Starting phenix.real_space_refine
on Thu May 15 16:29:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h8x_34551/05_2025/8h8x_34551.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h8x_34551/05_2025/8h8x_34551.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8h8x_34551/05_2025/8h8x_34551.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h8x_34551/05_2025/8h8x_34551.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h8x_34551/05_2025/8h8x_34551.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h8x_34551/05_2025/8h8x_34551.cif"
  }
  resolution = 3.92
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    4274      2.51       5
     N    1166      2.21       5
     O    1262      1.98       5
     H    6667      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13418
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 13418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 850, 13418
          Classifications: {'peptide': 850}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 39, 'TRANS': 810}
          Chain breaks: 1
  Time building chain proxies: 6.66, per 1000 atoms: 0.50
  Number of scatterers: 13418
  At special positions: 0
  Unit cell: (75.5392, 100.433, 156.229, 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      49     16.00
     O    1262      8.00
     N    1166      7.00
     C    4274      6.00
     H    6667      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.46
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1602

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 4 sheets defined
      63.9% alpha, 2.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 17
      removed outlier: 4.401A  pdb=" N   LEU A  11 " --> pdb=" O   GLN A   7 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   THR A  12 " --> pdb=" O   LEU A   8 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ARG A  13 " --> pdb=" O   ASN A   9 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   SER A  14 " --> pdb=" O   ARG A  10 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU A  15 " --> pdb=" O   LEU A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 40
      removed outlier: 4.182A  pdb=" N   TYR A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
      Proline residue:  A  36  - end of helix
    Processing helix  chain 'A' and resid 42 through 50
    Processing helix  chain 'A' and resid 67 through 76
      removed outlier: 3.546A  pdb=" N   ILE A  71 " --> pdb=" O   SER A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 87
      removed outlier: 3.934A  pdb=" N   LEU A  83 " --> pdb=" O   GLU A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 109
      removed outlier: 3.986A  pdb=" N   LEU A 104 " --> pdb=" O   THR A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 120
      removed outlier: 3.529A  pdb=" N   LEU A 117 " --> pdb=" O   CYS A 113 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU A 118 " --> pdb=" O   MET A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 141
    Processing helix  chain 'A' and resid 144 through 152
      removed outlier: 3.523A  pdb=" N   GLN A 152 " --> pdb=" O   HIS A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 175
    Processing helix  chain 'A' and resid 176 through 186
    Processing helix  chain 'A' and resid 199 through 208
      removed outlier: 3.556A  pdb=" N   PHE A 203 " --> pdb=" O   THR A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 219
    Processing helix  chain 'A' and resid 232 through 240
      removed outlier: 3.612A  pdb=" N   CYS A 236 " --> pdb=" O   PRO A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 252
      removed outlier: 3.888A  pdb=" N   CYS A 245 " --> pdb=" O   TYR A 241 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   VAL A 247 " --> pdb=" O   GLU A 243 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU A 248 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLN A 250 " --> pdb=" O   GLU A 246 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   TYR A 251 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 261
      removed outlier: 3.888A  pdb=" N   THR A 258 " --> pdb=" O   ARG A 254 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE A 260 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 284
      removed outlier: 3.538A  pdb=" N   LEU A 273 " --> pdb=" O   ARG A 269 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ARG A 274 " --> pdb=" O   GLU A 270 " (cutoff:3.500A)
      removed outlier: 5.102A  pdb=" N   GLN A 275 " --> pdb=" O   ASN A 271 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLN A 282 " --> pdb=" O   GLU A 278 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   SER A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 308
      removed outlier: 4.133A  pdb=" N   LYS A 290 " --> pdb=" O   SER A 286 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLU A 297 " --> pdb=" O   THR A 293 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   VAL A 298 " --> pdb=" O   SER A 294 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   HIS A 304 " --> pdb=" O   THR A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 334
      removed outlier: 3.898A  pdb=" N   GLN A 316 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LYS A 318 " --> pdb=" O   ASP A 314 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU A 321 " --> pdb=" O   MET A 317 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ILE A 323 " --> pdb=" O   SER A 319 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ARG A 325 " --> pdb=" O   LEU A 321 " (cutoff:3.500A)
      removed outlier: 4.972A  pdb=" N   MET A 326 " --> pdb=" O   ARG A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 355
    Processing helix  chain 'A' and resid 357 through 359
      No H-bonds generated for 'chain 'A' and resid 357 through 359'
    Processing helix  chain 'A' and resid 360 through 382
      removed outlier: 3.666A  pdb=" N   TRP A 364 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU A 369 " --> pdb=" O   HIS A 365 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   TRP A 370 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU A 371 " --> pdb=" O   LEU A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 464
      removed outlier: 3.738A  pdb=" N   ALA A 449 " --> pdb=" O   ILE A 445 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   ASN A 450 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   ARG A 451 " --> pdb=" O   MET A 447 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU A 452 " --> pdb=" O   THR A 448 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   SER A 453 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ALA A 454 " --> pdb=" O   ASN A 450 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   VAL A 455 " --> pdb=" O   ARG A 451 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   CYS A 463 " --> pdb=" O   PHE A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 483
      removed outlier: 3.560A  pdb=" N   ILE A 477 " --> pdb=" O   SER A 473 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLU A 478 " --> pdb=" O   PRO A 474 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   PHE A 479 " --> pdb=" O   ARG A 475 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   HIS A 483 " --> pdb=" O   PHE A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 494
      removed outlier: 3.562A  pdb=" N   LYS A 488 " --> pdb=" O   ASP A 484 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   CYS A 489 " --> pdb=" O   GLU A 485 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE A 490 " --> pdb=" O   VAL A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 500
    Processing helix  chain 'A' and resid 502 through 508
    Processing helix  chain 'A' and resid 508 through 515
    Processing helix  chain 'A' and resid 515 through 520
      removed outlier: 4.058A  pdb=" N   ILE A 519 " --> pdb=" O   PHE A 515 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LYS A 520 " --> pdb=" O   MET A 516 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 515 through 520'
    Processing helix  chain 'A' and resid 524 through 530
    Processing helix  chain 'A' and resid 532 through 537
    Processing helix  chain 'A' and resid 561 through 573
      removed outlier: 3.894A  pdb=" N   GLU A 568 " --> pdb=" O   ARG A 564 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   SER A 571 " --> pdb=" O   CYS A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 579
    Processing helix  chain 'A' and resid 596 through 608
      removed outlier: 3.750A  pdb=" N   TRP A 600 " --> pdb=" O   VAL A 596 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   PHE A 601 " --> pdb=" O   VAL A 597 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ASN A 606 " --> pdb=" O   ASP A 602 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 614
    Processing helix  chain 'A' and resid 629 through 634
      removed outlier: 4.152A  pdb=" N   TYR A 632 " --> pdb=" O   SER A 629 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   VAL A 633 " --> pdb=" O   ASN A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 638 through 654
      removed outlier: 3.639A  pdb=" N   PHE A 643 " --> pdb=" O   ASN A 639 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ALA A 644 " --> pdb=" O   TYR A 640 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLY A 645 " --> pdb=" O   PHE A 641 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLN A 646 " --> pdb=" O   ARG A 642 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ILE A 647 " --> pdb=" O   PHE A 643 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU A 648 " --> pdb=" O   ALA A 644 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   GLY A 649 " --> pdb=" O   GLY A 645 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   LEU A 650 " --> pdb=" O   GLN A 646 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 671
      removed outlier: 3.778A  pdb=" N   TYR A 667 " --> pdb=" O   THR A 663 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LYS A 668 " --> pdb=" O   ARG A 664 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ILE A 670 " --> pdb=" O   PHE A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 683
      removed outlier: 3.774A  pdb=" N   SER A 682 " --> pdb=" O   ASP A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 684 through 697
      removed outlier: 3.837A  pdb=" N   ALA A 688 " --> pdb=" O   ASP A 684 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE A 694 " --> pdb=" O   ASN A 690 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU A 695 " --> pdb=" O   LEU A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 698 through 702
      removed outlier: 3.566A  pdb=" N   ASP A 701 " --> pdb=" O   ASP A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 736 through 765
      removed outlier: 3.519A  pdb=" N   THR A 745 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   MET A 749 " --> pdb=" O   THR A 745 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ALA A 752 " --> pdb=" O   ARG A 748 " (cutoff:3.500A)
      Proline residue:  A 755  - end of helix
      removed outlier: 3.611A  pdb=" N   ASN A 758 " --> pdb=" O   GLN A 754 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   ALA A 759 " --> pdb=" O   PRO A 755 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   PHE A 760 " --> pdb=" O   GLN A 756 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   GLY A 763 " --> pdb=" O   ALA A 759 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 774
      removed outlier: 4.052A  pdb=" N   ILE A 773 " --> pdb=" O   PRO A 769 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   GLN A 774 " --> pdb=" O   PRO A 770 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 769 through 774'
    Processing helix  chain 'A' and resid 780 through 787
      removed outlier: 4.047A  pdb=" N   LEU A 784 " --> pdb=" O   GLU A 780 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LEU A 785 " --> pdb=" O   LEU A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 792 through 799
      removed outlier: 3.512A  pdb=" N   ASN A 799 " --> pdb=" O   ASP A 795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 810 through 821
      removed outlier: 3.604A  pdb=" N   TRP A 817 " --> pdb=" O   ILE A 813 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLU A 818 " --> pdb=" O   GLN A 814 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL A 819 " --> pdb=" O   TRP A 815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 824 through 837
      removed outlier: 3.728A  pdb=" N   ARG A 828 " --> pdb=" O   THR A 824 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   LEU A 830 " --> pdb=" O   GLU A 826 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLN A 833 " --> pdb=" O   VAL A 829 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 844 through 849
      removed outlier: 3.916A  pdb=" N   ALA A 847 " --> pdb=" O   GLY A 844 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 887 through 904
      removed outlier: 4.772A  pdb=" N   LEU A 896 " --> pdb=" O   LYS A 892 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   HIS A 900 " --> pdb=" O   LEU A 896 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   CYS A 901 " --> pdb=" O   VAL A 897 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 555 through 557
    Processing sheet with id=AA2, first strand: chain 'A' and resid 616 through 618
    Processing sheet with id=AA3, first strand: chain 'A' and resid 709 through 713
      removed outlier: 3.587A  pdb=" N   VAL A 721 " --> pdb=" O   VAL A 710 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 801 through 802
      removed outlier: 6.684A  pdb=" N   GLU A 801 " --> pdb=" O   ILE A 860 " (cutoff:3.500A)
      removed outlier: 8.705A  pdb=" N   ALA A 862 " --> pdb=" O   GLU A 801 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   THR A 859 " --> pdb=" O   LEU A 880 " (cutoff:3.500A)
      removed outlier: 8.231A  pdb=" N   LEU A 882 " --> pdb=" O   THR A 859 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ALA A 861 " --> pdb=" O   LEU A 882 " (cutoff:3.500A)

    259 hydrogen bonds defined for protein.
    720 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: 4.20

  Time building geometry restraints manager: 4.15 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 6645
        1.03 -     1.22: 23
        1.22 -     1.42: 2892
        1.42 -     1.61: 3930
        1.61 -     1.81: 76
  Bond restraints: 13566
  Sorted by residual:
  bond pdb=" CB  VAL A 324 "
       pdb=" CG1 VAL A 324 "
    ideal  model  delta    sigma   weight residual
    1.521  1.431  0.090 3.30e-02 9.18e+02 7.40e+00
  bond pdb=" CA  ASP A 621 "
       pdb=" C   ASP A 621 "
    ideal  model  delta    sigma   weight residual
    1.523  1.487  0.036 1.41e-02 5.03e+03 6.55e+00
  bond pdb=" CG  LEU A 320 "
       pdb=" CD1 LEU A 320 "
    ideal  model  delta    sigma   weight residual
    1.521  1.438  0.083 3.30e-02 9.18e+02 6.35e+00
  bond pdb=" CG  LEU A 321 "
       pdb=" CD2 LEU A 321 "
    ideal  model  delta    sigma   weight residual
    1.521  1.442  0.079 3.30e-02 9.18e+02 5.80e+00
  bond pdb=" CA  PHE A 524 "
       pdb=" CB  PHE A 524 "
    ideal  model  delta    sigma   weight residual
    1.534  1.500  0.034 1.45e-02 4.76e+03 5.35e+00
  ... (remaining 13561 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 23093
        1.66 -     3.32: 1278
        3.32 -     4.98: 107
        4.98 -     6.64: 16
        6.64 -     8.30: 3
  Bond angle restraints: 24497
  Sorted by residual:
  angle pdb=" N   LEU A 535 "
        pdb=" CA  LEU A 535 "
        pdb=" C   LEU A 535 "
      ideal   model   delta    sigma   weight residual
     113.18  107.77    5.41 1.33e+00 5.65e-01 1.65e+01
  angle pdb=" N   LYS A 350 "
        pdb=" CA  LYS A 350 "
        pdb=" CB  LYS A 350 "
      ideal   model   delta    sigma   weight residual
     114.17  109.88    4.29 1.14e+00 7.69e-01 1.41e+01
  angle pdb=" N   THR A 623 "
        pdb=" CA  THR A 623 "
        pdb=" C   THR A 623 "
      ideal   model   delta    sigma   weight residual
     113.55  109.34    4.21 1.26e+00 6.30e-01 1.11e+01
  angle pdb=" N   ASP A 541 "
        pdb=" CA  ASP A 541 "
        pdb=" C   ASP A 541 "
      ideal   model   delta    sigma   weight residual
     111.55  107.72    3.83 1.37e+00 5.33e-01 7.82e+00
  angle pdb=" N   ILE A 498 "
        pdb=" CA  ILE A 498 "
        pdb=" CB  ILE A 498 "
      ideal   model   delta    sigma   weight residual
     111.23  106.85    4.38 1.65e+00 3.67e-01 7.06e+00
  ... (remaining 24492 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.63: 5719
       14.63 -    29.27: 489
       29.27 -    43.90: 139
       43.90 -    58.53: 57
       58.53 -    73.16: 5
  Dihedral angle restraints: 6409
    sinusoidal: 3493
      harmonic: 2916
  Sorted by residual:
  dihedral pdb=" CA  HIS A 534 "
           pdb=" C   HIS A 534 "
           pdb=" N   LEU A 535 "
           pdb=" CA  LEU A 535 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.57   35.43     0      5.00e+00 4.00e-02 5.02e+01
  dihedral pdb=" CA  LEU A 706 "
           pdb=" C   LEU A 706 "
           pdb=" N   THR A 707 "
           pdb=" CA  THR A 707 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.92  -31.08     0      5.00e+00 4.00e-02 3.86e+01
  dihedral pdb=" CA  PRO A 540 "
           pdb=" C   PRO A 540 "
           pdb=" N   ASP A 541 "
           pdb=" CA  ASP A 541 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.38   28.62     0      5.00e+00 4.00e-02 3.28e+01
  ... (remaining 6406 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 603
       0.036 -    0.071: 295
       0.071 -    0.107: 100
       0.107 -    0.143: 40
       0.143 -    0.179: 6
  Chirality restraints: 1044
  Sorted by residual:
  chirality pdb=" CB  VAL A 455 "
            pdb=" CA  VAL A 455 "
            pdb=" CG1 VAL A 455 "
            pdb=" CG2 VAL A 455 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.97e-01
  chirality pdb=" CG  LEU A 321 "
            pdb=" CB  LEU A 321 "
            pdb=" CD1 LEU A 321 "
            pdb=" CD2 LEU A 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.20e-01
  chirality pdb=" CA  PRO A 540 "
            pdb=" N   PRO A 540 "
            pdb=" C   PRO A 540 "
            pdb=" CB  PRO A 540 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.33e-01
  ... (remaining 1041 not shown)

  Planarity restraints: 2028
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 459 "   -0.022 2.00e-02 2.50e+03   1.57e-02 7.37e+00
        pdb=" CG  PHE A 459 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 459 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 459 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 459 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 459 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 459 "    0.000 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 459 "    0.005 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 459 "   -0.003 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 459 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 459 "   -0.004 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 459 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 534 "    0.013 2.00e-02 2.50e+03   2.63e-02 6.92e+00
        pdb=" C   HIS A 534 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   HIS A 534 "    0.018 2.00e-02 2.50e+03
        pdb=" N   LEU A 535 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 547 "   -0.037 5.00e-02 4.00e+02   5.58e-02 4.98e+00
        pdb=" N   PRO A 548 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 548 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 548 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 2025 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.25: 1587
        2.25 -     2.84: 30500
        2.84 -     3.43: 32464
        3.43 -     4.01: 42752
        4.01 -     4.60: 67443
  Nonbonded interactions: 174746
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 335 "
            pdb=" H   ASP A 343 "
     model   vdw
     1.663 2.450
  nonbonded pdb=" O   ILE A 753 "
            pdb=" H   GLN A 756 "
     model   vdw
     1.668 2.450
  nonbonded pdb=" O   PHE A 708 "
            pdb=" H   LEU A 723 "
     model   vdw
     1.688 2.450
  nonbonded pdb=" O   HIS A 534 "
            pdb="HE21 GLN A 539 "
     model   vdw
     1.690 2.450
  nonbonded pdb=" HG  SER A 619 "
            pdb=" OG1 THR A 624 "
     model   vdw
     1.691 2.450
  ... (remaining 174741 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  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:             0.220
  Extract box with map and model:          0.570
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     30.080
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
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      :  0.011   0.090   6899  Z= 0.446
  Angle     :  0.894   8.290   9356  Z= 0.508
  Chirality :  0.050   0.179   1044
  Planarity :  0.006   0.056   1219
  Dihedral  :  9.886  73.163   2558
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.16 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.57 (0.25), residues: 846
  helix: -3.12 (0.18), residues: 378
  sheet: -2.02 (1.01), residues: 19
  loop : -1.61 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.004   TRP A 796 
 HIS   0.014   0.003   HIS A 654 
 PHE   0.046   0.004   PHE A 459 
 TYR   0.028   0.003   TYR A 667 
 ARG   0.009   0.001   ARG A  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.32507 (  259)
  hydrogen bonds       : angle      10.80296 (  720)
  covalent geometry    : bond        0.01074 ( 6899)
  covalent geometry    : angle       0.89390 ( 9356)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 MET cc_start: 0.8846 (mtp) cc_final: 0.8589 (mmm)
REVERT: A  524 PHE cc_start: 0.7147 (m-80) cc_final: 0.6905 (m-10)
REVERT: A  751 ARG cc_start: 0.7671 (tpt90) cc_final: 0.7033 (tpm170)
REVERT: A  822 ASP cc_start: 0.7983 (m-30) cc_final: 0.7780 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.5275
  time to fit residues: 75.2900
Evaluate side-chains
  74 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    0.5980
   chunk 64 optimal weight:   10.0000
   chunk 35 optimal weight:    0.6980
   chunk 22 optimal weight:    7.9990
   chunk 43 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 66 optimal weight:   30.0000
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 49 optimal weight:    5.9990
   chunk 77 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 141 ASN
A 257 GLN
A 669 HIS
A 697 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.121445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.094767 restraints weight = 65164.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.098459 restraints weight = 32706.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.100752 restraints weight = 21119.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6899  Z= 0.132
  Angle     :  0.621   5.982   9356  Z= 0.334
  Chirality :  0.038   0.138   1044
  Planarity :  0.005   0.052   1219
  Dihedral  :  6.070  27.517    917
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  5.17 %
    Favored  : 94.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.56 (0.26), residues: 846
  helix: -1.62 (0.20), residues: 437
  sheet: -1.78 (1.04), residues: 19
  loop : -1.66 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 600 
 HIS   0.005   0.001   HIS A 669 
 PHE   0.013   0.001   PHE A 327 
 TYR   0.017   0.001   TYR A 313 
 ARG   0.003   0.000   ARG A 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05314 (  259)
  hydrogen bonds       : angle       6.24040 (  720)
  covalent geometry    : bond        0.00266 ( 6899)
  covalent geometry    : angle       0.62093 ( 9356)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 TRP cc_start: 0.8615 (t-100) cc_final: 0.7842 (t-100)
REVERT: A  751 ARG cc_start: 0.7678 (tpt90) cc_final: 0.6965 (tpm170)
  outliers start: 4
  outliers final: 3
  residues processed: 93
  average time/residue: 0.4495
  time to fit residues: 55.6060
Evaluate side-chains
  75 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  148 HIS
Chi-restraints excluded: chain A residue  677 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 7 optimal weight:   20.0000
   chunk 46 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 51 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
A 536 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.119465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.091925 restraints weight = 64297.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.095576 restraints weight = 31809.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.097833 restraints weight = 20603.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.3524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6899  Z= 0.143
  Angle     :  0.557   5.207   9356  Z= 0.299
  Chirality :  0.037   0.135   1044
  Planarity :  0.004   0.058   1219
  Dihedral  :  5.519  23.834    917
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  7.28 %
    Favored  : 92.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.27), residues: 846
  helix: -0.92 (0.22), residues: 439
  sheet: -1.06 (1.19), residues: 19
  loop : -1.56 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 817 
 HIS   0.006   0.001   HIS A 558 
 PHE   0.013   0.001   PHE A 531 
 TYR   0.010   0.001   TYR A 313 
 ARG   0.005   0.000   ARG A 514 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04670 (  259)
  hydrogen bonds       : angle       5.68631 (  720)
  covalent geometry    : bond        0.00308 ( 6899)
  covalent geometry    : angle       0.55678 ( 9356)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 1.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 LEU cc_start: 0.9106 (tt) cc_final: 0.8845 (tt)
REVERT: A  742 GLN cc_start: 0.8904 (tp-100) cc_final: 0.8566 (tp-100)
REVERT: A  751 ARG cc_start: 0.7629 (tpt90) cc_final: 0.6932 (tpm170)
REVERT: A  879 MET cc_start: 0.8493 (ttt) cc_final: 0.8072 (tpp)
REVERT: A  882 LEU cc_start: 0.8273 (mp) cc_final: 0.7603 (tp)
  outliers start: 4
  outliers final: 3
  residues processed: 83
  average time/residue: 0.4827
  time to fit residues: 52.8148
Evaluate side-chains
  68 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  148 HIS
Chi-restraints excluded: chain A residue  677 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0870
   chunk 71 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 54 optimal weight:    0.2980
   overall best weight:    0.8360

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.120499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.093536 restraints weight = 64415.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.097075 restraints weight = 32164.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.099313 restraints weight = 20968.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.4120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6899  Z= 0.099
  Angle     :  0.517   5.887   9356  Z= 0.271
  Chirality :  0.036   0.131   1044
  Planarity :  0.004   0.048   1219
  Dihedral  :  5.114  23.888    917
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  7.68 %
    Favored  : 91.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.28), residues: 846
  helix: -0.32 (0.23), residues: 448
  sheet: -0.77 (1.22), residues: 19
  loop : -1.41 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 600 
 HIS   0.003   0.001   HIS A  43 
 PHE   0.009   0.001   PHE A 531 
 TYR   0.008   0.001   TYR A 313 
 ARG   0.005   0.000   ARG A 514 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03685 (  259)
  hydrogen bonds       : angle       5.19099 (  720)
  covalent geometry    : bond        0.00213 ( 6899)
  covalent geometry    : angle       0.51700 ( 9356)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 1.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  742 GLN cc_start: 0.8915 (tp-100) cc_final: 0.8566 (tp-100)
REVERT: A  751 ARG cc_start: 0.7474 (tpt90) cc_final: 0.6816 (tpm170)
REVERT: A  879 MET cc_start: 0.8460 (ttt) cc_final: 0.7993 (tpp)
REVERT: A  882 LEU cc_start: 0.8158 (mp) cc_final: 0.7570 (tt)
  outliers start: 4
  outliers final: 2
  residues processed: 73
  average time/residue: 0.4119
  time to fit residues: 40.7729
Evaluate side-chains
  65 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 HIS
Chi-restraints excluded: chain A residue  677 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 80 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 4 optimal weight:    9.9990
   chunk 42 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A  27 ASN
A 129 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.118762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.095053 restraints weight = 64880.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.095088 restraints weight = 30910.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.095583 restraints weight = 26754.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.4498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6899  Z= 0.126
  Angle     :  0.521   6.588   9356  Z= 0.275
  Chirality :  0.037   0.129   1044
  Planarity :  0.004   0.048   1219
  Dihedral  :  4.897  22.370    917
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  7.15 %
    Favored  : 91.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.29), residues: 846
  helix:  0.15 (0.24), residues: 442
  sheet: -0.97 (1.20), residues: 18
  loop : -1.25 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 796 
 HIS   0.004   0.001   HIS A 654 
 PHE   0.012   0.001   PHE A 531 
 TYR   0.008   0.001   TYR A 202 
 ARG   0.001   0.000   ARG A 564 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03702 (  259)
  hydrogen bonds       : angle       5.09687 (  720)
  covalent geometry    : bond        0.00279 ( 6899)
  covalent geometry    : angle       0.52059 ( 9356)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 1.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  742 GLN cc_start: 0.8926 (tp-100) cc_final: 0.8579 (tp-100)
REVERT: A  751 ARG cc_start: 0.7572 (tpt90) cc_final: 0.6902 (tpm170)
REVERT: A  879 MET cc_start: 0.8562 (ttt) cc_final: 0.7925 (tpp)
  outliers start: 7
  outliers final: 5
  residues processed: 70
  average time/residue: 0.3919
  time to fit residues: 37.8029
Evaluate side-chains
  67 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  120 TYR
Chi-restraints excluded: chain A residue  148 HIS
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  592 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 4 optimal weight:    9.9990
   chunk 16 optimal weight:    8.9990
   chunk 27 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 39 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 73 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.120011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.092723 restraints weight = 65697.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.096308 restraints weight = 32480.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.098551 restraints weight = 21110.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.4763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6899  Z= 0.103
  Angle     :  0.499   5.863   9356  Z= 0.260
  Chirality :  0.036   0.128   1044
  Planarity :  0.004   0.047   1219
  Dihedral  :  4.737  22.990    917
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  7.68 %
    Favored  : 91.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.29), residues: 846
  helix:  0.50 (0.24), residues: 444
  sheet: -0.92 (1.15), residues: 19
  loop : -1.22 (0.33), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 796 
 HIS   0.004   0.001   HIS A 517 
 PHE   0.013   0.001   PHE A 331 
 TYR   0.007   0.001   TYR A 532 
 ARG   0.001   0.000   ARG A 514 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03377 (  259)
  hydrogen bonds       : angle       4.84116 (  720)
  covalent geometry    : bond        0.00229 ( 6899)
  covalent geometry    : angle       0.49950 ( 9356)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  742 GLN cc_start: 0.8908 (tp-100) cc_final: 0.8538 (tp-100)
REVERT: A  751 ARG cc_start: 0.7433 (tpt90) cc_final: 0.6782 (tpm170)
REVERT: A  879 MET cc_start: 0.8431 (ttt) cc_final: 0.8075 (tpp)
REVERT: A  882 LEU cc_start: 0.8301 (mp) cc_final: 0.7584 (tt)
  outliers start: 4
  outliers final: 2
  residues processed: 64
  average time/residue: 0.3765
  time to fit residues: 33.4686
Evaluate side-chains
  63 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 HIS
Chi-restraints excluded: chain A residue  592 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 29 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 58 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9990
   chunk 53 optimal weight:    8.9990
   chunk 4 optimal weight:    9.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.119549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.092385 restraints weight = 65307.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.095909 restraints weight = 32570.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.098087 restraints weight = 21237.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.4981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6899  Z= 0.114
  Angle     :  0.501   5.567   9356  Z= 0.262
  Chirality :  0.036   0.124   1044
  Planarity :  0.004   0.048   1219
  Dihedral  :  4.641  21.953    917
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  7.95 %
    Favored  : 91.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.30), residues: 846
  helix:  0.65 (0.24), residues: 446
  sheet: -0.64 (0.98), residues: 29
  loop : -1.24 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 796 
 HIS   0.004   0.001   HIS A 517 
 PHE   0.012   0.001   PHE A 531 
 TYR   0.007   0.001   TYR A 202 
 ARG   0.001   0.000   ARG A 514 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03381 (  259)
  hydrogen bonds       : angle       4.78911 (  720)
  covalent geometry    : bond        0.00254 ( 6899)
  covalent geometry    : angle       0.50088 ( 9356)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 1.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  742 GLN cc_start: 0.8876 (tp-100) cc_final: 0.8537 (tp-100)
REVERT: A  751 ARG cc_start: 0.7484 (tpt90) cc_final: 0.6779 (tpm170)
REVERT: A  879 MET cc_start: 0.8476 (ttt) cc_final: 0.8090 (tpp)
REVERT: A  882 LEU cc_start: 0.8353 (mp) cc_final: 0.7674 (tt)
  outliers start: 4
  outliers final: 4
  residues processed: 65
  average time/residue: 0.3825
  time to fit residues: 34.6254
Evaluate side-chains
  67 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  148 HIS
Chi-restraints excluded: chain A residue  592 MET
Chi-restraints excluded: chain A residue  693 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 64 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   chunk 77 optimal weight:    0.6980
   chunk 66 optimal weight:    0.5980
   chunk 83 optimal weight:    0.6980
   chunk 38 optimal weight:    6.9990
   chunk 69 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 50 optimal weight:    4.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.120286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.093167 restraints weight = 65910.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.096737 restraints weight = 32779.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.098955 restraints weight = 21307.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.5152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6899  Z= 0.088
  Angle     :  0.479   5.202   9356  Z= 0.247
  Chirality :  0.035   0.129   1044
  Planarity :  0.004   0.046   1219
  Dihedral  :  4.475  22.128    917
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  7.95 %
    Favored  : 91.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.30), residues: 846
  helix:  0.82 (0.25), residues: 455
  sheet: -0.65 (0.98), residues: 30
  loop : -1.27 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 817 
 HIS   0.003   0.001   HIS A 534 
 PHE   0.010   0.001   PHE A 816 
 TYR   0.012   0.001   TYR A 885 
 ARG   0.002   0.000   ARG A 514 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03071 (  259)
  hydrogen bonds       : angle       4.55440 (  720)
  covalent geometry    : bond        0.00195 ( 6899)
  covalent geometry    : angle       0.47938 ( 9356)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 1.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  742 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8477 (tp-100)
REVERT: A  879 MET cc_start: 0.8435 (ttt) cc_final: 0.8004 (tpp)
REVERT: A  882 LEU cc_start: 0.8261 (mp) cc_final: 0.7708 (tp)
  outliers start: 6
  outliers final: 4
  residues processed: 67
  average time/residue: 0.4231
  time to fit residues: 39.6554
Evaluate side-chains
  66 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 62
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  148 HIS
Chi-restraints excluded: chain A residue  592 MET
Chi-restraints excluded: chain A residue  693 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 64 optimal weight:   10.0000
   chunk 8 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 84 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 252 HIS
A 754 GLN
A 758 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.117730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.090175 restraints weight = 65321.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.093664 restraints weight = 32496.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.095766 restraints weight = 21246.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.5229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6899  Z= 0.181
  Angle     :  0.550   5.202   9356  Z= 0.292
  Chirality :  0.037   0.133   1044
  Planarity :  0.004   0.048   1219
  Dihedral  :  4.722  20.764    917
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  8.34 %
    Favored  : 90.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.29), residues: 846
  helix:  0.59 (0.24), residues: 447
  sheet: -0.59 (0.98), residues: 29
  loop : -1.32 (0.34), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 796 
 HIS   0.006   0.001   HIS A 517 
 PHE   0.017   0.002   PHE A 531 
 TYR   0.013   0.002   TYR A 885 
 ARG   0.002   0.000   ARG A  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03775 (  259)
  hydrogen bonds       : angle       5.02121 (  720)
  covalent geometry    : bond        0.00403 ( 6899)
  covalent geometry    : angle       0.55003 ( 9356)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  742 GLN cc_start: 0.8856 (tp-100) cc_final: 0.8524 (tp-100)
REVERT: A  751 ARG cc_start: 0.7532 (tpt90) cc_final: 0.6812 (tpm170)
REVERT: A  879 MET cc_start: 0.8463 (ttt) cc_final: 0.7982 (tpp)
REVERT: A  882 LEU cc_start: 0.8341 (mp) cc_final: 0.7801 (tp)
  outliers start: 5
  outliers final: 4
  residues processed: 72
  average time/residue: 0.4512
  time to fit residues: 43.9012
Evaluate side-chains
  68 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  120 TYR
Chi-restraints excluded: chain A residue  148 HIS
Chi-restraints excluded: chain A residue  592 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 52 optimal weight:    7.9990
   chunk 57 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 64 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.118556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.090514 restraints weight = 63013.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.093740 restraints weight = 30144.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.095530 restraints weight = 21323.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.5438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6899  Z= 0.097
  Angle     :  0.492   5.372   9356  Z= 0.254
  Chirality :  0.036   0.136   1044
  Planarity :  0.004   0.046   1219
  Dihedral  :  4.519  22.667    917
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  8.61 %
    Favored  : 90.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.30), residues: 846
  helix:  0.83 (0.25), residues: 454
  sheet: -0.67 (0.99), residues: 30
  loop : -1.20 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 817 
 HIS   0.003   0.001   HIS A 517 
 PHE   0.009   0.001   PHE A 816 
 TYR   0.008   0.001   TYR A 885 
 ARG   0.002   0.000   ARG A 514 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03181 (  259)
  hydrogen bonds       : angle       4.63487 (  720)
  covalent geometry    : bond        0.00217 ( 6899)
  covalent geometry    : angle       0.49154 ( 9356)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 1.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  742 GLN cc_start: 0.8918 (tp-100) cc_final: 0.8575 (tp-100)
REVERT: A  751 ARG cc_start: 0.7753 (tpt90) cc_final: 0.6933 (tpm170)
REVERT: A  879 MET cc_start: 0.8714 (ttt) cc_final: 0.7892 (tpp)
REVERT: A  882 LEU cc_start: 0.8363 (mp) cc_final: 0.7777 (tp)
  outliers start: 3
  outliers final: 3
  residues processed: 68
  average time/residue: 0.4132
  time to fit residues: 38.5052
Evaluate side-chains
  68 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  148 HIS
Chi-restraints excluded: chain A residue  592 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 35 optimal weight:    0.0980
   chunk 14 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0570
   chunk 10 optimal weight:    0.7980
   chunk 50 optimal weight:    7.9990
   chunk 41 optimal weight:    0.2980
   chunk 53 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   overall best weight:    0.4098

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

Flipped N/Q/H residues before XYZ refinement:
A 522 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.119580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.091927 restraints weight = 62931.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.094456 restraints weight = 29570.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.095421 restraints weight = 20006.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.5656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6899  Z= 0.086
  Angle     :  0.485   6.316   9356  Z= 0.247
  Chirality :  0.036   0.124   1044
  Planarity :  0.003   0.047   1219
  Dihedral  :  4.277  21.763    917
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  8.87 %
    Favored  : 90.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.30), residues: 846
  helix:  1.09 (0.25), residues: 455
  sheet: -0.63 (0.95), residues: 30
  loop : -1.12 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 137 
 HIS   0.005   0.001   HIS A  43 
 PHE   0.009   0.001   PHE A 816 
 TYR   0.007   0.001   TYR A 885 
 ARG   0.002   0.000   ARG A 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02884 (  259)
  hydrogen bonds       : angle       4.37561 (  720)
  covalent geometry    : bond        0.00196 ( 6899)
  covalent geometry    : angle       0.48541 ( 9356)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4248.93 seconds
wall clock time: 73 minutes 56.08 seconds (4436.08 seconds total)