Starting phenix.real_space_refine
on Sat May 24 04:42:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g40_51020/05_2025/9g40_51020.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g40_51020/05_2025/9g40_51020.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9g40_51020/05_2025/9g40_51020.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g40_51020/05_2025/9g40_51020.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g40_51020/05_2025/9g40_51020.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g40_51020/05_2025/9g40_51020.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    7932      2.51       5
     N    2160      2.21       5
     O    2285      1.98       5
     H   12457      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 24900
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "F"
      Number of atoms: 10098
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 617, 10098
          Classifications: {'peptide': 617}
          Link IDs: {'PTRANS': 15, 'TRANS': 601}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 12901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 797, 12901
          Classifications: {'peptide': 797}
          Link IDs: {'PTRANS': 26, 'TRANS': 770}
          Chain breaks: 3
    Chain: "X"
      Number of atoms: 679
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 679
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 1, 'TRANS': 43}
          Chain breaks: 1
    Chain: "u"
      Number of atoms: 611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 611
          Classifications: {'peptide': 34}
          Link IDs: {'TRANS': 33}
    Chain: "v"
      Number of atoms: 611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 611
          Classifications: {'peptide': 34}
          Link IDs: {'TRANS': 33}
  Time building chain proxies: 11.00, per 1000 atoms: 0.44
  Number of scatterers: 24900
  At special positions: 0
  Unit cell: (165.36, 127.2, 110.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      66     16.00
     O    2285      8.00
     N    2160      7.00
     C    7932      6.00
     H   12457      1.00
    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: 6.24
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2942

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 5 sheets defined
      76.1% alpha, 2.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.67
  Creating SS restraints...
    Processing helix  chain 'F' and resid 249 through 262
      removed outlier: 3.524A  pdb=" N   LEU F 253 " --> pdb=" O   THR F 249 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 281 through 285
      removed outlier: 3.843A  pdb=" N   ASN F 285 " --> pdb=" O   GLY F 282 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 287 through 316
      removed outlier: 3.788A  pdb=" N   GLU F 299 " --> pdb=" O   VAL F 295 " (cutoff:3.500A)
      removed outlier: 5.341A  pdb=" N   LEU F 300 " --> pdb=" O   ARG F 296 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   GLY F 301 " --> pdb=" O   LEU F 297 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 321 through 350
      removed outlier: 3.508A  pdb=" N   GLN F 350 " --> pdb=" O   HIS F 346 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 366 through 389
      removed outlier: 5.675A  pdb=" N   ASP F 376 " --> pdb=" O   VAL F 372 " (cutoff:3.500A)
      Proline residue:  F 377  - end of helix
    Processing helix  chain 'F' and resid 396 through 405
      removed outlier: 3.890A  pdb=" N   ALA F 400 " --> pdb=" O   GLY F 396 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 411 through 439
      removed outlier: 3.631A  pdb=" N   HIS F 427 " --> pdb=" O   SER F 423 " (cutoff:3.500A)
      Proline residue:  F 428  - end of helix
    Processing helix  chain 'F' and resid 461 through 466
      removed outlier: 3.586A  pdb=" N   LYS F 466 " --> pdb=" O   LEU F 462 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 470 through 474
    Processing helix  chain 'F' and resid 479 through 499
      removed outlier: 3.997A  pdb=" N   HIS F 497 " --> pdb=" O   ILE F 493 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   VAL F 499 " --> pdb=" O   PHE F 495 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 532 through 556
    Processing helix  chain 'F' and resid 557 through 569
    Processing helix  chain 'F' and resid 573 through 589
      removed outlier: 4.076A  pdb=" N   ILE F 577 " --> pdb=" O   GLN F 573 " (cutoff:3.500A)
      Proline residue:  F 586  - end of helix
      removed outlier: 3.926A  pdb=" N   VAL F 589 " --> pdb=" O   LYS F 585 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 591 through 595
      removed outlier: 3.614A  pdb=" N   THR F 594 " --> pdb=" O   PRO F 591 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 596 through 611
      removed outlier: 3.702A  pdb=" N   LEU F 600 " --> pdb=" O   TYR F 596 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 617 through 623
      removed outlier: 3.545A  pdb=" N   ARG F 623 " --> pdb=" O   GLU F 619 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 636 through 640
      removed outlier: 4.168A  pdb=" N   VAL F 640 " --> pdb=" O   THR F 636 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 636 through 640'
    Processing helix  chain 'F' and resid 648 through 655
    Processing helix  chain 'F' and resid 656 through 694
      removed outlier: 3.772A  pdb=" N   ARG F 692 " --> pdb=" O   MET F 688 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 700 through 729
    Processing helix  chain 'F' and resid 731 through 744
      removed outlier: 3.771A  pdb=" N   ARG F 743 " --> pdb=" O   ASN F 739 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 746 through 765
    Processing helix  chain 'F' and resid 771 through 819
    Processing helix  chain 'F' and resid 825 through 869
      Proline residue:  F 844  - end of helix
    Processing helix  chain 'F' and resid 874 through 883
    Processing helix  chain 'F' and resid 893 through 897
    Processing helix  chain 'G' and resid 4 through 18
    Processing helix  chain 'G' and resid 25 through 34
      removed outlier: 3.741A  pdb=" N   LYS G  34 " --> pdb=" O   ASP G  30 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 57
      removed outlier: 3.674A  pdb=" N   PHE G  56 " --> pdb=" O   LYS G  52 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 59 through 74
      removed outlier: 3.524A  pdb=" N   PHE G  63 " --> pdb=" O   THR G  59 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 77 through 89
      removed outlier: 3.962A  pdb=" N   MET G  89 " --> pdb=" O   LEU G  85 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 116
    Processing helix  chain 'G' and resid 149 through 170
      removed outlier: 3.579A  pdb=" N   SER G 153 " --> pdb=" O   THR G 149 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 178 through 182
    Processing helix  chain 'G' and resid 209 through 225
    Processing helix  chain 'G' and resid 253 through 264
    Processing helix  chain 'G' and resid 264 through 280
    Processing helix  chain 'G' and resid 281 through 284
      removed outlier: 6.202A  pdb=" N   GLU G 284 " --> pdb=" O   SER G 281 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 281 through 284'
    Processing helix  chain 'G' and resid 285 through 316
      removed outlier: 4.275A  pdb=" N   ASN G 289 " --> pdb=" O   TYR G 285 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   GLN G 316 " --> pdb=" O   GLN G 312 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 320 through 349
      removed outlier: 3.636A  pdb=" N   GLN G 329 " --> pdb=" O   TRP G 325 " (cutoff:3.500A)
      Proline residue:  G 330  - end of helix
    Processing helix  chain 'G' and resid 352 through 366
    Processing helix  chain 'G' and resid 369 through 396
      Proline residue:  G 386  - end of helix
    Processing helix  chain 'G' and resid 415 through 422
      removed outlier: 4.323A  pdb=" N   ILE G 419 " --> pdb=" O   ARG G 415 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 440 through 445
      removed outlier: 3.881A  pdb=" N   GLN G 444 " --> pdb=" O   SER G 441 " (cutoff:3.500A)
      removed outlier: 5.090A  pdb=" N   LYS G 445 " --> pdb=" O   PHE G 442 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 446 through 463
      removed outlier: 3.501A  pdb=" N   CYS G 463 " --> pdb=" O   VAL G 459 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 481 through 505
    Processing helix  chain 'G' and resid 508 through 519
    Processing helix  chain 'G' and resid 524 through 540
      removed outlier: 5.466A  pdb=" N   GLU G 537 " --> pdb=" O   ASP G 533 " (cutoff:3.500A)
      removed outlier: 5.625A  pdb=" N   GLU G 538 " --> pdb=" O   LEU G 534 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   LYS G 540 " --> pdb=" O   GLU G 536 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 542 through 546
    Processing helix  chain 'G' and resid 547 through 561
      removed outlier: 3.994A  pdb=" N   LEU G 551 " --> pdb=" O   THR G 547 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 581 through 591
    Processing helix  chain 'G' and resid 604 through 608
    Processing helix  chain 'G' and resid 631 through 662
      removed outlier: 3.628A  pdb=" N   ASN G 662 " --> pdb=" O   VAL G 658 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 663 through 667
      removed outlier: 4.109A  pdb=" N   ARG G 667 " --> pdb=" O   ALA G 664 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 673 through 677
    Processing helix  chain 'G' and resid 678 through 699
      removed outlier: 4.142A  pdb=" N   LEU G 682 " --> pdb=" O   GLY G 678 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 701 through 715
      removed outlier: 3.768A  pdb=" N   ARG G 714 " --> pdb=" O   GLU G 710 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 718 through 737
      removed outlier: 3.537A  pdb=" N   VAL G 722 " --> pdb=" O   ASN G 718 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   CYS G 737 " --> pdb=" O   CYS G 733 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 741 through 772
    Processing helix  chain 'G' and resid 823 through 851
      removed outlier: 3.631A  pdb=" N   ALA G 834 " --> pdb=" O   LYS G 830 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER G 849 " --> pdb=" O   ILE G 845 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 853 through 863
    Processing helix  chain 'G' and resid 865 through 868
      removed outlier: 4.199A  pdb=" N   TYR G 868 " --> pdb=" O   ASN G 865 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 865 through 868'
    Processing helix  chain 'G' and resid 869 through 878
      removed outlier: 3.611A  pdb=" N   GLU G 873 " --> pdb=" O   THR G 869 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLU G 878 " --> pdb=" O   ARG G 874 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 34 through 46
      removed outlier: 3.518A  pdb=" N   GLY X  46 " --> pdb=" O   ALA X  42 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 56 through 63
      removed outlier: 4.206A  pdb=" N   LEU X  60 " --> pdb=" O   ILE X  56 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU X  61 " --> pdb=" O   LEU X  57 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 66 through 80
    Processing helix  chain 'u' and resid 63 through 91
      removed outlier: 4.406A  pdb=" N   LEU u  77 " --> pdb=" O   GLU u  73 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   LYS u  78 " --> pdb=" O   ASN u  74 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   TYR u  82 " --> pdb=" O   LYS u  78 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   GLU u  91 " --> pdb=" O   ARG u  87 " (cutoff:3.500A)
    Processing helix  chain 'v' and resid 59 through 91
      removed outlier: 3.680A  pdb=" N   PHE v  63 " --> pdb=" O   ASN v  59 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLU v  64 " --> pdb=" O   MET v  60 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   GLU v  91 " --> pdb=" O   ARG v  87 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'F' and resid 270 through 272
      removed outlier: 3.527A  pdb=" N   CYS F 277 " --> pdb=" O   SER F 272 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 624 through 628
      removed outlier: 3.760A  pdb=" N   ASP F 644 " --> pdb=" O   ASP F 625 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'G' and resid 233 through 236
      removed outlier: 3.844A  pdb=" N   THR G 245 " --> pdb=" O   GLN G 236 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'G' and resid 409 through 411
    Processing sheet with id=AA5, first strand: chain 'G' and resid 573 through 577

    841 hydrogen bonds defined for protein.
    2472 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: 8.38

  Time building geometry restraints manager: 7.52 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 12434
        1.03 -     1.23: 23
        1.23 -     1.42: 5347
        1.42 -     1.62: 7233
        1.62 -     1.81: 109
  Bond restraints: 25146
  Sorted by residual:
  bond pdb=" CA  ARG G 184 "
       pdb=" CB  ARG G 184 "
    ideal  model  delta    sigma   weight residual
    1.522  1.532 -0.010 7.00e-03 2.04e+04 1.97e+00
  bond pdb=" CA  ARG G 184 "
       pdb=" C   ARG G 184 "
    ideal  model  delta    sigma   weight residual
    1.531  1.523  0.008 7.40e-03 1.83e+04 1.29e+00
  bond pdb=" CB  PRO G 440 "
       pdb=" CG  PRO G 440 "
    ideal  model  delta    sigma   weight residual
    1.492  1.544 -0.052 5.00e-02 4.00e+02 1.09e+00
  bond pdb=" CA  ALA G 673 "
       pdb=" CB  ALA G 673 "
    ideal  model  delta    sigma   weight residual
    1.541  1.530  0.011 1.20e-02 6.94e+03 8.38e-01
  bond pdb=" CA  GLU G 284 "
       pdb=" C   GLU G 284 "
    ideal  model  delta    sigma   weight residual
    1.523  1.534 -0.011 1.34e-02 5.57e+03 7.02e-01
  ... (remaining 25141 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.16: 43261
        1.16 -     2.31: 2027
        2.31 -     3.47: 70
        3.47 -     4.63: 27
        4.63 -     5.78: 5
  Bond angle restraints: 45390
  Sorted by residual:
  angle pdb=" N   ALA G 673 "
        pdb=" CA  ALA G 673 "
        pdb=" CB  ALA G 673 "
      ideal   model   delta    sigma   weight residual
     114.17  110.06    4.11 1.14e+00 7.69e-01 1.30e+01
  angle pdb=" CA  GLU G 284 "
        pdb=" C   GLU G 284 "
        pdb=" N   TYR G 285 "
      ideal   model   delta    sigma   weight residual
     116.84  122.62   -5.78 1.71e+00 3.42e-01 1.14e+01
  angle pdb=" CA  GLU G 284 "
        pdb=" C   GLU G 284 "
        pdb=" O   GLU G 284 "
      ideal   model   delta    sigma   weight residual
     120.51  116.59    3.92 1.43e+00 4.89e-01 7.50e+00
  angle pdb=" N   ASN G  77 "
        pdb=" CA  ASN G  77 "
        pdb=" CB  ASN G  77 "
      ideal   model   delta    sigma   weight residual
     113.65  110.02    3.63 1.47e+00 4.63e-01 6.09e+00
  angle pdb=" N   LEU G 264 "
        pdb=" CA  LEU G 264 "
        pdb=" C   LEU G 264 "
      ideal   model   delta    sigma   weight residual
     109.81  115.25   -5.44 2.21e+00 2.05e-01 6.06e+00
  ... (remaining 45385 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.96: 10879
       16.96 -    33.92: 634
       33.92 -    50.89: 162
       50.89 -    67.85: 60
       67.85 -    84.81: 7
  Dihedral angle restraints: 11742
    sinusoidal: 6377
      harmonic: 5365
  Sorted by residual:
  dihedral pdb=" CA  ASP G 253 "
           pdb=" CB  ASP G 253 "
           pdb=" CG  ASP G 253 "
           pdb=" OD1 ASP G 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.93   57.93     1      2.00e+01 2.50e-03 1.13e+01
  dihedral pdb=" N   ASP G 220 "
           pdb=" CA  ASP G 220 "
           pdb=" CB  ASP G 220 "
           pdb=" CG  ASP G 220 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.06  -59.94     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   ASN G 831 "
           pdb=" CA  ASN G 831 "
           pdb=" CB  ASN G 831 "
           pdb=" CG  ASN G 831 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.59   59.59     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 11739 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1344
       0.028 -    0.056: 427
       0.056 -    0.084: 87
       0.084 -    0.112: 45
       0.112 -    0.140: 11
  Chirality restraints: 1914
  Sorted by residual:
  chirality pdb=" CA  ILE F 474 "
            pdb=" N   ILE F 474 "
            pdb=" C   ILE F 474 "
            pdb=" CB  ILE F 474 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.91e-01
  chirality pdb=" CA  VAL F 626 "
            pdb=" N   VAL F 626 "
            pdb=" C   VAL F 626 "
            pdb=" CB  VAL F 626 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  VAL F 280 "
            pdb=" N   VAL F 280 "
            pdb=" C   VAL F 280 "
            pdb=" CB  VAL F 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.61e-01
  ... (remaining 1911 not shown)

  Planarity restraints: 3657
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP F 376 "    0.030 5.00e-02 4.00e+02   4.51e-02 3.25e+00
        pdb=" N   PRO F 377 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO F 377 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO F 377 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN G 688 "    0.007 2.00e-02 2.50e+03   1.47e-02 2.16e+00
        pdb=" C   ASN G 688 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   ASN G 688 "    0.010 2.00e-02 2.50e+03
        pdb=" N   PHE G 689 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG G 685 "    0.007 2.00e-02 2.50e+03   1.40e-02 1.95e+00
        pdb=" C   ARG G 685 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   ARG G 685 "    0.009 2.00e-02 2.50e+03
        pdb=" N   MET G 686 "    0.008 2.00e-02 2.50e+03
  ... (remaining 3654 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 1154
        2.15 -     2.77: 49287
        2.77 -     3.38: 71626
        3.38 -     3.99: 83656
        3.99 -     4.60: 132179
  Nonbonded interactions: 337902
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU G 538 "
            pdb=" H   GLU G 538 "
     model   vdw
     1.543 2.450
  nonbonded pdb=" OE1 GLU G 537 "
            pdb=" H   GLU G 537 "
     model   vdw
     1.568 2.450
  nonbonded pdb=" OE1 GLU G  93 "
            pdb=" H   GLU G  93 "
     model   vdw
     1.571 2.450
  nonbonded pdb=" OE1 GLU G 536 "
            pdb=" H   GLU G 536 "
     model   vdw
     1.585 2.450
  nonbonded pdb=" OE1 GLU G 413 "
            pdb=" H   GLU G 413 "
     model   vdw
     1.591 2.450
  ... (remaining 337897 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 'u'
  selection = chain 'v'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.390
  Extract box with map and model:          0.900
  Check model and map are aligned:         0.180
  Set scattering table:                    0.220
  Process input model:                     48.860
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   55.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
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      :  0.002   0.052  12689  Z= 0.109
  Angle     :  0.469   5.784  17124  Z= 0.267
  Chirality :  0.032   0.140   1914
  Planarity :  0.003   0.045   2182
  Dihedral  : 11.676  84.808   4757
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  :  7.42 %
    Favored  : 90.31 %
  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:  1.89 (0.23), residues: 1505
  helix:  2.21 (0.16), residues: 1054
  sheet: -1.27 (1.57), residues: 10
  loop : -1.12 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 638 
 HIS   0.003   0.001   HIS G 580 
 PHE   0.010   0.001   PHE F 327 
 TYR   0.010   0.001   TYR G 484 
 ARG   0.003   0.000   ARG G  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12818 (  841)
  hydrogen bonds       : angle       5.35870 ( 2472)
  covalent geometry    : bond        0.00210 (12689)
  covalent geometry    : angle       0.46867 (17124)

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

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

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 202
  time to evaluate  : 1.946 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  292 ASP cc_start: 0.7881 (m-30) cc_final: 0.7674 (m-30)
REVERT: F  299 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8257 (pm20)
REVERT: F  336 ARG cc_start: 0.8841 (tmm160) cc_final: 0.8543 (ttp80)
REVERT: F  371 LEU cc_start: 0.9386 (mp) cc_final: 0.9186 (mm)
REVERT: F  379 MET cc_start: 0.8882 (mtt) cc_final: 0.8649 (tmm)
REVERT: F  605 GLU cc_start: 0.9097 (tp30) cc_final: 0.8894 (tp30)
REVERT: F  708 HIS cc_start: 0.6421 (OUTLIER) cc_final: 0.5911 (m90)
REVERT: F  723 TYR cc_start: 0.8553 (t80) cc_final: 0.7476 (t80)
REVERT: F  797 ARG cc_start: 0.9116 (tpt-90) cc_final: 0.8735 (tpp-160)
REVERT: G   39 TYR cc_start: 0.8503 (p90) cc_final: 0.8068 (p90)
REVERT: G  221 LEU cc_start: 0.9496 (mt) cc_final: 0.9260 (mt)
REVERT: G  238 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6305 (mp)
REVERT: G  698 MET cc_start: 0.7367 (ttp) cc_final: 0.6891 (mmm)
REVERT: G  715 SER cc_start: 0.9669 (m) cc_final: 0.9355 (p)
REVERT: G  864 PHE cc_start: 0.8862 (t80) cc_final: 0.8342 (p90)
REVERT: X   57 LEU cc_start: 0.9143 (mm) cc_final: 0.8900 (tp)
REVERT: v   60 MET cc_start: 0.7994 (ptt) cc_final: 0.7667 (tmm)
  outliers start: 31
  outliers final: 13
  residues processed: 225
  average time/residue: 0.5855
  time to fit residues: 185.4387
Evaluate side-chains
  166 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 151
  time to evaluate  : 1.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    0.9980
   chunk 113 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 76 optimal weight:    0.0980
   chunk 60 optimal weight:    4.9990
   chunk 117 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 87 optimal weight:    2.9990
   chunk 136 optimal weight:    2.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** F 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 329 GLN
G 711 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.068135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.055793 restraints weight = 216136.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.057968 restraints weight = 111134.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.059449 restraints weight = 69390.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  12689  Z= 0.155
  Angle     :  0.559   6.703  17124  Z= 0.310
  Chirality :  0.035   0.137   1914
  Planarity :  0.005   0.077   2182
  Dihedral  :  3.743  17.336   1675
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.22), residues: 1505
  helix:  2.03 (0.16), residues: 1056
  sheet: -1.10 (1.50), residues: 10
  loop : -1.36 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F 638 
 HIS   0.010   0.001   HIS G 580 
 PHE   0.021   0.002   PHE G 832 
 TYR   0.014   0.001   TYR G 327 
 ARG   0.006   0.000   ARG F 675 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04719 (  841)
  hydrogen bonds       : angle       4.63832 ( 2472)
  covalent geometry    : bond        0.00327 (12689)
  covalent geometry    : angle       0.55897 (17124)

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

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

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 2.019 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  292 ASP cc_start: 0.7682 (m-30) cc_final: 0.7478 (m-30)
REVERT: F  299 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8255 (mt-10)
REVERT: F  336 ARG cc_start: 0.8784 (tmm160) cc_final: 0.8489 (ttp80)
REVERT: F  371 LEU cc_start: 0.9502 (mp) cc_final: 0.9282 (mm)
REVERT: F  496 LEU cc_start: 0.9551 (mt) cc_final: 0.9345 (mt)
REVERT: F  605 GLU cc_start: 0.9026 (tp30) cc_final: 0.8795 (tp30)
REVERT: F  797 ARG cc_start: 0.9149 (tpt-90) cc_final: 0.8779 (tpp-160)
REVERT: G   39 TYR cc_start: 0.8170 (p90) cc_final: 0.7811 (p90)
REVERT: G  221 LEU cc_start: 0.9380 (mt) cc_final: 0.9102 (mt)
REVERT: G  258 GLU cc_start: 0.8864 (tt0) cc_final: 0.8446 (tp30)
REVERT: G  446 MET cc_start: 0.8301 (mmm) cc_final: 0.8075 (mmm)
REVERT: G  698 MET cc_start: 0.7965 (ttp) cc_final: 0.7737 (mmm)
REVERT: v   60 MET cc_start: 0.8072 (ptt) cc_final: 0.7678 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.5869
  time to fit residues: 147.2403
Evaluate side-chains
  154 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 2.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 56 optimal weight:    0.0070
   chunk 17 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 128 optimal weight:    3.9990
   chunk 115 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 144 optimal weight:    6.9990
   overall best weight:    3.0006

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

Flipped N/Q/H residues before XYZ refinement:
F 597 GLN
** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 329 GLN
G 458 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.066596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.054353 restraints weight = 220781.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.056434 restraints weight = 113626.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.057833 restraints weight = 71425.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.2404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  12689  Z= 0.257
  Angle     :  0.577   5.740  17124  Z= 0.335
  Chirality :  0.035   0.168   1914
  Planarity :  0.005   0.054   2182
  Dihedral  :  3.912  16.285   1675
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.22), residues: 1505
  helix:  1.68 (0.16), residues: 1058
  sheet: -3.67 (1.05), residues: 12
  loop : -1.81 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 638 
 HIS   0.008   0.001   HIS G 580 
 PHE   0.017   0.002   PHE G 326 
 TYR   0.029   0.002   TYR G 427 
 ARG   0.007   0.000   ARG G 415 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04593 (  841)
  hydrogen bonds       : angle       4.80250 ( 2472)
  covalent geometry    : bond        0.00494 (12689)
  covalent geometry    : angle       0.57697 (17124)

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

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

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 2.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  299 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8176 (mt-10)
REVERT: F  496 LEU cc_start: 0.9582 (mt) cc_final: 0.9298 (mt)
REVERT: F  797 ARG cc_start: 0.9170 (tpt-90) cc_final: 0.8805 (tpp-160)
REVERT: G   39 TYR cc_start: 0.8240 (p90) cc_final: 0.7878 (p90)
REVERT: G  561 MET cc_start: 0.8088 (tmm) cc_final: 0.7699 (tmm)
REVERT: G  769 MET cc_start: 0.8146 (tmm) cc_final: 0.7945 (tmm)
REVERT: u   65 ASN cc_start: 0.9364 (p0) cc_final: 0.8763 (p0)
REVERT: v   60 MET cc_start: 0.8049 (ptt) cc_final: 0.7689 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.5803
  time to fit residues: 136.7607
Evaluate side-chains
  141 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 2.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 118 optimal weight:    5.9990
   chunk 26 optimal weight:    0.6980
   chunk 57 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.067280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.054966 restraints weight = 218264.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.057108 restraints weight = 111902.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.058571 restraints weight = 69684.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  12689  Z= 0.142
  Angle     :  0.516   5.379  17124  Z= 0.289
  Chirality :  0.034   0.158   1914
  Planarity :  0.004   0.077   2182
  Dihedral  :  3.874  17.456   1675
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.22), residues: 1505
  helix:  1.82 (0.16), residues: 1062
  sheet: -3.46 (1.15), residues: 12
  loop : -1.63 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 463 
 HIS   0.006   0.001   HIS G 580 
 PHE   0.025   0.002   PHE G 828 
 TYR   0.013   0.001   TYR G 494 
 ARG   0.004   0.000   ARG F 415 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04208 (  841)
  hydrogen bonds       : angle       4.45860 ( 2472)
  covalent geometry    : bond        0.00301 (12689)
  covalent geometry    : angle       0.51637 (17124)

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

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

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 1.857 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  299 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8101 (mt-10)
REVERT: F  677 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8903 (tm-30)
REVERT: F  723 TYR cc_start: 0.8007 (t80) cc_final: 0.7204 (t80)
REVERT: F  797 ARG cc_start: 0.9123 (tpt-90) cc_final: 0.8771 (tpp-160)
REVERT: G   39 TYR cc_start: 0.8248 (p90) cc_final: 0.8040 (p90)
REVERT: G  408 MET cc_start: 0.8237 (mmp) cc_final: 0.7888 (mmp)
REVERT: G  561 MET cc_start: 0.8057 (tmm) cc_final: 0.7541 (tmm)
REVERT: G  769 MET cc_start: 0.8181 (tmm) cc_final: 0.7976 (tmm)
REVERT: u   65 ASN cc_start: 0.9358 (p0) cc_final: 0.8722 (p0)
REVERT: v   60 MET cc_start: 0.8202 (ptt) cc_final: 0.7776 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.5460
  time to fit residues: 131.1280
Evaluate side-chains
  145 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 119 optimal weight:    2.9990
   chunk 140 optimal weight:    0.0870
   chunk 39 optimal weight:    2.9990
   chunk 146 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 141 optimal weight:    3.9990
   chunk 126 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 133 optimal weight:    0.9980
   overall best weight:    1.8164

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

Flipped N/Q/H residues before XYZ refinement:
** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.067053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.054605 restraints weight = 220093.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.056766 restraints weight = 111345.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.058220 restraints weight = 69111.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  12689  Z= 0.179
  Angle     :  0.522   5.458  17124  Z= 0.295
  Chirality :  0.034   0.130   1914
  Planarity :  0.004   0.047   2182
  Dihedral  :  3.847  15.978   1675
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.20 (0.22), residues: 1505
  helix:  1.76 (0.16), residues: 1069
  sheet: -1.65 (1.28), residues: 10
  loop : -1.71 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 638 
 HIS   0.007   0.001   HIS G 580 
 PHE   0.014   0.001   PHE G 326 
 TYR   0.022   0.001   TYR G 427 
 ARG   0.004   0.000   ARG G 415 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04132 (  841)
  hydrogen bonds       : angle       4.46151 ( 2472)
  covalent geometry    : bond        0.00363 (12689)
  covalent geometry    : angle       0.52197 (17124)

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

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

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 1.877 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  299 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8149 (mt-10)
REVERT: F  723 TYR cc_start: 0.8056 (t80) cc_final: 0.7292 (t80)
REVERT: F  797 ARG cc_start: 0.9130 (tpt-90) cc_final: 0.8796 (tpp-160)
REVERT: G   39 TYR cc_start: 0.8161 (p90) cc_final: 0.7958 (p90)
REVERT: G  769 MET cc_start: 0.8163 (tmm) cc_final: 0.7962 (tmm)
REVERT: u   65 ASN cc_start: 0.9328 (p0) cc_final: 0.8692 (p0)
REVERT: v   60 MET cc_start: 0.8189 (ptt) cc_final: 0.7769 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.5488
  time to fit residues: 128.1259
Evaluate side-chains
  138 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 1.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 119 optimal weight:    0.5980
   chunk 111 optimal weight:    0.7980
   chunk 114 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 127 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 118 optimal weight:    0.6980
   chunk 142 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.067888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.055358 restraints weight = 214970.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.057532 restraints weight = 107922.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.059043 restraints weight = 66972.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.2882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  12689  Z= 0.123
  Angle     :  0.503   5.333  17124  Z= 0.276
  Chirality :  0.034   0.133   1914
  Planarity :  0.004   0.047   2182
  Dihedral  :  3.792  17.487   1675
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  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:  1.42 (0.22), residues: 1505
  helix:  1.91 (0.16), residues: 1064
  sheet: -1.38 (1.44), residues: 10
  loop : -1.54 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP G 394 
 HIS   0.005   0.001   HIS G 580 
 PHE   0.029   0.001   PHE G 828 
 TYR   0.026   0.001   TYR G 427 
 ARG   0.003   0.000   ARG F 318 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03987 (  841)
  hydrogen bonds       : angle       4.26418 ( 2472)
  covalent geometry    : bond        0.00271 (12689)
  covalent geometry    : angle       0.50297 (17124)

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

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

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 2.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  292 ASP cc_start: 0.8008 (m-30) cc_final: 0.7805 (m-30)
REVERT: F  299 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8257 (mt-10)
REVERT: F  481 ASP cc_start: 0.9470 (m-30) cc_final: 0.9087 (p0)
REVERT: F  723 TYR cc_start: 0.8032 (t80) cc_final: 0.7264 (t80)
REVERT: F  797 ARG cc_start: 0.9127 (tpt-90) cc_final: 0.8789 (tpp-160)
REVERT: G  769 MET cc_start: 0.8157 (tmm) cc_final: 0.7952 (tmm)
REVERT: u   65 ASN cc_start: 0.9312 (p0) cc_final: 0.8683 (p0)
REVERT: v   60 MET cc_start: 0.8182 (ptt) cc_final: 0.7756 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.5690
  time to fit residues: 139.3130
Evaluate side-chains
  145 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 139 optimal weight:    4.9990
   chunk 123 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 71 optimal weight:   10.0000
   chunk 54 optimal weight:   30.0000
   chunk 80 optimal weight:    0.8980
   chunk 101 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 100 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.067381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.054811 restraints weight = 216737.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.056999 restraints weight = 109398.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.058508 restraints weight = 67555.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.2955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12689  Z= 0.155
  Angle     :  0.505   5.386  17124  Z= 0.283
  Chirality :  0.034   0.133   1914
  Planarity :  0.004   0.046   2182
  Dihedral  :  3.767  16.147   1675
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  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:  1.32 (0.22), residues: 1505
  helix:  1.84 (0.16), residues: 1073
  sheet: -1.56 (1.26), residues: 10
  loop : -1.67 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G 180 
 HIS   0.005   0.001   HIS F 754 
 PHE   0.015   0.001   PHE G 832 
 TYR   0.022   0.001   TYR G 404 
 ARG   0.003   0.000   ARG F 318 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03886 (  841)
  hydrogen bonds       : angle       4.33109 ( 2472)
  covalent geometry    : bond        0.00319 (12689)
  covalent geometry    : angle       0.50510 (17124)

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

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

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 1.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  292 ASP cc_start: 0.8040 (m-30) cc_final: 0.7837 (m-30)
REVERT: F  299 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8287 (mt-10)
REVERT: F  481 ASP cc_start: 0.9438 (m-30) cc_final: 0.9020 (p0)
REVERT: F  797 ARG cc_start: 0.9103 (tpt-90) cc_final: 0.8791 (tpp-160)
REVERT: G   39 TYR cc_start: 0.8185 (p90) cc_final: 0.7882 (p90)
REVERT: G  408 MET cc_start: 0.8268 (mmp) cc_final: 0.7793 (mmp)
REVERT: G  715 SER cc_start: 0.9539 (m) cc_final: 0.9196 (p)
REVERT: u   65 ASN cc_start: 0.9283 (p0) cc_final: 0.8680 (p0)
REVERT: v   60 MET cc_start: 0.8188 (ptt) cc_final: 0.7778 (tmm)
REVERT: v   78 LYS cc_start: 0.9047 (mmpt) cc_final: 0.8703 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.5615
  time to fit residues: 134.0255
Evaluate side-chains
  146 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 2.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 100 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   chunk 118 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 116 optimal weight:    1.9990
   chunk 133 optimal weight:    1.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.067541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.054989 restraints weight = 216327.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.057192 restraints weight = 108789.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.058696 restraints weight = 67261.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.3077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  12689  Z= 0.140
  Angle     :  0.502   5.748  17124  Z= 0.280
  Chirality :  0.033   0.125   1914
  Planarity :  0.004   0.047   2182
  Dihedral  :  3.768  15.672   1675
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  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:  1.37 (0.22), residues: 1505
  helix:  1.87 (0.16), residues: 1072
  sheet: -1.44 (1.34), residues: 10
  loop : -1.63 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 638 
 HIS   0.005   0.001   HIS F 687 
 PHE   0.030   0.001   PHE G 828 
 TYR   0.020   0.001   TYR G 404 
 ARG   0.003   0.000   ARG F 318 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03841 (  841)
  hydrogen bonds       : angle       4.30103 ( 2472)
  covalent geometry    : bond        0.00294 (12689)
  covalent geometry    : angle       0.50229 (17124)

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

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

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 2.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  292 ASP cc_start: 0.8046 (m-30) cc_final: 0.7844 (m-30)
REVERT: F  299 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8266 (mt-10)
REVERT: F  481 ASP cc_start: 0.9472 (m-30) cc_final: 0.9076 (p0)
REVERT: F  496 LEU cc_start: 0.9617 (mt) cc_final: 0.9400 (mt)
REVERT: F  581 MET cc_start: 0.8877 (ttt) cc_final: 0.8661 (ttt)
REVERT: F  723 TYR cc_start: 0.8020 (t80) cc_final: 0.7217 (t80)
REVERT: F  797 ARG cc_start: 0.9105 (tpt-90) cc_final: 0.8793 (tpp-160)
REVERT: G   39 TYR cc_start: 0.8164 (p90) cc_final: 0.7855 (p90)
REVERT: G  715 SER cc_start: 0.9496 (m) cc_final: 0.9099 (p)
REVERT: v   60 MET cc_start: 0.8187 (ptt) cc_final: 0.7769 (tmm)
REVERT: v   78 LYS cc_start: 0.9078 (mmpt) cc_final: 0.8685 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.5516
  time to fit residues: 128.9441
Evaluate side-chains
  144 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 2.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 118 optimal weight:    3.9990
   chunk 82 optimal weight:    0.3980
   chunk 120 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 128 optimal weight:    6.9990
   chunk 9 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.067091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.054736 restraints weight = 218474.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.056891 restraints weight = 111784.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.058329 restraints weight = 69794.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.3132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12689  Z= 0.159
  Angle     :  0.510   5.657  17124  Z= 0.285
  Chirality :  0.034   0.131   1914
  Planarity :  0.005   0.095   2182
  Dihedral  :  3.774  15.908   1675
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  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:  1.28 (0.22), residues: 1505
  helix:  1.81 (0.16), residues: 1074
  sheet: -1.57 (1.26), residues: 10
  loop : -1.71 (0.29), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP G 180 
 HIS   0.005   0.001   HIS F 687 
 PHE   0.022   0.001   PHE F 839 
 TYR   0.017   0.001   TYR G 404 
 ARG   0.004   0.000   ARG F 415 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03834 (  841)
  hydrogen bonds       : angle       4.30808 ( 2472)
  covalent geometry    : bond        0.00329 (12689)
  covalent geometry    : angle       0.50970 (17124)

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

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

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 2.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  250 GLU cc_start: 0.7987 (tp30) cc_final: 0.7581 (tp30)
REVERT: F  292 ASP cc_start: 0.8048 (m-30) cc_final: 0.7846 (m-30)
REVERT: F  299 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8259 (mt-10)
REVERT: F  481 ASP cc_start: 0.9412 (m-30) cc_final: 0.9005 (p0)
REVERT: F  496 LEU cc_start: 0.9621 (mt) cc_final: 0.9405 (mt)
REVERT: F  723 TYR cc_start: 0.8056 (t80) cc_final: 0.7285 (t80)
REVERT: F  797 ARG cc_start: 0.9092 (tpt-90) cc_final: 0.8790 (tpp-160)
REVERT: G   39 TYR cc_start: 0.8177 (p90) cc_final: 0.7859 (p90)
REVERT: G  258 GLU cc_start: 0.8953 (tt0) cc_final: 0.8274 (tp30)
REVERT: G  715 SER cc_start: 0.9492 (m) cc_final: 0.9090 (p)
REVERT: X   70 VAL cc_start: 0.9007 (m) cc_final: 0.8768 (m)
REVERT: v   60 MET cc_start: 0.8185 (ptt) cc_final: 0.7864 (tmm)
REVERT: v   78 LYS cc_start: 0.9040 (mmpt) cc_final: 0.8690 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.5410
  time to fit residues: 128.8444
Evaluate side-chains
  146 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 1.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   chunk 108 optimal weight:    0.7980
   chunk 131 optimal weight:    0.6980
   chunk 48 optimal weight:    4.9990
   chunk 115 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 117 optimal weight:    0.5980
   chunk 118 optimal weight:    3.9990
   chunk 97 optimal weight:    0.2980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.067826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.055459 restraints weight = 214590.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.057588 restraints weight = 108697.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.059063 restraints weight = 67881.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.3159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  12689  Z= 0.112
  Angle     :  0.498   6.025  17124  Z= 0.272
  Chirality :  0.033   0.130   1914
  Planarity :  0.004   0.076   2182
  Dihedral  :  3.715  15.384   1675
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.54 (0.22), residues: 1505
  helix:  2.00 (0.16), residues: 1068
  sheet: -1.28 (1.42), residues: 10
  loop : -1.52 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 638 
 HIS   0.004   0.001   HIS G 580 
 PHE   0.021   0.001   PHE G 828 
 TYR   0.017   0.001   TYR G 404 
 ARG   0.004   0.000   ARG G 871 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03706 (  841)
  hydrogen bonds       : angle       4.13846 ( 2472)
  covalent geometry    : bond        0.00247 (12689)
  covalent geometry    : angle       0.49794 (17124)

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

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

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3010 Ramachandran restraints generated.
    1505 Oldfield, 0 Emsley, 1505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 2.690 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  250 GLU cc_start: 0.7794 (tp30) cc_final: 0.7523 (tp30)
REVERT: F  292 ASP cc_start: 0.8064 (m-30) cc_final: 0.7851 (m-30)
REVERT: F  299 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8212 (mt-10)
REVERT: F  481 ASP cc_start: 0.9439 (m-30) cc_final: 0.9062 (p0)
REVERT: F  581 MET cc_start: 0.8883 (ttt) cc_final: 0.8643 (ttt)
REVERT: F  723 TYR cc_start: 0.8021 (t80) cc_final: 0.7221 (t80)
REVERT: F  797 ARG cc_start: 0.9080 (tpt-90) cc_final: 0.8775 (tpp-160)
REVERT: G   39 TYR cc_start: 0.8069 (p90) cc_final: 0.7741 (p90)
REVERT: G  258 GLU cc_start: 0.8906 (tt0) cc_final: 0.8338 (tp30)
REVERT: G  446 MET cc_start: 0.8418 (mmm) cc_final: 0.8054 (mmm)
REVERT: G  715 SER cc_start: 0.9475 (m) cc_final: 0.9076 (p)
REVERT: X   70 VAL cc_start: 0.8860 (m) cc_final: 0.8656 (m)
REVERT: v   60 MET cc_start: 0.8230 (ptt) cc_final: 0.7883 (tmm)
REVERT: v   78 LYS cc_start: 0.9024 (mmpt) cc_final: 0.8685 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.5553
  time to fit residues: 131.9996
Evaluate side-chains
  147 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 105 optimal weight:    0.7980
   chunk 138 optimal weight:    3.9990
   chunk 92 optimal weight:    4.9990
   chunk 132 optimal weight:    4.9990
   chunk 137 optimal weight:    1.9990
   chunk 148 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0670
   chunk 147 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.067957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.055304 restraints weight = 216270.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.057589 restraints weight = 108355.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.059114 restraints weight = 66635.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.3202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  12689  Z= 0.112
  Angle     :  0.497   6.286  17124  Z= 0.270
  Chirality :  0.033   0.138   1914
  Planarity :  0.004   0.067   2182
  Dihedral  :  3.664  15.277   1675
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.61 (0.22), residues: 1505
  helix:  2.03 (0.16), residues: 1070
  sheet: -1.02 (1.49), residues: 10
  loop : -1.48 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP G 180 
 HIS   0.004   0.001   HIS G 580 
 PHE   0.020   0.001   PHE G 828 
 TYR   0.015   0.001   TYR G 404 
 ARG   0.004   0.000   ARG G 871 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03636 (  841)
  hydrogen bonds       : angle       4.08682 ( 2472)
  covalent geometry    : bond        0.00244 (12689)
  covalent geometry    : angle       0.49694 (17124)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7108.62 seconds
wall clock time: 123 minutes 45.52 seconds (7425.52 seconds total)