Starting phenix.real_space_refine
on Wed Feb  4 13:08:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qim_53190/02_2026/9qim_53190_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qim_53190/02_2026/9qim_53190.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qim_53190/02_2026/9qim_53190.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qim_53190/02_2026/9qim_53190.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qim_53190/02_2026/9qim_53190_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qim_53190/02_2026/9qim_53190_neut.cif"
  }
  resolution = 3.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     S      50      5.16       5
     C    6623      2.51       5
     N    1760      2.21       5
     O    1991      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10433
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2346
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2346
          Classifications: {'peptide': 293}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 275}
    Chain: "B"
      Number of atoms: 8020
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1012, 8020
          Classifications: {'peptide': 1012}
          Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 50, 'TRANS': 956}
    Chain: "B"
      Number of atoms: 67
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 67
          Unusual residues: {'ATP': 1, 'IHP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.12, per 1000 atoms: 0.20
  Number of scatterers: 10433
  At special positions: 0
  Unit cell: (82.5, 104.775, 134.475, 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      50     16.00
     P       9     15.00
     O    1991      8.00
     N    1760      7.00
     C    6623      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.94
  Conformation dependent library (CDL) restraints added in 526.2 milliseconds
  

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2484

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 9 sheets defined
      50.0% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4522 through 4534
      removed outlier: 4.085A  pdb=" N   LYS A4534 " --> pdb=" O   ALA A4530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4559 through 4566
    Processing helix  chain 'A' and resid 4571 through 4589
      removed outlier: 3.567A  pdb=" N   ALA A4575 " --> pdb=" O   SER A4571 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LEU A4578 " --> pdb=" O   ARG A4574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4676 through 4680
    Processing helix  chain 'A' and resid 4687 through 4699
    Processing helix  chain 'A' and resid 4703 through 4708
      removed outlier: 3.619A  pdb=" N   GLU A4708 " --> pdb=" O   TYR A4705 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4711 through 4715
    Processing helix  chain 'A' and resid 4717 through 4738
    Processing helix  chain 'A' and resid 4740 through 4746
    Processing helix  chain 'A' and resid 4748 through 4750
      No H-bonds generated for 'chain 'A' and resid 4748 through 4750'
    Processing helix  chain 'A' and resid 4751 through 4779
      removed outlier: 5.406A  pdb=" N   VAL A4764 " --> pdb=" O   TYR A4760 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   GLU A4765 " --> pdb=" O   LEU A4761 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLN A4779 " --> pdb=" O   ALA A4775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4786 through 4811
    Processing helix  chain 'B' and resid 40 through 52
      removed outlier: 6.978A  pdb=" N   ARG B  46 " --> pdb=" O   ALA B  42 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   GLN B  47 " --> pdb=" O   LEU B  43 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   VAL B  50 " --> pdb=" O   ARG B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 60
      removed outlier: 3.550A  pdb=" N   LYS B  58 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 84
    Processing helix  chain 'B' and resid 97 through 103
      removed outlier: 3.503A  pdb=" N   GLY B 102 " --> pdb=" O   TRP B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 115
    Processing helix  chain 'B' and resid 117 through 128
      removed outlier: 3.548A  pdb=" N   VAL B 122 " --> pdb=" O   ARG B 118 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   LYS B 124 " --> pdb=" O   GLU B 120 " (cutoff:3.500A)
      removed outlier: 5.262A  pdb=" N   HIS B 125 " --> pdb=" O   ALA B 121 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   GLU B 128 " --> pdb=" O   LYS B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 154
      removed outlier: 3.861A  pdb=" N   LYS B 153 " --> pdb=" O   PHE B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 163 through 176
      removed outlier: 3.686A  pdb=" N   SER B 176 " --> pdb=" O   ASP B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 257
    Processing helix  chain 'B' and resid 301 through 306
    Processing helix  chain 'B' and resid 320 through 340
    Processing helix  chain 'B' and resid 347 through 365
      removed outlier: 3.526A  pdb=" N   GLU B 363 " --> pdb=" O   THR B 359 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   THR B 364 " --> pdb=" O   SER B 360 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LEU B 365 " --> pdb=" O   ILE B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 382
    Processing helix  chain 'B' and resid 387 through 408
    Processing helix  chain 'B' and resid 421 through 427
      removed outlier: 4.191A  pdb=" N   VAL B 425 " --> pdb=" O   ALA B 421 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   SER B 427 " --> pdb=" O   ASP B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 436
    Processing helix  chain 'B' and resid 443 through 451
      removed outlier: 3.726A  pdb=" N   CYS B 449 " --> pdb=" O   ALA B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 460
    Processing helix  chain 'B' and resid 469 through 483
    Processing helix  chain 'B' and resid 502 through 508
      removed outlier: 3.553A  pdb=" N   ASN B 507 " --> pdb=" O   SER B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 517
    Processing helix  chain 'B' and resid 520 through 533
      removed outlier: 3.645A  pdb=" N   LEU B 530 " --> pdb=" O   ALA B 526 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   LYS B 531 " --> pdb=" O   ASP B 527 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ILE B 532 " --> pdb=" O   ALA B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 546 through 550
    Processing helix  chain 'B' and resid 554 through 561
    Processing helix  chain 'B' and resid 571 through 585
    Processing helix  chain 'B' and resid 610 through 614
    Processing helix  chain 'B' and resid 623 through 629
    Processing helix  chain 'B' and resid 633 through 650
      removed outlier: 3.593A  pdb=" N   THR B 637 " --> pdb=" O   ALA B 633 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 650 through 663
    Processing helix  chain 'B' and resid 665 through 675
    Processing helix  chain 'B' and resid 681 through 691
    Processing helix  chain 'B' and resid 695 through 712
    Processing helix  chain 'B' and resid 712 through 722
    Processing helix  chain 'B' and resid 751 through 769
    Processing helix  chain 'B' and resid 774 through 778
    Processing helix  chain 'B' and resid 779 through 788
    Processing helix  chain 'B' and resid 817 through 834
    Processing helix  chain 'B' and resid 857 through 873
    Processing helix  chain 'B' and resid 879 through 888
    Processing helix  chain 'B' and resid 894 through 915
      removed outlier: 3.545A  pdb=" N   THR B 898 " --> pdb=" O   ILE B 894 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS B 911 " --> pdb=" O   LEU B 907 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 917 through 920
    Processing helix  chain 'B' and resid 967 through 980
    Processing helix  chain 'B' and resid 1000 through 1006
      removed outlier: 3.618A  pdb=" N   LYS B1003 " --> pdb=" O   GLY B1000 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1008 through 1014
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4537 through 4540
      removed outlier: 3.765A  pdb=" N   SER A4596 " --> pdb=" O   THR A4614 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ASP A4602 " --> pdb=" O   ILE A4608 " (cutoff:3.500A)
      removed outlier: 7.260A  pdb=" N   ILE A4608 " --> pdb=" O   ASP A4602 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 4543 through 4545
    Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 138
      removed outlier: 6.246A  pdb=" N   VAL B  88 " --> pdb=" O   THR B 136 " (cutoff:3.500A)
      removed outlier: 7.627A  pdb=" N   SER B 138 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ILE B  90 " --> pdb=" O   SER B 138 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   VAL B  64 " --> pdb=" O   THR B  89 " (cutoff:3.500A)
      removed outlier: 7.741A  pdb=" N   HIS B  91 " --> pdb=" O   VAL B  64 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   LEU B  66 " --> pdb=" O   HIS B  91 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   HIS B  63 " --> pdb=" O   CYS B 156 " (cutoff:3.500A)
      removed outlier: 8.247A  pdb=" N   VAL B 158 " --> pdb=" O   HIS B  63 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   PHE B  65 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   THR B 160 " --> pdb=" O   PHE B  65 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   SER B  67 " --> pdb=" O   THR B 160 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 202 through 205
    Processing sheet with id=AA5, first strand: chain 'B' and resid 260 through 262
      removed outlier: 4.793A  pdb=" N   PHE B 244 " --> pdb=" O   VAL B 291 " (cutoff:3.500A)
      removed outlier: 5.767A  pdb=" N   ILE B 250 " --> pdb=" O   GLY B 285 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   GLY B 285 " --> pdb=" O   ILE B 250 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   GLY B 286 " --> pdb=" O   ILE B 218 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   SER B 272 " --> pdb=" O   VAL B 265 " (cutoff:3.500A)
      removed outlier: 5.545A  pdb=" N   VAL B 265 " --> pdb=" O   SER B 272 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 538 through 541
      removed outlier: 6.210A  pdb=" N   ILE B 493 " --> pdb=" O   ASP B 539 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   HIS B 541 " --> pdb=" O   ILE B 493 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   VAL B 495 " --> pdb=" O   HIS B 541 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   SER B 591 " --> pdb=" O   THR B 566 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   VAL B 602 " --> pdb=" O   LYS B 922 " (cutoff:3.500A)
      removed outlier: 7.386A  pdb=" N   LYS B 922 " --> pdb=" O   VAL B 602 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 944 through 947
      removed outlier: 6.802A  pdb=" N   ILE B 950 " --> pdb=" O   ILE B 946 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 958 through 961
      removed outlier: 6.505A  pdb=" N   TRP B 958 " --> pdb=" O   ARG B1044 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   TYR B1046 " --> pdb=" O   TRP B 958 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   VAL B 960 " --> pdb=" O   TYR B1046 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   SER B1027 " --> pdb=" O   MET B 985 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   MET B 985 " --> pdb=" O   SER B1027 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   VAL B 986 " --> pdb=" O   LEU B 993 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 958 through 961
      removed outlier: 6.505A  pdb=" N   TRP B 958 " --> pdb=" O   ARG B1044 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   TYR B1046 " --> pdb=" O   TRP B 958 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   VAL B 960 " --> pdb=" O   TYR B1046 " (cutoff:3.500A)

    512 hydrogen bonds defined for protein.
    1404 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.00

  Time building geometry restraints manager: 1.25 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3392
        1.34 -     1.46: 2035
        1.46 -     1.58: 5164
        1.58 -     1.69: 11
        1.69 -     1.81: 73
  Bond restraints: 10675
  Sorted by residual:
  bond pdb=" C1' ATP B1102 "
       pdb=" O4' ATP B1102 "
    ideal  model  delta    sigma   weight residual
    1.416  1.404  0.012 1.30e-02 5.92e+03 7.84e-01
  bond pdb=" C   ILE B 930 "
       pdb=" N   PRO B 931 "
    ideal  model  delta    sigma   weight residual
    1.338  1.352 -0.014 1.90e-02 2.77e+03 5.31e-01
  bond pdb=" CB  MET A4790 "
       pdb=" CG  MET A4790 "
    ideal  model  delta    sigma   weight residual
    1.520  1.502  0.018 3.00e-02 1.11e+03 3.77e-01
  bond pdb=" C   GLU A4726 "
       pdb=" O   GLU A4726 "
    ideal  model  delta    sigma   weight residual
    1.236  1.243 -0.007 1.15e-02 7.56e+03 3.64e-01
  bond pdb=" C2' ATP B1102 "
       pdb=" C3' ATP B1102 "
    ideal  model  delta    sigma   weight residual
    1.531  1.538 -0.007 1.20e-02 6.94e+03 3.45e-01
  ... (remaining 10670 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 14388
        2.03 -     4.05: 96
        4.05 -     6.08: 6
        6.08 -     8.10: 0
        8.10 -    10.13: 1
  Bond angle restraints: 14491
  Sorted by residual:
  angle pdb=" CA  LEU B 828 "
        pdb=" CB  LEU B 828 "
        pdb=" CG  LEU B 828 "
      ideal   model   delta    sigma   weight residual
     116.30  126.43  -10.13 3.50e+00 8.16e-02 8.37e+00
  angle pdb=" C2' ATP B1102 "
        pdb=" C3' ATP B1102 "
        pdb=" C4' ATP B1102 "
      ideal   model   delta    sigma   weight residual
     102.49  104.34   -1.85 1.00e+00 1.00e+00 3.43e+00
  angle pdb=" C1' ATP B1102 "
        pdb=" O4' ATP B1102 "
        pdb=" C4' ATP B1102 "
      ideal   model   delta    sigma   weight residual
     109.40  106.58    2.82 1.61e+00 3.87e-01 3.08e+00
  angle pdb=" C   ILE B 930 "
        pdb=" N   PRO B 931 "
        pdb=" CA  PRO B 931 "
      ideal   model   delta    sigma   weight residual
     127.00  131.03   -4.03 2.40e+00 1.74e-01 2.82e+00
  angle pdb=" C3  IHP B1101 "
        pdb=" C4  IHP B1101 "
        pdb=" C5  IHP B1101 "
      ideal   model   delta    sigma   weight residual
     107.91  112.90   -4.99 3.00e+00 1.11e-01 2.77e+00
  ... (remaining 14486 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.12: 6136
       17.12 -    34.24: 302
       34.24 -    51.36: 52
       51.36 -    68.48: 19
       68.48 -    85.60: 4
  Dihedral angle restraints: 6513
    sinusoidal: 2689
      harmonic: 3824
  Sorted by residual:
  dihedral pdb=" CA  LYS B 922 "
           pdb=" C   LYS B 922 "
           pdb=" N   ASN B 923 "
           pdb=" CA  ASN B 923 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.61   15.39     0      5.00e+00 4.00e-02 9.47e+00
  dihedral pdb=" CA  GLU B 435 "
           pdb=" CB  GLU B 435 "
           pdb=" CG  GLU B 435 "
           pdb=" CD  GLU B 435 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -123.47  -56.53     3      1.50e+01 4.44e-03 9.40e+00
  dihedral pdb=" CB  MET A4790 "
           pdb=" CG  MET A4790 "
           pdb=" SD  MET A4790 "
           pdb=" CE  MET A4790 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  112.56  -52.56     3      1.50e+01 4.44e-03 9.13e+00
  ... (remaining 6510 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1028
       0.029 -    0.057: 381
       0.057 -    0.086: 113
       0.086 -    0.114: 85
       0.114 -    0.143: 12
  Chirality restraints: 1619
  Sorted by residual:
  chirality pdb=" CA  ILE B 622 "
            pdb=" N   ILE B 622 "
            pdb=" C   ILE B 622 "
            pdb=" CB  ILE B 622 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.08e-01
  chirality pdb=" CA  ILE B 493 "
            pdb=" N   ILE B 493 "
            pdb=" C   ILE B 493 "
            pdb=" CB  ILE B 493 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.16e-01
  chirality pdb=" CA  VAL B 814 "
            pdb=" N   VAL B 814 "
            pdb=" C   VAL B 814 "
            pdb=" CB  VAL B 814 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.99e-01
  ... (remaining 1616 not shown)

  Planarity restraints: 1858
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 267 "   -0.025 5.00e-02 4.00e+02   3.82e-02 2.34e+00
        pdb=" N   PRO B 268 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO B 268 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 268 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A4656 "   -0.025 5.00e-02 4.00e+02   3.73e-02 2.22e+00
        pdb=" N   PRO A4657 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A4657 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A4657 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 497 "   -0.020 5.00e-02 4.00e+02   3.05e-02 1.49e+00
        pdb=" N   PRO B 498 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO B 498 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 498 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1855 not shown)

  Histogram of nonbonded interaction distances:
        2.57 -     3.03: 6439
        3.03 -     3.50: 10769
        3.50 -     3.97: 17221
        3.97 -     4.43: 20180
        4.43 -     4.90: 31116
  Nonbonded interactions: 85725
  Sorted by model distance:
  nonbonded pdb=" N   THR A4647 "
            pdb=" OG1 THR A4647 "
     model   vdw
     2.568 2.496
  nonbonded pdb=" O2' ATP B1102 "
            pdb=" O3' ATP B1102 "
     model   vdw
     2.593 2.432
  nonbonded pdb=" N   PHE B 271 "
            pdb=" O   PHE B 271 "
     model   vdw
     2.621 2.496
  nonbonded pdb=" N   SER B 267 "
            pdb=" O   SER B 267 "
     model   vdw
     2.629 2.496
  nonbonded pdb=" N   CYS B 546 "
            pdb=" O   CYS B 546 "
     model   vdw
     2.631 2.496
  ... (remaining 85720 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.300
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8645
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   0.018  10675  Z= 0.096
  Angle     :  0.438  10.125  14491  Z= 0.230
  Chirality :  0.039   0.143   1619
  Planarity :  0.003   0.038   1858
  Dihedral  : 11.005  85.600   4029
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.20 %
    Favored  : 96.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.24), residues: 1301
  helix:  1.89 (0.22), residues: 571
  sheet:  1.14 (0.38), residues: 189
  loop :  0.85 (0.28), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A4805 
 TYR   0.009   0.001   TYR A4621 
 PHE   0.014   0.001   PHE B 656 
 TRP   0.009   0.001   TRP B 660 
 HIS   0.002   0.000   HIS A4793 

Details of bonding type rmsd
  covalent geometry    : bond        0.00194 (10675)
  covalent geometry    : angle       0.43788 (14491)
  hydrogen bonds       : bond        0.15154 (  508)
  hydrogen bonds       : angle       6.11318 ( 1404)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4542 MET cc_start: 0.9481 (mtt) cc_final: 0.9143 (mpp)
REVERT: A 4740 MET cc_start: 0.9638 (mtt) cc_final: 0.9273 (mpp)
REVERT: B  253 MET cc_start: 0.8240 (mtt) cc_final: 0.7979 (mtt)
REVERT: B  992 MET cc_start: 0.8732 (ttp) cc_final: 0.8062 (tmm)
REVERT: B  993 LEU cc_start: 0.9506 (tt) cc_final: 0.9271 (tt)
REVERT: B 1009 MET cc_start: 0.9433 (mmm) cc_final: 0.8933 (mmm)
  outliers start: 3
  outliers final: 0
  residues processed: 39
  average time/residue: 0.1058
  time to fit residues: 6.3251
Evaluate side-chains
  32 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 98 optimal weight:    0.5980
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    0.7980
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 129 optimal weight:    7.9990
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A4722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 713 HIS
B 760 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.048479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.031394 restraints weight = 57676.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.032682 restraints weight = 28754.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.033534 restraints weight = 18914.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.034107 restraints weight = 14484.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.034460 restraints weight = 12203.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.0707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10675  Z= 0.165
  Angle     :  0.491   8.837  14491  Z= 0.255
  Chirality :  0.040   0.138   1619
  Planarity :  0.003   0.038   1858
  Dihedral  :  5.810  79.050   1469
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  4.33 %
    Favored  : 94.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.94 (0.24), residues: 1301
  helix:  2.03 (0.22), residues: 575
  sheet:  0.82 (0.40), residues: 173
  loop :  0.80 (0.28), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 809 
 TYR   0.010   0.001   TYR B 921 
 PHE   0.014   0.001   PHE B 656 
 TRP   0.008   0.001   TRP B 660 
 HIS   0.002   0.001   HIS B 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (10675)
  covalent geometry    : angle       0.49127 (14491)
  hydrogen bonds       : bond        0.04166 (  508)
  hydrogen bonds       : angle       4.92265 ( 1404)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 30
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4532 MET cc_start: 0.9374 (mmm) cc_final: 0.8795 (mmm)
REVERT: A 4542 MET cc_start: 0.9446 (mtt) cc_final: 0.9096 (mpp)
REVERT: A 4790 MET cc_start: 0.8593 (mmt) cc_final: 0.8304 (mmt)
REVERT: B  253 MET cc_start: 0.8011 (mtt) cc_final: 0.7718 (mtt)
REVERT: B  601 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8123 (tm-30)
REVERT: B  992 MET cc_start: 0.8651 (ttp) cc_final: 0.8013 (tmm)
REVERT: B 1009 MET cc_start: 0.9381 (mmm) cc_final: 0.8878 (mmm)
  outliers start: 8
  outliers final: 4
  residues processed: 35
  average time/residue: 0.0927
  time to fit residues: 5.1948
Evaluate side-chains
  35 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  601 GLU
Chi-restraints excluded: chain B residue  768 VAL
Chi-restraints excluded: chain B residue  813 HIS
Chi-restraints excluded: chain B residue  938 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 112 optimal weight:    5.9990
   chunk 61 optimal weight:   10.0000
   chunk 77 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 126 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   chunk 4 optimal weight:    6.9990
   chunk 39 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 122 optimal weight:    6.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A4722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 234 ASN
B 599 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.047806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.030699 restraints weight = 58615.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.031964 restraints weight = 29327.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.032778 restraints weight = 19341.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.033332 restraints weight = 14947.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.033693 restraints weight = 12616.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.1108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  10675  Z= 0.206
  Angle     :  0.514   7.477  14491  Z= 0.263
  Chirality :  0.040   0.172   1619
  Planarity :  0.003   0.039   1858
  Dihedral  :  5.937  82.040   1469
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  5.02 %
    Favored  : 94.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.90 (0.24), residues: 1301
  helix:  2.07 (0.22), residues: 576
  sheet:  0.66 (0.40), residues: 169
  loop :  0.73 (0.28), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 822 
 TYR   0.010   0.001   TYR B 921 
 PHE   0.013   0.001   PHE B 183 
 TRP   0.009   0.001   TRP B 696 
 HIS   0.004   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 (10675)
  covalent geometry    : angle       0.51386 (14491)
  hydrogen bonds       : bond        0.03845 (  508)
  hydrogen bonds       : angle       4.70835 ( 1404)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 33
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4532 MET cc_start: 0.9396 (mmm) cc_final: 0.8854 (mmm)
REVERT: A 4542 MET cc_start: 0.9402 (mtt) cc_final: 0.9035 (mpp)
REVERT: A 4790 MET cc_start: 0.8634 (mmt) cc_final: 0.8412 (mmt)
REVERT: B  253 MET cc_start: 0.8050 (mtt) cc_final: 0.7770 (mtt)
REVERT: B  992 MET cc_start: 0.8579 (ttp) cc_final: 0.8104 (tmm)
REVERT: B  993 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9199 (mm)
REVERT: B 1009 MET cc_start: 0.9417 (mmm) cc_final: 0.8918 (mmm)
  outliers start: 9
  outliers final: 4
  residues processed: 40
  average time/residue: 0.0940
  time to fit residues: 5.9778
Evaluate side-chains
  36 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  768 VAL
Chi-restraints excluded: chain B residue  813 HIS
Chi-restraints excluded: chain B residue  938 THR
Chi-restraints excluded: chain B residue  993 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 77 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 117 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 91 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 48 optimal weight:    6.9990
   chunk 123 optimal weight:    0.9990
   chunk 96 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A4722 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 = 0.3269 r_free = 0.3269 target = 0.048806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.031723 restraints weight = 57909.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.033013 restraints weight = 28668.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.033875 restraints weight = 18898.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.034461 restraints weight = 14432.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.034820 restraints weight = 12109.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.1165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  10675  Z= 0.087
  Angle     :  0.430   7.959  14491  Z= 0.224
  Chirality :  0.039   0.150   1619
  Planarity :  0.003   0.040   1858
  Dihedral  :  5.689  78.553   1469
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  4.59 %
    Favored  : 94.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.01 (0.24), residues: 1301
  helix:  2.20 (0.22), residues: 576
  sheet:  0.75 (0.41), residues: 173
  loop :  0.73 (0.28), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A4574 
 TYR   0.006   0.001   TYR A4557 
 PHE   0.010   0.001   PHE B 881 
 TRP   0.005   0.001   TRP B  99 
 HIS   0.002   0.000   HIS B 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00181 (10675)
  covalent geometry    : angle       0.42957 (14491)
  hydrogen bonds       : bond        0.03254 (  508)
  hydrogen bonds       : angle       4.38839 ( 1404)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 37
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4532 MET cc_start: 0.9363 (mmm) cc_final: 0.8779 (mmm)
REVERT: A 4542 MET cc_start: 0.9385 (mtt) cc_final: 0.9029 (mpp)
REVERT: B  216 ILE cc_start: 0.9523 (OUTLIER) cc_final: 0.9322 (tt)
REVERT: B  253 MET cc_start: 0.7925 (mtt) cc_final: 0.7702 (mtt)
REVERT: B  844 MET cc_start: 0.6605 (ppp) cc_final: 0.6309 (ppp)
REVERT: B 1009 MET cc_start: 0.9381 (mmm) cc_final: 0.8906 (mmm)
  outliers start: 10
  outliers final: 5
  residues processed: 46
  average time/residue: 0.0804
  time to fit residues: 6.0011
Evaluate side-chains
  37 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 4551 LEU
Chi-restraints excluded: chain A residue 4769 GLN
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  216 ILE
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  938 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 23 optimal weight:    2.9990
   chunk 120 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 41 optimal weight:    0.1980
   chunk 108 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 116 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 82 optimal weight:   10.0000
   chunk 119 optimal weight:    5.9990
   overall best weight:    2.2388

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

Flipped N/Q/H residues before XYZ refinement:
** A4722 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 = 0.3247 r_free = 0.3247 target = 0.048062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.031047 restraints weight = 58494.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.032324 restraints weight = 28961.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.033161 restraints weight = 19059.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.033721 restraints weight = 14663.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.034054 restraints weight = 12389.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          0.1351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10675  Z= 0.158
  Angle     :  0.479  11.178  14491  Z= 0.243
  Chirality :  0.039   0.147   1619
  Planarity :  0.003   0.038   1858
  Dihedral  :  5.725  79.173   1469
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  5.80 %
    Favored  : 93.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.04 (0.24), residues: 1301
  helix:  2.27 (0.22), residues: 576
  sheet:  0.67 (0.40), residues: 169
  loop :  0.72 (0.28), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A4788 
 TYR   0.008   0.001   TYR B 921 
 PHE   0.012   0.001   PHE B 656 
 TRP   0.007   0.001   TRP B 696 
 HIS   0.003   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (10675)
  covalent geometry    : angle       0.47902 (14491)
  hydrogen bonds       : bond        0.03377 (  508)
  hydrogen bonds       : angle       4.35718 ( 1404)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4532 MET cc_start: 0.9359 (mmm) cc_final: 0.8790 (mmm)
REVERT: A 4542 MET cc_start: 0.9429 (mtt) cc_final: 0.9031 (mpp)
REVERT: A 4790 MET cc_start: 0.8323 (mmt) cc_final: 0.8095 (mmt)
REVERT: B  253 MET cc_start: 0.8027 (mtt) cc_final: 0.7739 (mtt)
REVERT: B  985 MET cc_start: 0.9040 (ptt) cc_final: 0.8668 (ptm)
REVERT: B 1009 MET cc_start: 0.9415 (mmm) cc_final: 0.8861 (mmm)
  outliers start: 7
  outliers final: 5
  residues processed: 40
  average time/residue: 0.0765
  time to fit residues: 4.9811
Evaluate side-chains
  36 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 4551 LEU
Chi-restraints excluded: chain A residue 4769 GLN
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  600 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 84 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   chunk 126 optimal weight:    7.9990
   chunk 56 optimal weight:    3.9990
   chunk 25 optimal weight:   10.0000
   chunk 75 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 128 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 116 optimal weight:    0.8980
   chunk 86 optimal weight:    4.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A4722 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 = 0.3251 r_free = 0.3251 target = 0.048183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.031089 restraints weight = 59062.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.032369 restraints weight = 29277.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.033208 restraints weight = 19304.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.033766 restraints weight = 14869.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.034139 restraints weight = 12522.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.1514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10675  Z= 0.139
  Angle     :  0.471   8.792  14491  Z= 0.237
  Chirality :  0.039   0.141   1619
  Planarity :  0.003   0.039   1858
  Dihedral  :  5.686  78.611   1469
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  6.32 %
    Favored  : 92.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.04 (0.24), residues: 1301
  helix:  2.28 (0.22), residues: 576
  sheet:  0.67 (0.40), residues: 169
  loop :  0.70 (0.28), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A4574 
 TYR   0.007   0.001   TYR B 921 
 PHE   0.012   0.001   PHE B 656 
 TRP   0.006   0.001   TRP B 696 
 HIS   0.002   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (10675)
  covalent geometry    : angle       0.47094 (14491)
  hydrogen bonds       : bond        0.03265 (  508)
  hydrogen bonds       : angle       4.28857 ( 1404)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4532 MET cc_start: 0.9350 (mmm) cc_final: 0.8786 (mmm)
REVERT: A 4542 MET cc_start: 0.9413 (mtt) cc_final: 0.9024 (mpp)
REVERT: B  253 MET cc_start: 0.7994 (mtt) cc_final: 0.7766 (mtt)
REVERT: B 1009 MET cc_start: 0.9399 (mmm) cc_final: 0.8866 (mmm)
  outliers start: 8
  outliers final: 7
  residues processed: 42
  average time/residue: 0.0820
  time to fit residues: 5.6209
Evaluate side-chains
  40 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 4551 LEU
Chi-restraints excluded: chain A residue 4769 GLN
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  216 ILE
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain B residue  938 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 124 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 78 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 77 optimal weight:    0.0010
   chunk 95 optimal weight:    6.9990
   chunk 128 optimal weight:    2.9990
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
** A4722 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 = 0.3270 r_free = 0.3270 target = 0.048779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.031722 restraints weight = 57838.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.033006 restraints weight = 28512.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.033852 restraints weight = 18729.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.034407 restraints weight = 14387.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.034786 restraints weight = 12159.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.1560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  10675  Z= 0.086
  Angle     :  0.449   8.563  14491  Z= 0.225
  Chirality :  0.039   0.143   1619
  Planarity :  0.003   0.039   1858
  Dihedral  :  5.560  76.325   1469
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  6.84 %
    Favored  : 92.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.09 (0.24), residues: 1301
  helix:  2.28 (0.22), residues: 578
  sheet:  0.80 (0.41), residues: 169
  loop :  0.75 (0.28), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A4788 
 TYR   0.006   0.001   TYR A4557 
 PHE   0.012   0.001   PHE B 656 
 TRP   0.006   0.001   TRP B  99 
 HIS   0.002   0.000   HIS A4792 

Details of bonding type rmsd
  covalent geometry    : bond        0.00184 (10675)
  covalent geometry    : angle       0.44943 (14491)
  hydrogen bonds       : bond        0.03104 (  508)
  hydrogen bonds       : angle       4.16439 ( 1404)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4532 MET cc_start: 0.9336 (mmm) cc_final: 0.8743 (mmm)
REVERT: A 4542 MET cc_start: 0.9405 (mtt) cc_final: 0.9026 (mpp)
REVERT: B  253 MET cc_start: 0.7925 (mtt) cc_final: 0.7676 (mtt)
REVERT: B 1009 MET cc_start: 0.9373 (mmm) cc_final: 0.8896 (mmm)
  outliers start: 7
  outliers final: 5
  residues processed: 38
  average time/residue: 0.0838
  time to fit residues: 5.2112
Evaluate side-chains
  38 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 4769 GLN
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain B residue  938 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 125 optimal weight:    0.0030
   chunk 110 optimal weight:    6.9990
   chunk 123 optimal weight:    0.6980
   chunk 40 optimal weight:    5.9990
   chunk 115 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 105 optimal weight:    0.7980
   chunk 82 optimal weight:    7.9990
   chunk 62 optimal weight:    0.0060
   chunk 48 optimal weight:   10.0000
   overall best weight:    0.4606

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

Flipped N/Q/H residues before XYZ refinement:
** A4722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 720 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.049227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.032183 restraints weight = 57674.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.033497 restraints weight = 28387.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.034357 restraints weight = 18581.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.034940 restraints weight = 14229.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.035327 restraints weight = 11962.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  10675  Z= 0.077
  Angle     :  0.438   8.411  14491  Z= 0.219
  Chirality :  0.039   0.137   1619
  Planarity :  0.003   0.038   1858
  Dihedral  :  5.359  72.886   1469
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  6.75 %
    Favored  : 92.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.18 (0.24), residues: 1301
  helix:  2.37 (0.22), residues: 573
  sheet:  0.91 (0.40), residues: 169
  loop :  0.77 (0.28), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A4785 
 TYR   0.007   0.001   TYR A4557 
 PHE   0.013   0.001   PHE B 656 
 TRP   0.007   0.001   TRP B  99 
 HIS   0.002   0.000   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00160 (10675)
  covalent geometry    : angle       0.43827 (14491)
  hydrogen bonds       : bond        0.02870 (  508)
  hydrogen bonds       : angle       4.02275 ( 1404)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4532 MET cc_start: 0.9325 (mmm) cc_final: 0.8722 (mmm)
REVERT: A 4542 MET cc_start: 0.9408 (mtt) cc_final: 0.9031 (mpp)
REVERT: A 4790 MET cc_start: 0.8770 (mmt) cc_final: 0.7927 (mpp)
REVERT: B  253 MET cc_start: 0.7881 (mtt) cc_final: 0.7646 (mtt)
REVERT: B  844 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.5853 (ppp)
REVERT: B  985 MET cc_start: 0.8904 (ptt) cc_final: 0.8345 (ppp)
REVERT: B 1009 MET cc_start: 0.9319 (mmm) cc_final: 0.8845 (mmm)
  outliers start: 6
  outliers final: 4
  residues processed: 39
  average time/residue: 0.0806
  time to fit residues: 5.1803
Evaluate side-chains
  37 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 4769 GLN
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain B residue  844 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 86 optimal weight:    6.9990
   chunk 103 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 125 optimal weight:    5.9990
   chunk 8 optimal weight:    0.5980
   chunk 87 optimal weight:    0.0270
   chunk 9 optimal weight:    9.9990
   chunk 68 optimal weight:    0.0370
   chunk 100 optimal weight:    0.9980
   chunk 94 optimal weight:    7.9990
   chunk 116 optimal weight:    2.9990
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
** A4722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A4778 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.049111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.032106 restraints weight = 57794.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.033407 restraints weight = 28481.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.034259 restraints weight = 18626.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.034843 restraints weight = 14281.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.035233 restraints weight = 11994.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  10675  Z= 0.081
  Angle     :  0.437   9.042  14491  Z= 0.217
  Chirality :  0.038   0.147   1619
  Planarity :  0.003   0.038   1858
  Dihedral  :  5.307  72.985   1469
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  7.27 %
    Favored  : 92.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.22 (0.24), residues: 1301
  helix:  2.42 (0.22), residues: 573
  sheet:  0.82 (0.39), residues: 174
  loop :  0.80 (0.28), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A4574 
 TYR   0.006   0.001   TYR B 282 
 PHE   0.014   0.001   PHE B 656 
 TRP   0.006   0.001   TRP B  99 
 HIS   0.002   0.000   HIS B 515 

Details of bonding type rmsd
  covalent geometry    : bond        0.00176 (10675)
  covalent geometry    : angle       0.43665 (14491)
  hydrogen bonds       : bond        0.02837 (  508)
  hydrogen bonds       : angle       4.01291 ( 1404)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4532 MET cc_start: 0.9299 (mmm) cc_final: 0.8683 (mmm)
REVERT: A 4542 MET cc_start: 0.9410 (mtt) cc_final: 0.9040 (mpp)
REVERT: B  253 MET cc_start: 0.7894 (mtt) cc_final: 0.7630 (mtt)
REVERT: B  844 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.5942 (ppp)
REVERT: B 1009 MET cc_start: 0.9305 (mmm) cc_final: 0.8939 (mmm)
  outliers start: 5
  outliers final: 4
  residues processed: 36
  average time/residue: 0.0908
  time to fit residues: 5.3396
Evaluate side-chains
  37 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 4769 GLN
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain B residue  844 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 85 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0970
   chunk 1 optimal weight:    0.0020
   chunk 78 optimal weight:    0.5980
   chunk 42 optimal weight:    6.9990
   chunk 43 optimal weight:    0.7980
   chunk 12 optimal weight:   10.0000
   chunk 71 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A4722 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 = 0.3364 r_free = 0.3364 target = 0.051717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.035609 restraints weight = 57819.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.036951 restraints weight = 27743.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.037815 restraints weight = 17663.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.038403 restraints weight = 13263.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.038759 restraints weight = 10987.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  10675  Z= 0.077
  Angle     :  0.442  10.140  14491  Z= 0.220
  Chirality :  0.039   0.150   1619
  Planarity :  0.003   0.038   1858
  Dihedral  :  5.250  72.376   1469
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  7.27 %
    Favored  : 92.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.20 (0.24), residues: 1301
  helix:  2.39 (0.22), residues: 573
  sheet:  0.86 (0.39), residues: 174
  loop :  0.79 (0.28), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A4785 
 TYR   0.007   0.001   TYR A4557 
 PHE   0.013   0.001   PHE B 656 
 TRP   0.006   0.001   TRP B  99 
 HIS   0.002   0.000   HIS B1001 

Details of bonding type rmsd
  covalent geometry    : bond        0.00163 (10675)
  covalent geometry    : angle       0.44181 (14491)
  hydrogen bonds       : bond        0.02828 (  508)
  hydrogen bonds       : angle       3.98563 ( 1404)

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

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

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2602 Ramachandran restraints generated.
    1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4532 MET cc_start: 0.9263 (mmm) cc_final: 0.8645 (mmm)
REVERT: A 4542 MET cc_start: 0.9424 (mtt) cc_final: 0.9086 (mpp)
REVERT: A 4790 MET cc_start: 0.8818 (mmt) cc_final: 0.7765 (mpp)
REVERT: B  253 MET cc_start: 0.7764 (mtt) cc_final: 0.7499 (mtt)
REVERT: B  844 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.5986 (ppp)
REVERT: B  985 MET cc_start: 0.8870 (ptt) cc_final: 0.8499 (pmm)
REVERT: B 1009 MET cc_start: 0.9202 (mmm) cc_final: 0.8927 (mmm)
  outliers start: 5
  outliers final: 4
  residues processed: 38
  average time/residue: 0.0822
  time to fit residues: 5.1639
Evaluate side-chains
  37 residues out of total 1155 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 4769 GLN
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain B residue  844 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9980
   chunk 18 optimal weight:    9.9990
   chunk 90 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
** A4722 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 = 0.3334 r_free = 0.3334 target = 0.050317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.032983 restraints weight = 58137.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.034341 restraints weight = 28032.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.035241 restraints weight = 18195.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.035840 restraints weight = 13824.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.036211 restraints weight = 11549.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10675  Z= 0.096
  Angle     :  0.441   8.763  14491  Z= 0.222
  Chirality :  0.039   0.153   1619
  Planarity :  0.003   0.037   1858
  Dihedral  :  5.259  73.185   1469
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  7.45 %
    Favored  : 92.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.04 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.23 (0.24), residues: 1301
  helix:  2.43 (0.22), residues: 573
  sheet:  0.81 (0.39), residues: 174
  loop :  0.81 (0.28), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A4574 
 TYR   0.007   0.001   TYR B 282 
 PHE   0.013   0.001   PHE B 656 
 TRP   0.005   0.001   TRP B  99 
 HIS   0.003   0.000   HIS B1001 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 (10675)
  covalent geometry    : angle       0.44148 (14491)
  hydrogen bonds       : bond        0.02860 (  508)
  hydrogen bonds       : angle       4.00676 ( 1404)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1804.17 seconds
wall clock time: 31 minutes 53.70 seconds (1913.70 seconds total)