Starting phenix.real_space_refine
on Wed Feb  4 16:46:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qia_53183/02_2026/9qia_53183_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qia_53183/02_2026/9qia_53183.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.38
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qia_53183/02_2026/9qia_53183.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qia_53183/02_2026/9qia_53183.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qia_53183/02_2026/9qia_53183_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qia_53183/02_2026/9qia_53183_neut.cif"
  }
  resolution = 4.38
  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=   0.015
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       7      5.49       5
     S      52      5.16       5
     C    7260      2.51       5
     N    1934      2.21       5
     O    2175      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 64 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: 11428
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2331
          Classifications: {'peptide': 291}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 273}
    Chain: "B"
      Number of atoms: 7834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 988, 7834
          Classifications: {'peptide': 988}
          Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 47, 'TRANS': 935}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 602
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "E"
      Number of atoms: 603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 603
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "B"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 36
          Unusual residues: {'IHP': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'AMP%rna2p': 1}
          Classifications: {'RNA_mixed': 1}
          Modifications used: {'rna2p': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 2.32, per 1000 atoms: 0.20
  Number of scatterers: 11428
  At special positions: 0
  Unit cell: (94.35, 100.3, 131.75, 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      52     16.00
     P       7     15.00
     O    2175      8.00
     N    1934      7.00
     C    7260      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.86
  Conformation dependent library (CDL) restraints added in 589.8 milliseconds
  

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2716

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 12 sheets defined
      47.7% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4524 through 4533
    Processing helix  chain 'A' and resid 4559 through 4566
    Processing helix  chain 'A' and resid 4572 through 4586
      removed outlier: 3.777A  pdb=" N   VAL A4583 " --> pdb=" O   ALA A4579 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   THR A4584 " --> pdb=" O   GLN A4580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4667 through 4671
    Processing helix  chain 'A' and resid 4687 through 4699
    Processing helix  chain 'A' and resid 4703 through 4708
      removed outlier: 3.833A  pdb=" N   PHE A4706 " --> pdb=" O   GLU A4703 " (cutoff:3.500A)
      removed outlier: 3.979A  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 4739
    Processing helix  chain 'A' and resid 4740 through 4746
    Processing helix  chain 'A' and resid 4751 through 4762
    Processing helix  chain 'A' and resid 4762 through 4780
      removed outlier: 4.162A  pdb=" N   TYR A4780 " --> pdb=" O   ASP A4776 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4786 through 4810
      removed outlier: 3.689A  pdb=" N   GLN A4803 " --> pdb=" O   ARG A4799 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLU A4806 " --> pdb=" O   ALA A4802 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 52
      removed outlier: 7.288A  pdb=" N   ARG B  46 " --> pdb=" O   ALA B  42 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   GLN B  47 " --> pdb=" O   LEU B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 60
    Processing helix  chain 'B' and resid 70 through 84
    Processing helix  chain 'B' and resid 98 through 103
    Processing helix  chain 'B' and resid 108 through 115
    Processing helix  chain 'B' and resid 117 through 128
      removed outlier: 3.949A  pdb=" N   VAL B 122 " --> pdb=" O   ARG B 118 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   LYS B 124 " --> pdb=" O   GLU B 120 " (cutoff:3.500A)
      removed outlier: 5.214A  pdb=" N   HIS B 125 " --> pdb=" O   ALA B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 154
      removed outlier: 3.514A  pdb=" N   ASP B 152 " --> pdb=" O   SER B 149 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LYS B 153 " --> pdb=" O   PHE B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 163 through 176
    Processing helix  chain 'B' and resid 253 through 257
    Processing helix  chain 'B' and resid 301 through 308
      removed outlier: 3.756A  pdb=" N   LYS B 307 " --> pdb=" O   GLU B 303 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   HIS B 308 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 340
      removed outlier: 3.583A  pdb=" N   GLU B 324 " --> pdb=" O   GLU B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 365
      removed outlier: 3.639A  pdb=" N   GLU B 363 " --> pdb=" O   THR B 359 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   THR B 364 " --> pdb=" O   SER B 360 " (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: 4.466A  pdb=" N   VAL B 425 " --> pdb=" O   ALA B 421 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   SER B 427 " --> pdb=" O   ASP B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 437
    Processing helix  chain 'B' and resid 443 through 450
    Processing helix  chain 'B' and resid 451 through 459
      removed outlier: 3.626A  pdb=" N   CYS B 455 " --> pdb=" O   GLY B 451 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 483
      removed outlier: 3.535A  pdb=" N   CYS B 473 " --> pdb=" O   GLY B 469 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLU B 474 " --> pdb=" O   ALA B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 509
      removed outlier: 4.314A  pdb=" N   ARG B 508 " --> pdb=" O   SER B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 517
      removed outlier: 3.876A  pdb=" N   ILE B 517 " --> pdb=" O   PRO B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 531
      removed outlier: 3.877A  pdb=" N   LYS B 531 " --> pdb=" O   ASP B 527 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 547 through 552
      removed outlier: 4.201A  pdb=" N   THR B 551 " --> pdb=" O   THR B 548 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 554 through 561
    Processing helix  chain 'B' and resid 570 through 583
    Processing helix  chain 'B' and resid 610 through 614
      removed outlier: 3.561A  pdb=" N   HIS B 614 " --> pdb=" O   TYR B 611 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 623 through 628
    Processing helix  chain 'B' and resid 633 through 650
      removed outlier: 3.563A  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
      removed outlier: 3.516A  pdb=" N   LEU B 716 " --> pdb=" O   ASN B 712 " (cutoff:3.500A)
    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 821 through 834
    Processing helix  chain 'B' and resid 839 through 843
      removed outlier: 3.567A  pdb=" N   GLN B 843 " --> pdb=" O   SER B 840 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 857 through 873
      removed outlier: 3.848A  pdb=" N   TYR B 873 " --> pdb=" O   ARG B 869 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 879 through 889
    Processing helix  chain 'B' and resid 894 through 915
      removed outlier: 3.548A  pdb=" N   THR B 898 " --> pdb=" O   ILE B 894 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ILE B 910 " --> pdb=" O   ALA B 906 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LYS B 911 " --> pdb=" O   LEU B 907 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLY B 915 " --> pdb=" O   LYS B 911 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 967 through 980
    Processing helix  chain 'B' and resid 1001 through 1007
      removed outlier: 3.676A  pdb=" N   LYS B1006 " --> pdb=" O   LYS B1003 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1008 through 1014
    Processing helix  chain 'C' and resid 22 through 34
    Processing helix  chain 'C' and resid 56 through 60
      removed outlier: 3.594A  pdb=" N   TYR C  59 " --> pdb=" O   LEU C  56 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 22 through 35
      removed outlier: 3.577A  pdb=" N   ILE E  30 " --> pdb=" O   VAL E  26 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLN E  31 " --> pdb=" O   LYS E  27 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ASP E  32 " --> pdb=" O   ALA E  28 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   LYS E  33 " --> pdb=" O   LYS E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 37 through 41
      removed outlier: 3.553A  pdb=" N   GLN E  41 " --> pdb=" O   PRO E  38 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 60
      removed outlier: 3.735A  pdb=" N   TYR E  59 " --> pdb=" O   THR E  55 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4537 through 4540
      removed outlier: 3.839A  pdb=" N   CYS A4601 " --> pdb=" O   ASP A4538 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   ILE A4608 " --> pdb=" O   ASP A4602 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   PHE A4626 " --> pdb=" O   ILE A4613 " (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: 6.134A  pdb=" N   VAL B  64 " --> pdb=" O   THR B  89 " (cutoff:3.500A)
      removed outlier: 7.803A  pdb=" N   HIS B  91 " --> pdb=" O   VAL B  64 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   LEU B  66 " --> pdb=" O   HIS B  91 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   HIS B  63 " --> pdb=" O   CYS B 156 " (cutoff:3.500A)
      removed outlier: 8.494A  pdb=" N   VAL B 158 " --> pdb=" O   HIS B  63 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   PHE B  65 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER B 185 " --> pdb=" O   PHE B 196 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 203 through 205
    Processing sheet with id=AA5, first strand: chain 'B' and resid 218 through 222
      removed outlier: 3.709A  pdb=" N   ILE B 228 " --> pdb=" O   THR B 222 " (cutoff:3.500A)
      removed outlier: 5.995A  pdb=" N   SER B 272 " --> pdb=" O   VAL B 265 " (cutoff:3.500A)
      removed outlier: 5.746A  pdb=" N   VAL B 265 " --> pdb=" O   SER B 272 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 260 through 262
      removed outlier: 4.581A  pdb=" N   PHE B 244 " --> pdb=" O   VAL B 291 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 538 through 541
      removed outlier: 6.545A  pdb=" N   ILE B 493 " --> pdb=" O   ASP B 539 " (cutoff:3.500A)
      removed outlier: 8.101A  pdb=" N   HIS B 541 " --> pdb=" O   ILE B 493 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   VAL B 495 " --> pdb=" O   HIS B 541 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   THR B 496 " --> pdb=" O   LEU B 465 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   ASN B 462 " --> pdb=" O   VAL B 563 " (cutoff:3.500A)
      removed outlier: 8.197A  pdb=" N   ILE B 565 " --> pdb=" O   ASN B 462 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   PHE B 464 " --> pdb=" O   ILE B 565 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ILE B 564 " --> pdb=" O   LEU B 589 " (cutoff:3.500A)
      removed outlier: 8.682A  pdb=" N   SER B 591 " --> pdb=" O   ILE B 564 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   THR B 566 " --> pdb=" O   SER B 591 " (cutoff:3.500A)
      removed outlier: 9.301A  pdb=" N   THR B 593 " --> pdb=" O   THR B 566 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU B 588 " --> pdb=" O   ILE B 603 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   CYS B 924 " --> pdb=" O   THR B 600 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 944 through 945
    Processing sheet with id=AA9, first strand: chain 'B' and resid 958 through 961
      removed outlier: 6.670A  pdb=" N   TRP B 958 " --> pdb=" O   ARG B1044 " (cutoff:3.500A)
      removed outlier: 7.922A  pdb=" N   TYR B1046 " --> pdb=" O   TRP B 958 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   VAL B 960 " --> pdb=" O   TYR B1046 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   VAL B1043 " --> pdb=" O   LEU B1024 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   SER B1027 " --> pdb=" O   MET B 985 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   MET B 985 " --> pdb=" O   SER B1027 " (cutoff:3.500A)
      removed outlier: 5.050A  pdb=" N   GLN B 988 " --> pdb=" O   MET B 992 " (cutoff:3.500A)
      removed outlier: 5.027A  pdb=" N   MET B 992 " --> pdb=" O   GLN B 988 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 958 through 961
      removed outlier: 6.670A  pdb=" N   TRP B 958 " --> pdb=" O   ARG B1044 " (cutoff:3.500A)
      removed outlier: 7.922A  pdb=" N   TYR B1046 " --> pdb=" O   TRP B 958 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   VAL B 960 " --> pdb=" O   TYR B1046 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   VAL B1043 " --> pdb=" O   LEU B1024 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 48 through 49
      removed outlier: 3.885A  pdb=" N   HIS C  68 " --> pdb=" O   ILE C  44 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 12 through 16
      removed outlier: 4.259A  pdb=" N   SER E  65 " --> pdb=" O   GLN E   2 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ARG E  42 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)

    513 hydrogen bonds defined for protein.
    1413 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: 2.48

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3728
        1.35 -     1.47: 2606
        1.47 -     1.59: 5259
        1.59 -     1.71: 7
        1.71 -     1.83: 77
  Bond restraints: 11677
  Sorted by residual:
  bond pdb=" N   ILE B 622 "
       pdb=" CA  ILE B 622 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.036 8.70e-03 1.32e+04 1.72e+01
  bond pdb=" CA  SER E  20 "
       pdb=" CB  SER E  20 "
    ideal  model  delta    sigma   weight residual
    1.539  1.498  0.040 1.20e-02 6.94e+03 1.13e+01
  bond pdb=" N   ASN A4656 "
       pdb=" CA  ASN A4656 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.034 1.18e-02 7.18e+03 8.40e+00
  bond pdb=" CZ  ARG A4654 "
       pdb=" NH2 ARG A4654 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.57e+00
  bond pdb=" CZ  ARG C  74 "
       pdb=" NH2 ARG C  74 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 5.98e+00
  ... (remaining 11672 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 15506
        1.84 -     3.67: 273
        3.67 -     5.51: 43
        5.51 -     7.34: 6
        7.34 -     9.18: 2
  Bond angle restraints: 15830
  Sorted by residual:
  angle pdb=" N   CYS A4666 "
        pdb=" CA  CYS A4666 "
        pdb=" CB  CYS A4666 "
      ideal   model   delta    sigma   weight residual
     110.65  103.95    6.70 1.56e+00 4.11e-01 1.85e+01
  angle pdb=" CA  ARG C  74 "
        pdb=" C   ARG C  74 "
        pdb=" N   GLY C  75 "
      ideal   model   delta    sigma   weight residual
     115.51  120.83   -5.32 1.24e+00 6.50e-01 1.84e+01
  angle pdb=" CA  THR E  22 "
        pdb=" CB  THR E  22 "
        pdb=" OG1 THR E  22 "
      ideal   model   delta    sigma   weight residual
     109.60  103.44    6.16 1.50e+00 4.44e-01 1.69e+01
  angle pdb=" CA  PRO E  19 "
        pdb=" C   PRO E  19 "
        pdb=" O   PRO E  19 "
      ideal   model   delta    sigma   weight residual
     121.95  117.33    4.62 1.25e+00 6.40e-01 1.37e+01
  angle pdb=" N   SER B 625 "
        pdb=" CA  SER B 625 "
        pdb=" C   SER B 625 "
      ideal   model   delta    sigma   weight residual
     111.33  106.97    4.36 1.21e+00 6.83e-01 1.30e+01
  ... (remaining 15825 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.80: 6582
       16.80 -    33.61: 415
       33.61 -    50.41: 98
       50.41 -    67.22: 17
       67.22 -    84.02: 4
  Dihedral angle restraints: 7116
    sinusoidal: 2935
      harmonic: 4181
  Sorted by residual:
  dihedral pdb=" CA  SER B 625 "
           pdb=" C   SER B 625 "
           pdb=" N   THR B 626 "
           pdb=" CA  THR B 626 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.27   23.73     0      5.00e+00 4.00e-02 2.25e+01
  dihedral pdb=" CA  ASP C  52 "
           pdb=" C   ASP C  52 "
           pdb=" N   GLY C  53 "
           pdb=" CA  GLY C  53 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.56  -21.44     0      5.00e+00 4.00e-02 1.84e+01
  dihedral pdb=" CA  LYS C  63 "
           pdb=" C   LYS C  63 "
           pdb=" N   GLU C  64 "
           pdb=" CA  GLU C  64 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.61   20.39     0      5.00e+00 4.00e-02 1.66e+01
  ... (remaining 7113 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1568
       0.064 -    0.128: 201
       0.128 -    0.193: 10
       0.193 -    0.257: 3
       0.257 -    0.321: 1
  Chirality restraints: 1783
  Sorted by residual:
  chirality pdb=" CA  ARG C  74 "
            pdb=" N   ARG C  74 "
            pdb=" C   ARG C  74 "
            pdb=" CB  ARG C  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.58e+00
  chirality pdb=" CA  PHE B 624 "
            pdb=" N   PHE B 624 "
            pdb=" C   PHE B 624 "
            pdb=" CB  PHE B 624 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.46e+00
  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    2.67   -0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 1780 not shown)

  Planarity restraints: 2030
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A4673 "    0.072 2.00e-02 2.50e+03   3.37e-02 2.83e+01
        pdb=" CG  TRP A4673 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP A4673 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP A4673 "   -0.040 2.00e-02 2.50e+03
        pdb=" NE1 TRP A4673 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A4673 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A4673 "   -0.038 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A4673 "    0.026 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A4673 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A4673 "    0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 625 "    0.020 2.00e-02 2.50e+03   4.00e-02 1.60e+01
        pdb=" C   SER B 625 "   -0.069 2.00e-02 2.50e+03
        pdb=" O   SER B 625 "    0.026 2.00e-02 2.50e+03
        pdb=" N   THR B 626 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A4654 "    0.152 9.50e-02 1.11e+02   6.81e-02 2.95e+00
        pdb=" NE  ARG A4654 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  ARG A4654 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A4654 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG A4654 "    0.007 2.00e-02 2.50e+03
  ... (remaining 2027 not shown)

  Histogram of nonbonded interaction distances:
        1.32 -     2.04: 2
        2.04 -     2.75: 1357
        2.75 -     3.47: 17502
        3.47 -     4.18: 27332
        4.18 -     4.90: 47627
  Nonbonded interactions: 93820
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 625 "
            pdb=" C   ALA C  76 "
     model   vdw
     1.324 3.270
  nonbonded pdb=" SG  CYS A4666 "
            pdb=" CB  ALA C  76 "
     model   vdw
     1.835 3.820
  nonbonded pdb=" OG  SER B 625 "
            pdb=" O   ALA C  76 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" CB  ASN A4671 "
            pdb=" CZ3 TRP A4673 "
     model   vdw
     2.315 3.740
  nonbonded pdb=" CD1 TYR B 611 "
            pdb=" NH1 ARG E  72 "
     model   vdw
     2.372 3.420
  ... (remaining 93815 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = (chain 'E' and (resid 1 through 75 or (resid 76 and (name N or name CA or name C \ 
 or name O or name CB ))))
}

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:             2.560
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.490
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
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      :  0.003   0.045  11678  Z= 0.177
  Angle     :  0.605   9.176  15830  Z= 0.338
  Chirality :  0.043   0.321   1783
  Planarity :  0.004   0.068   2030
  Dihedral  : 12.017  84.021   4400
  Min Nonbonded Distance : 1.324

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  1.18 %
    Favored  : 98.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.76 %
    Cis-general     : 0.07 %
    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:  1.05 (0.23), residues: 1421
  helix:  1.57 (0.22), residues: 566
  sheet:  0.42 (0.35), residues: 208
  loop :  0.10 (0.26), residues: 647

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A4654 
 TYR   0.011   0.001   TYR A4660 
 PHE   0.013   0.001   PHE B 966 
 TRP   0.072   0.003   TRP A4673 
 HIS   0.005   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (11677)
  covalent geometry    : angle       0.60490 (15830)
  hydrogen bonds       : bond        0.16808 (  510)
  hydrogen bonds       : angle       6.68401 ( 1413)
  Misc. bond           : bond        0.00123 (    1)

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

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

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4532 MET cc_start: 0.9062 (mtp) cc_final: 0.8835 (mtp)
REVERT: A 4626 PHE cc_start: 0.9123 (m-80) cc_final: 0.8915 (m-80)
REVERT: B   69 MET cc_start: 0.8611 (mmp) cc_final: 0.7888 (mmm)
REVERT: B  329 MET cc_start: 0.9770 (mmm) cc_final: 0.9270 (mmm)
REVERT: B  479 PHE cc_start: 0.9761 (m-80) cc_final: 0.9376 (m-80)
REVERT: B  492 MET cc_start: 0.8918 (tpt) cc_final: 0.8707 (tpt)
REVERT: B  844 MET cc_start: 0.8953 (pmm) cc_final: 0.8306 (pmm)
REVERT: C    3 ILE cc_start: 0.8887 (tp) cc_final: 0.8583 (mp)
REVERT: E    1 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.6804 (tmm)
REVERT: E   14 THR cc_start: 0.9228 (m) cc_final: 0.8811 (t)
REVERT: E   33 LYS cc_start: 0.7966 (mtpt) cc_final: 0.7481 (tptt)
  outliers start: 6
  outliers final: 2
  residues processed: 86
  average time/residue: 0.1017
  time to fit residues: 13.1667
Evaluate side-chains
  63 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9990
   overall best weight:    3.1386

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

Flipped N/Q/H residues before XYZ refinement:
A4536 GLN
A4696 GLN
B 171 ASN
** E  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.038583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.032824 restraints weight = 168957.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.033622 restraints weight = 105349.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.034184 restraints weight = 73659.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.034608 restraints weight = 55606.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.034926 restraints weight = 43807.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.1083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11678  Z= 0.148
  Angle     :  0.544   6.698  15830  Z= 0.285
  Chirality :  0.040   0.169   1783
  Planarity :  0.004   0.043   2030
  Dihedral  :  5.065  48.656   1576
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.76 %
    Cis-general     : 0.07 %
    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:  1.25 (0.23), residues: 1421
  helix:  1.75 (0.22), residues: 578
  sheet:  0.69 (0.34), residues: 195
  loop :  0.13 (0.27), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  74 
 TYR   0.020   0.001   TYR A4528 
 PHE   0.016   0.001   PHE A4598 
 TRP   0.010   0.001   TRP B 660 
 HIS   0.007   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (11677)
  covalent geometry    : angle       0.54441 (15830)
  hydrogen bonds       : bond        0.03500 (  510)
  hydrogen bonds       : angle       5.05570 ( 1413)
  Misc. bond           : bond        0.00070 (    1)

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

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

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4532 MET cc_start: 0.8742 (mtp) cc_final: 0.8392 (mtp)
REVERT: B   69 MET cc_start: 0.8550 (mmp) cc_final: 0.7844 (mmm)
REVERT: B  329 MET cc_start: 0.9733 (mmm) cc_final: 0.9226 (mmm)
REVERT: B  479 PHE cc_start: 0.9764 (m-80) cc_final: 0.9406 (m-80)
REVERT: B  591 SER cc_start: 0.9123 (m) cc_final: 0.8911 (t)
REVERT: B  844 MET cc_start: 0.8765 (pmm) cc_final: 0.8215 (pmm)
REVERT: B  992 MET cc_start: 0.8493 (pmm) cc_final: 0.8261 (pmm)
REVERT: C    3 ILE cc_start: 0.8809 (tp) cc_final: 0.8468 (mp)
REVERT: E    1 MET cc_start: 0.8067 (ttp) cc_final: 0.6766 (tmm)
REVERT: E   14 THR cc_start: 0.9040 (m) cc_final: 0.8799 (t)
REVERT: E   33 LYS cc_start: 0.7948 (mtpt) cc_final: 0.7596 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.0994
  time to fit residues: 10.8957
Evaluate side-chains
  60 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 87 optimal weight:    6.9990
   chunk 71 optimal weight:    5.9990
   chunk 75 optimal weight:    0.0770
   chunk 110 optimal weight:    5.9990
   chunk 127 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   chunk 109 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 49 optimal weight:    5.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    3.2146

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

Flipped N/Q/H residues before XYZ refinement:
** A4696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A4758 HIS
B 171 ASN
** E  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.037810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.032107 restraints weight = 172427.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.032892 restraints weight = 106470.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.033441 restraints weight = 73904.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.033866 restraints weight = 55815.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.034183 restraints weight = 43947.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.1712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11678  Z= 0.146
  Angle     :  0.545   6.469  15830  Z= 0.281
  Chirality :  0.040   0.177   1783
  Planarity :  0.004   0.051   2030
  Dihedral  :  5.120  46.104   1576
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.76 %
    Cis-general     : 0.07 %
    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:  1.22 (0.23), residues: 1421
  helix:  1.73 (0.22), residues: 582
  sheet:  0.60 (0.35), residues: 201
  loop :  0.12 (0.27), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  74 
 TYR   0.009   0.001   TYR A4528 
 PHE   0.017   0.001   PHE B 757 
 TRP   0.012   0.001   TRP B 660 
 HIS   0.005   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (11677)
  covalent geometry    : angle       0.54452 (15830)
  hydrogen bonds       : bond        0.03303 (  510)
  hydrogen bonds       : angle       4.81558 ( 1413)
  Misc. bond           : bond        0.00003 (    1)

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

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

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4532 MET cc_start: 0.8834 (mtp) cc_final: 0.8452 (mtp)
REVERT: B   69 MET cc_start: 0.8525 (mmp) cc_final: 0.7813 (mmm)
REVERT: B  329 MET cc_start: 0.9692 (mmm) cc_final: 0.9185 (mmm)
REVERT: B  479 PHE cc_start: 0.9723 (m-80) cc_final: 0.9364 (m-80)
REVERT: B  844 MET cc_start: 0.8657 (pmm) cc_final: 0.8071 (pmm)
REVERT: C    3 ILE cc_start: 0.8710 (tp) cc_final: 0.8345 (mp)
REVERT: E    1 MET cc_start: 0.8244 (ttp) cc_final: 0.7445 (tmm)
REVERT: E   33 LYS cc_start: 0.8016 (mtpt) cc_final: 0.7767 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0996
  time to fit residues: 10.6615
Evaluate side-chains
  53 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 120 optimal weight:    5.9990
   chunk 110 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 140 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 54 optimal weight:    8.9990
   chunk 123 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A4696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 171 ASN
** E  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.038452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.032630 restraints weight = 169818.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.033431 restraints weight = 103856.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.033985 restraints weight = 71873.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.034412 restraints weight = 54225.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.034747 restraints weight = 42665.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  11678  Z= 0.109
  Angle     :  0.511   6.394  15830  Z= 0.260
  Chirality :  0.040   0.167   1783
  Planarity :  0.004   0.053   2030
  Dihedral  :  4.965  48.699   1576
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.76 %
    Cis-general     : 0.07 %
    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:  1.32 (0.23), residues: 1421
  helix:  1.85 (0.22), residues: 581
  sheet:  0.83 (0.35), residues: 195
  loop :  0.05 (0.26), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 869 
 TYR   0.007   0.001   TYR E  59 
 PHE   0.012   0.001   PHE B 711 
 TRP   0.010   0.001   TRP B 660 
 HIS   0.005   0.001   HIS B 858 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (11677)
  covalent geometry    : angle       0.51102 (15830)
  hydrogen bonds       : bond        0.02872 (  510)
  hydrogen bonds       : angle       4.63712 ( 1413)
  Misc. bond           : bond        0.00010 (    1)

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

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

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4532 MET cc_start: 0.8771 (mtp) cc_final: 0.8413 (mtp)
REVERT: A 4688 PHE cc_start: 0.9353 (t80) cc_final: 0.9150 (t80)
REVERT: B   69 MET cc_start: 0.8396 (mmp) cc_final: 0.7918 (mmm)
REVERT: B  479 PHE cc_start: 0.9776 (m-80) cc_final: 0.9395 (m-80)
REVERT: B  492 MET cc_start: 0.9162 (tpt) cc_final: 0.8962 (tpt)
REVERT: B  844 MET cc_start: 0.8642 (pmm) cc_final: 0.8011 (pmm)
REVERT: B  904 LEU cc_start: 0.9863 (tp) cc_final: 0.9500 (tt)
REVERT: B  907 LEU cc_start: 0.9809 (tp) cc_final: 0.9579 (tp)
REVERT: B  908 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9025 (mm-30)
REVERT: B  985 MET cc_start: 0.8780 (ppp) cc_final: 0.8410 (ppp)
REVERT: C    3 ILE cc_start: 0.8851 (tp) cc_final: 0.8560 (mp)
REVERT: E    1 MET cc_start: 0.8389 (ttp) cc_final: 0.7994 (tmm)
REVERT: E   14 THR cc_start: 0.9168 (m) cc_final: 0.8915 (t)
REVERT: E   33 LYS cc_start: 0.8073 (mtpt) cc_final: 0.7819 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.0990
  time to fit residues: 10.3874
Evaluate side-chains
  53 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 127 optimal weight:    4.9990
   chunk 109 optimal weight:    9.9990
   chunk 18 optimal weight:    0.8980
   chunk 30 optimal weight:    8.9990
   chunk 139 optimal weight:    9.9990
   chunk 128 optimal weight:   30.0000
   chunk 108 optimal weight:    6.9990
   chunk 107 optimal weight:    5.9990
   chunk 35 optimal weight:    8.9990
   chunk 24 optimal weight:    0.9990
   chunk 104 optimal weight:    6.9990
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A4696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 171 ASN
** E  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.036097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.030622 restraints weight = 176550.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.031382 restraints weight = 108893.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.031911 restraints weight = 75857.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.032314 restraints weight = 57561.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.032608 restraints weight = 45566.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11678  Z= 0.174
  Angle     :  0.575   7.257  15830  Z= 0.296
  Chirality :  0.041   0.165   1783
  Planarity :  0.004   0.050   2030
  Dihedral  :  5.229  56.748   1576
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.76 %
    Cis-general     : 0.07 %
    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:  1.12 (0.23), residues: 1421
  helix:  1.69 (0.22), residues: 582
  sheet:  0.60 (0.35), residues: 206
  loop : -0.02 (0.27), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 869 
 TYR   0.011   0.002   TYR A4705 
 PHE   0.014   0.002   PHE A4598 
 TRP   0.009   0.001   TRP B 660 
 HIS   0.009   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (11677)
  covalent geometry    : angle       0.57488 (15830)
  hydrogen bonds       : bond        0.03105 (  510)
  hydrogen bonds       : angle       4.80187 ( 1413)
  Misc. bond           : bond        0.00002 (    1)

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

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

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: A 4532 MET cc_start: 0.8788 (mtp) cc_final: 0.8507 (mtt)
REVERT: A 4688 PHE cc_start: 0.9386 (t80) cc_final: 0.9099 (t80)
REVERT: B   69 MET cc_start: 0.8524 (mmp) cc_final: 0.8059 (mmm)
REVERT: B  329 MET cc_start: 0.9610 (mmt) cc_final: 0.9128 (mmm)
REVERT: B  461 LEU cc_start: 0.9413 (mt) cc_final: 0.9196 (mt)
REVERT: B  479 PHE cc_start: 0.9722 (m-80) cc_final: 0.9364 (m-80)
REVERT: B  844 MET cc_start: 0.8753 (pmm) cc_final: 0.8310 (pmm)
REVERT: B  904 LEU cc_start: 0.9845 (tp) cc_final: 0.9443 (tt)
REVERT: B  908 GLU cc_start: 0.9440 (mm-30) cc_final: 0.9011 (mm-30)
REVERT: C    4 PHE cc_start: 0.8150 (m-80) cc_final: 0.7448 (m-80)
REVERT: E    1 MET cc_start: 0.8612 (ttp) cc_final: 0.8236 (tmm)
REVERT: E   33 LYS cc_start: 0.7979 (mtpt) cc_final: 0.7694 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0968
  time to fit residues: 9.1979
Evaluate side-chains
  48 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 92 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 45 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   chunk 1 optimal weight:    8.9990
   chunk 74 optimal weight:    8.9990
   chunk 115 optimal weight:    5.9990
   chunk 122 optimal weight:    0.9980
   chunk 78 optimal weight:   10.0000
   chunk 111 optimal weight:    5.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
B 171 ASN
** E  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.035381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.029999 restraints weight = 178250.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.030745 restraints weight = 109083.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.031269 restraints weight = 75857.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.031667 restraints weight = 57096.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.031963 restraints weight = 44987.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11678  Z= 0.177
  Angle     :  0.588   7.376  15830  Z= 0.302
  Chirality :  0.041   0.165   1783
  Planarity :  0.004   0.048   2030
  Dihedral  :  5.446  61.177   1576
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 14.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.76 %
    Cis-general     : 0.07 %
    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:  0.91 (0.23), residues: 1421
  helix:  1.52 (0.22), residues: 589
  sheet:  0.36 (0.35), residues: 211
  loop : -0.12 (0.27), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B1004 
 TYR   0.011   0.001   TYR B 994 
 PHE   0.016   0.002   PHE C   4 
 TRP   0.014   0.001   TRP B 660 
 HIS   0.009   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (11677)
  covalent geometry    : angle       0.58813 (15830)
  hydrogen bonds       : bond        0.03096 (  510)
  hydrogen bonds       : angle       4.86488 ( 1413)
  Misc. bond           : bond        0.00016 (    1)

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

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

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
REVERT: A 4532 MET cc_start: 0.8683 (mtp) cc_final: 0.8359 (mtt)
REVERT: A 4688 PHE cc_start: 0.9392 (t80) cc_final: 0.9075 (t80)
REVERT: B   69 MET cc_start: 0.8622 (mmp) cc_final: 0.8170 (mmm)
REVERT: B  329 MET cc_start: 0.9680 (mmm) cc_final: 0.9198 (mmm)
REVERT: B  479 PHE cc_start: 0.9724 (m-80) cc_final: 0.9354 (m-80)
REVERT: B  844 MET cc_start: 0.8776 (pmm) cc_final: 0.8286 (pmm)
REVERT: B  904 LEU cc_start: 0.9841 (tp) cc_final: 0.9467 (tt)
REVERT: B  907 LEU cc_start: 0.9817 (tp) cc_final: 0.9601 (tp)
REVERT: B  908 GLU cc_start: 0.9461 (mm-30) cc_final: 0.9034 (mm-30)
REVERT: B  985 MET cc_start: 0.8928 (ppp) cc_final: 0.8605 (ppp)
REVERT: E    1 MET cc_start: 0.8704 (ttp) cc_final: 0.8493 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0834
  time to fit residues: 8.2267
Evaluate side-chains
  47 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 126 optimal weight:   20.0000
   chunk 8 optimal weight:    0.9990
   chunk 137 optimal weight:    0.3980
   chunk 79 optimal weight:    6.9990
   chunk 83 optimal weight:    0.0980
   chunk 2 optimal weight:    0.0060
   chunk 21 optimal weight:    2.9990
   chunk 61 optimal weight:    7.9990
   chunk 58 optimal weight:    6.9990
   chunk 76 optimal weight:    8.9990
   chunk 85 optimal weight:    6.9990
   overall best weight:    0.9000

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

Flipped N/Q/H residues before XYZ refinement:
B 171 ASN
** B 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.037925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.032295 restraints weight = 168430.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.033088 restraints weight = 100881.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.033652 restraints weight = 69572.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.034065 restraints weight = 51308.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.034380 restraints weight = 40190.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.3118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  11678  Z= 0.090
  Angle     :  0.519   6.621  15830  Z= 0.261
  Chirality :  0.040   0.149   1783
  Planarity :  0.004   0.050   2030
  Dihedral  :  5.050  61.258   1576
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.76 %
    Cis-general     : 0.07 %
    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:  1.28 (0.23), residues: 1421
  helix:  1.82 (0.22), residues: 581
  sheet:  1.01 (0.35), residues: 191
  loop : -0.04 (0.26), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  74 
 TYR   0.007   0.001   TYR B 769 
 PHE   0.009   0.001   PHE B 966 
 TRP   0.010   0.001   TRP B 660 
 HIS   0.005   0.001   HIS B 599 

Details of bonding type rmsd
  covalent geometry    : bond        0.00191 (11677)
  covalent geometry    : angle       0.51880 (15830)
  hydrogen bonds       : bond        0.02726 (  510)
  hydrogen bonds       : angle       4.58419 ( 1413)
  Misc. bond           : bond        0.00025 (    1)

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

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

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4532 MET cc_start: 0.8719 (mtp) cc_final: 0.8460 (mtt)
REVERT: A 4688 PHE cc_start: 0.9398 (t80) cc_final: 0.9124 (t80)
REVERT: B   69 MET cc_start: 0.8624 (mmp) cc_final: 0.8116 (mmm)
REVERT: B  479 PHE cc_start: 0.9758 (m-80) cc_final: 0.9365 (m-80)
REVERT: B  844 MET cc_start: 0.8828 (pmm) cc_final: 0.8371 (pmm)
REVERT: B  904 LEU cc_start: 0.9840 (tp) cc_final: 0.9479 (tt)
REVERT: B  908 GLU cc_start: 0.9513 (mm-30) cc_final: 0.9058 (mm-30)
REVERT: C    4 PHE cc_start: 0.8423 (m-80) cc_final: 0.7737 (m-80)
REVERT: E    1 MET cc_start: 0.8734 (ttp) cc_final: 0.8025 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0837
  time to fit residues: 8.9925
Evaluate side-chains
  49 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   chunk 119 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0770
   chunk 86 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 121 optimal weight:    5.9990
   chunk 58 optimal weight:   10.0000
   chunk 137 optimal weight:    0.6980
   overall best weight:    1.6742

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

Flipped N/Q/H residues before XYZ refinement:
B 114 ASN
B 171 ASN
** B 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.037308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.031722 restraints weight = 170941.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.032512 restraints weight = 102737.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.033065 restraints weight = 70283.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.033468 restraints weight = 52139.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.033782 restraints weight = 40954.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.3289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  11678  Z= 0.098
  Angle     :  0.505   6.553  15830  Z= 0.255
  Chirality :  0.039   0.147   1783
  Planarity :  0.003   0.048   2030
  Dihedral  :  4.902  58.049   1576
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.76 %
    Cis-general     : 0.07 %
    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:  1.34 (0.23), residues: 1421
  helix:  1.90 (0.22), residues: 581
  sheet:  0.65 (0.35), residues: 212
  loop :  0.09 (0.27), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  74 
 TYR   0.007   0.001   TYR B 769 
 PHE   0.012   0.001   PHE B1028 
 TRP   0.009   0.001   TRP B 660 
 HIS   0.005   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 (11677)
  covalent geometry    : angle       0.50513 (15830)
  hydrogen bonds       : bond        0.02689 (  510)
  hydrogen bonds       : angle       4.50594 ( 1413)
  Misc. bond           : bond        0.00022 (    1)

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

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

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
REVERT: A 4532 MET cc_start: 0.8728 (mtp) cc_final: 0.8430 (mtt)
REVERT: A 4688 PHE cc_start: 0.9394 (t80) cc_final: 0.9171 (t80)
REVERT: B   69 MET cc_start: 0.8725 (mmp) cc_final: 0.8203 (mmm)
REVERT: B  329 MET cc_start: 0.9627 (mmt) cc_final: 0.9133 (mmm)
REVERT: B  479 PHE cc_start: 0.9758 (m-80) cc_final: 0.9353 (m-80)
REVERT: B  624 PHE cc_start: 0.9131 (t80) cc_final: 0.8918 (t80)
REVERT: B  844 MET cc_start: 0.8780 (pmm) cc_final: 0.8283 (pmm)
REVERT: B  904 LEU cc_start: 0.9837 (tp) cc_final: 0.9502 (tt)
REVERT: B  908 GLU cc_start: 0.9513 (mm-30) cc_final: 0.9076 (mm-30)
REVERT: B  985 MET cc_start: 0.8984 (ppp) cc_final: 0.8536 (ppp)
REVERT: C    4 PHE cc_start: 0.8436 (m-80) cc_final: 0.7762 (m-80)
REVERT: E    1 MET cc_start: 0.8698 (ttp) cc_final: 0.8038 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0817
  time to fit residues: 8.8946
Evaluate side-chains
  49 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 63 optimal weight:   10.0000
   chunk 133 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 97 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 113 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 66 optimal weight:   20.0000
   chunk 109 optimal weight:    7.9990
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
B 171 ASN
** B 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.036972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.031447 restraints weight = 169145.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.032221 restraints weight = 101913.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.032770 restraints weight = 69956.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.033168 restraints weight = 52027.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.033473 restraints weight = 40942.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  11678  Z= 0.107
  Angle     :  0.517   8.281  15830  Z= 0.260
  Chirality :  0.040   0.154   1783
  Planarity :  0.003   0.048   2030
  Dihedral  :  4.919  58.688   1576
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.76 %
    Cis-general     : 0.07 %
    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:  1.39 (0.23), residues: 1421
  helix:  1.93 (0.22), residues: 581
  sheet:  0.96 (0.36), residues: 198
  loop :  0.04 (0.26), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  74 
 TYR   0.008   0.001   TYR A4528 
 PHE   0.010   0.001   PHE A4598 
 TRP   0.017   0.001   TRP B 660 
 HIS   0.005   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (11677)
  covalent geometry    : angle       0.51663 (15830)
  hydrogen bonds       : bond        0.02698 (  510)
  hydrogen bonds       : angle       4.51588 ( 1413)
  Misc. bond           : bond        0.00014 (    1)

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

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

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
REVERT: A 4532 MET cc_start: 0.8705 (mtp) cc_final: 0.8417 (mtt)
REVERT: A 4688 PHE cc_start: 0.9395 (t80) cc_final: 0.9152 (t80)
REVERT: B   69 MET cc_start: 0.8715 (mmp) cc_final: 0.8209 (mmm)
REVERT: B  329 MET cc_start: 0.9722 (mmm) cc_final: 0.9236 (mmm)
REVERT: B  479 PHE cc_start: 0.9758 (m-80) cc_final: 0.9357 (m-10)
REVERT: B  492 MET cc_start: 0.9172 (tpt) cc_final: 0.8969 (tpt)
REVERT: B  844 MET cc_start: 0.8769 (pmm) cc_final: 0.8264 (pmm)
REVERT: B  904 LEU cc_start: 0.9835 (tp) cc_final: 0.9499 (tt)
REVERT: B  908 GLU cc_start: 0.9518 (mm-30) cc_final: 0.9073 (mm-30)
REVERT: C    4 PHE cc_start: 0.8519 (m-80) cc_final: 0.7825 (m-80)
REVERT: E    1 MET cc_start: 0.8676 (ttp) cc_final: 0.8029 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.0752
  time to fit residues: 7.9116
Evaluate side-chains
  46 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 121 optimal weight:    2.9990
   chunk 107 optimal weight:    9.9990
   chunk 111 optimal weight:    2.9990
   chunk 44 optimal weight:   20.0000
   chunk 77 optimal weight:   10.0000
   chunk 123 optimal weight:   20.0000
   chunk 140 optimal weight:    5.9990
   chunk 131 optimal weight:    8.9990
   chunk 17 optimal weight:    0.8980
   chunk 130 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
B 171 ASN
** B 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.036923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.031392 restraints weight = 171001.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.032173 restraints weight = 102490.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.032723 restraints weight = 70431.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.033127 restraints weight = 52222.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.033433 restraints weight = 40953.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.3666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  11678  Z= 0.101
  Angle     :  0.507   6.496  15830  Z= 0.256
  Chirality :  0.039   0.143   1783
  Planarity :  0.003   0.048   2030
  Dihedral  :  4.853  57.230   1576
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.76 %
    Cis-general     : 0.07 %
    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:  1.36 (0.23), residues: 1421
  helix:  1.95 (0.22), residues: 581
  sheet:  0.63 (0.35), residues: 209
  loop :  0.08 (0.27), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  74 
 TYR   0.013   0.001   TYR A4660 
 PHE   0.009   0.001   PHE B 966 
 TRP   0.013   0.001   TRP B 660 
 HIS   0.004   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 (11677)
  covalent geometry    : angle       0.50689 (15830)
  hydrogen bonds       : bond        0.02632 (  510)
  hydrogen bonds       : angle       4.46861 ( 1413)
  Misc. bond           : bond        0.00011 (    1)

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

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

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2842 Ramachandran restraints generated.
    1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 4688 PHE cc_start: 0.9384 (t80) cc_final: 0.9139 (t80)
REVERT: B   69 MET cc_start: 0.8747 (mmp) cc_final: 0.8221 (mmm)
REVERT: B  479 PHE cc_start: 0.9759 (m-80) cc_final: 0.9357 (m-10)
REVERT: B  492 MET cc_start: 0.9175 (tpt) cc_final: 0.8965 (tpt)
REVERT: B  844 MET cc_start: 0.8754 (pmm) cc_final: 0.8236 (pmm)
REVERT: B  904 LEU cc_start: 0.9832 (tp) cc_final: 0.9501 (tt)
REVERT: B  908 GLU cc_start: 0.9518 (mm-30) cc_final: 0.9091 (mm-30)
REVERT: C    4 PHE cc_start: 0.8488 (m-80) cc_final: 0.7812 (m-80)
REVERT: E    1 MET cc_start: 0.8596 (ttp) cc_final: 0.8026 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0786
  time to fit residues: 8.2791
Evaluate side-chains
  45 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 132 optimal weight:    9.9990
   chunk 51 optimal weight:    9.9990
   chunk 12 optimal weight:    0.0670
   chunk 94 optimal weight:    0.9980
   chunk 118 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 104 optimal weight:    9.9990
   chunk 61 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 105 optimal weight:    8.9990
   overall best weight:    1.6124

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

Flipped N/Q/H residues before XYZ refinement:
B 171 ASN
** B 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.037191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.031662 restraints weight = 170183.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.032454 restraints weight = 101820.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.033013 restraints weight = 69306.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.033420 restraints weight = 51334.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.033719 restraints weight = 40243.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.3792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  11678  Z= 0.093
  Angle     :  0.504   6.523  15830  Z= 0.252
  Chirality :  0.040   0.144   1783
  Planarity :  0.003   0.048   2030
  Dihedral  :  4.789  58.123   1576
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.76 %
    Cis-general     : 0.07 %
    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:  1.40 (0.23), residues: 1421
  helix:  1.96 (0.22), residues: 582
  sheet:  0.68 (0.36), residues: 209
  loop :  0.12 (0.27), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  74 
 TYR   0.008   0.001   TYR A4528 
 PHE   0.009   0.001   PHE B 656 
 TRP   0.013   0.001   TRP B 660 
 HIS   0.004   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00199 (11677)
  covalent geometry    : angle       0.50397 (15830)
  hydrogen bonds       : bond        0.02585 (  510)
  hydrogen bonds       : angle       4.41671 ( 1413)
  Misc. bond           : bond        0.00022 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1679.52 seconds
wall clock time: 30 minutes 16.92 seconds (1816.92 seconds total)