.3677 r_free = 0.3677 target = 0.130023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.104623 restraints weight = 13750.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.108934 restraints weight = 7783.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.111936 restraints weight = 5324.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.2046

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= 0.158
  Angle     :  0.551  11.346  11689  Z= 0.272
  Chirality :  0.039   0.118   1277
  Planarity :  0.004   0.038   1533
  Dihedral  :  4.285  23.860   1174
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.10 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 15.90 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.25), residues: 1074
  helix: -0.74 (0.25), residues: 462
  sheet: -3.90 (0.91), residues: 20
  loop : -1.70 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 191 
 HIS   0.003   0.001   HIS B 116 
 PHE   0.009   0.001   PHE A 332 
 TYR   0.017   0.001   TYR B 638 
 ARG   0.002   0.000   ARG B 249 

*********************** 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
  69 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.892 
Fit side-chains
REVERT: A  487 ASP cc_start: 0.8728 (t0) cc_final: 0.8392 (t0)
REVERT: A  535 ASN cc_start: 0.8596 (t0) cc_final: 0.8329 (t0)
REVERT: A  608 TYR cc_start: 0.8350 (m-80) cc_final: 0.7966 (m-80)
REVERT: A  623 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7199 (mt-10)
REVERT: B  416 ILE cc_start: 0.8367 (mm) cc_final: 0.8037 (mt)
REVERT: B  542 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7863 (t0)
REVERT: B  623 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7259 (mt-10)
REVERT: B  668 TRP cc_start: 0.8485 (m100) cc_final: 0.8148 (m100)
  outliers start: 5
  outliers final: 2
  residues processed: 69
  average time/residue: 0.1473
  time to fit residues: 16.2163
Evaluate side-chains
  67 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain B residue   68 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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0470
   chunk 50 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 48 optimal weight:    0.5980
   chunk 94 optimal weight:    0.0770
   chunk 67 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0670
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.2774

-------------------------------------------------------------------------------
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 = 0.3690 r_free = 0.3690 target = 0.130589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.105749 restraints weight = 13646.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.110073 restraints weight = 7609.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.113095 restraints weight = 5162.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8589  Z= 0.144
  Angle     :  0.544  11.431  11689  Z= 0.267
  Chirality :  0.038   0.128   1277
  Planarity :  0.004   0.042   1533
  Dihedral  :  4.108  23.823   1174
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 16.49 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.25), residues: 1074
  helix: -0.61 (0.25), residues: 473
  sheet: -3.87 (0.90), residues: 20
  loop : -1.61 (0.25), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 191 
 HIS   0.003   0.000   HIS B 116 
 PHE   0.006   0.001   PHE A 657 
 TYR   0.023   0.001   TYR B 638 
 ARG   0.002   0.000   ARG B 114 

*********************** 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
  73 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.884 
Fit side-chains
REVERT: A  487 ASP cc_start: 0.8690 (t0) cc_final: 0.8374 (t0)
REVERT: A  535 ASN cc_start: 0.8602 (t0) cc_final: 0.8391 (t0)
REVERT: A  562 ASN cc_start: 0.8137 (t0) cc_final: 0.7935 (t0)
REVERT: A  608 TYR cc_start: 0.8374 (m-80) cc_final: 0.7990 (m-80)
REVERT: A  623 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7169 (mt-10)
REVERT: B  416 ILE cc_start: 0.8326 (mm) cc_final: 0.7994 (mt)
REVERT: B  419 ASP cc_start: 0.7813 (p0) cc_final: 0.7560 (p0)
REVERT: B  668 TRP cc_start: 0.8433 (m100) cc_final: 0.8084 (m100)
  outliers start: 5
  outliers final: 3
  residues processed: 73
  average time/residue: 0.1475
  time to fit residues: 16.9719
Evaluate side-chains
  70 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  544 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   chunk 88 optimal weight:    0.0870
   chunk 68 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   overall best weight:    0.6560

-------------------------------------------------------------------------------
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 = 0.3669 r_free = 0.3669 target = 0.128847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.104056 restraints weight = 13544.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.108225 restraints weight = 7655.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.111184 restraints weight = 5248.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.2176

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= 0.191
  Angle     :  0.571  12.062  11689  Z= 0.280
  Chirality :  0.040   0.128   1277
  Planarity :  0.004   0.071   1533
  Dihedral  :  4.245  24.027   1174
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 16.37 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.87 (0.25), residues: 1074
  helix: -0.63 (0.25), residues: 475
  sheet: -3.77 (0.95), residues: 20
  loop : -1.67 (0.25), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 191 
 HIS   0.003   0.001   HIS B 116 
 PHE   0.011   0.001   PHE A 332 
 TYR   0.023   0.001   TYR B 638 
 ARG   0.002   0.000   ARG B 187 

********************** 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
  74 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.962 
Fit side-chains
REVERT: A  487 ASP cc_start: 0.8794 (t0) cc_final: 0.8415 (t0)
REVERT: A  535 ASN cc_start: 0.8606 (t0) cc_final: 0.8382 (t0)
REVERT: A  608 TYR cc_start: 0.8365 (m-80) cc_final: 0.7995 (m-80)
REVERT: A  623 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7206 (mt-10)
REVERT: B  416 ILE cc_start: 0.8386 (mm) cc_final: 0.8046 (mt)
REVERT: B  542 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7813 (t0)
REVERT: B  668 TRP cc_start: 0.8460 (m100) cc_final: 0.8183 (m100)
  outliers start: 7
  outliers final: 4
  residues processed: 73
  average time/residue: 0.1635
  time to fit residues: 18.3985
Evaluate side-chains
  70 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
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  623 GLU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  542 ASP
Chi-restraints excluded: chain B residue  544 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 41 optimal weight:    0.2980
   chunk 49 optimal weight:    2.9990
   chunk 77 optimal weight:    0.3980
   chunk 107 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 75 optimal weight:    0.0270
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
A 529 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.129699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.104669 restraints weight = 13616.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.108924 restraints weight = 7669.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.111993 restraints weight = 5243.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8589  Z= 0.165
  Angle     :  0.560  12.120  11689  Z= 0.274
  Chirality :  0.039   0.128   1277
  Planarity :  0.004   0.068   1533
  Dihedral  :  4.203  23.860   1174
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 16.84 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.71 (0.25), residues: 1074
  helix: -0.48 (0.25), residues: 469
  sheet: -3.77 (0.95), residues: 20
  loop : -1.60 (0.25), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 191 
 HIS   0.003   0.001   HIS B 116 
 PHE   0.009   0.001   PHE A 332 
 TYR   0.023   0.001   TYR B 638 
 ARG   0.002   0.000   ARG B 418 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2297.21 seconds
wall clock time: 41 minutes 58.36 seconds (2518.36 seconds total)