Starting phenix.real_space_refine
on Thu Jul 31 10:00:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h8x_34551/07_2025/8h8x_34551.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h8x_34551/07_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_34551/07_2025/8h8x_34551.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h8x_34551/07_2025/8h8x_34551.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h8x_34551/07_2025/8h8x_34551.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h8x_34551/07_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.90, per 1000 atoms: 0.51
  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: 3.40
  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: 1.24
  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: 5.28

  Time building geometry restraints manager: 4.18 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:             42.010
  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:             0.240
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     32.050
  Find NCS groups from input model:        0.120
  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:             0.010
  Load rotamer database and sin/cos tables:3.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   78.310
-------------------------------------------------------------------------------
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  : 1.086 
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: 0.5319
  time to fit residues: 76.3320
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  : 1.065 
-------------------------------------------------------------------------------
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 = 51)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.094783 restraints weight = 65164.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.098449 restraints weight = 32674.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.100736 restraints weight = 21130.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
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  : 1.164 
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: 0.8588 (t-100) cc_final: 0.7825 (t-100)
REVERT: A  751 ARG cc_start: 0.7659 (tpt90) cc_final: 0.6956 (tpm170)
  outliers start: 4
  outliers final: 3
  residues processed: 93
  average time/residue: 0.4884
  time to fit residues: 61.2326
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  : 0.962 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 51 optimal weight:    6.9990
   chunk 9 optimal weight:    0.0670
   chunk 35 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    1.0722

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.120527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.093321 restraints weight = 64494.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.096941 restraints weight = 32444.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.099049 restraints weight = 21111.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.3562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6899  Z= 0.121
  Angle     :  0.543   5.477   9356  Z= 0.290
  Chirality :  0.037   0.135   1044
  Planarity :  0.005   0.069   1219
  Dihedral  :  5.415  23.689    917
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  7.02 %
    Favored  : 92.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.27), residues: 846
  helix: -0.81 (0.22), residues: 441
  sheet: -1.06 (1.24), residues: 18
  loop : -1.48 (0.31), residues: 387

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 816 
 TYR   0.010   0.001   TYR A 313 
 ARG   0.006   0.000   ARG A 514 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04501 (  259)
  hydrogen bonds       : angle       5.53456 (  720)
  covalent geometry    : bond        0.00260 ( 6899)
  covalent geometry    : angle       0.54276 ( 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
  84 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 LEU cc_start: 0.9082 (tt) cc_final: 0.8815 (tt)
REVERT: A  742 GLN cc_start: 0.8900 (tp-100) cc_final: 0.8545 (tp-100)
REVERT: A  751 ARG cc_start: 0.7609 (tpt90) cc_final: 0.6913 (tpm170)
REVERT: A  827 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6829 (mt-10)
REVERT: A  879 MET cc_start: 0.8474 (ttt) cc_final: 0.8117 (tpp)
  outliers start: 4
  outliers final: 3
  residues processed: 82
  average time/residue: 0.4399
  time to fit residues: 47.5013
Evaluate side-chains
  71 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 64 optimal weight:   10.0000
   chunk 71 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    1.3786

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.120074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.092811 restraints weight = 65342.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.096405 restraints weight = 32654.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.098641 restraints weight = 21328.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.4022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6899  Z= 0.124
  Angle     :  0.529   6.757   9356  Z= 0.279
  Chirality :  0.037   0.130   1044
  Planarity :  0.004   0.049   1219
  Dihedral  :  5.123  23.962    917
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  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: -1.24 (0.28), residues: 846
  helix: -0.27 (0.23), residues: 440
  sheet: -0.80 (1.20), residues: 19
  loop : -1.41 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 796 
 HIS   0.004   0.001   HIS A 517 
 PHE   0.012   0.001   PHE A 531 
 TYR   0.019   0.001   TYR A 120 
 ARG   0.004   0.000   ARG A 514 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03785 (  259)
  hydrogen bonds       : angle       5.27737 (  720)
  covalent geometry    : bond        0.00269 ( 6899)
  covalent geometry    : angle       0.52876 ( 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
  78 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.832 
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: 0.8920 (tp-100) cc_final: 0.8576 (tp-100)
REVERT: A  751 ARG cc_start: 0.7520 (tpt90) cc_final: 0.6846 (tpm170)
REVERT: A  879 MET cc_start: 0.8473 (ttt) cc_final: 0.7980 (tpp)
REVERT: A  882 LEU cc_start: 0.8182 (mp) cc_final: 0.7453 (tt)
  outliers start: 4
  outliers final: 3
  residues processed: 75
  average time/residue: 0.5406
  time to fit residues: 55.9488
Evaluate side-chains
  69 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 35 optimal weight:    0.3980
   chunk 80 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 4 optimal weight:   10.0000
   chunk 42 optimal weight:    0.1980
   chunk 15 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    1.3184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.119568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.092168 restraints weight = 65671.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.095803 restraints weight = 32423.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.098005 restraints weight = 20983.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.4424

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= 0.118
  Angle     :  0.512   6.078   9356  Z= 0.268
  Chirality :  0.036   0.130   1044
  Planarity :  0.004   0.049   1219
  Dihedral  :  4.907  22.664    917
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  7.95 %
    Favored  : 91.66 %
  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: -0.85 (0.29), residues: 846
  helix:  0.11 (0.24), residues: 443
  sheet: -0.75 (1.20), residues: 19
  loop : -1.32 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 796 
 HIS   0.005   0.001   HIS A 517 
 PHE   0.011   0.001   PHE A 531 
 TYR   0.012   0.001   TYR A 120 
 ARG   0.001   0.000   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03577 (  259)
  hydrogen bonds       : angle       5.10173 (  720)
  covalent geometry    : bond        0.00259 ( 6899)
  covalent geometry    : angle       0.51170 ( 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
  72 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 1.056 
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: 0.8927 (tp-100) cc_final: 0.8579 (tp-100)
REVERT: A  751 ARG cc_start: 0.7523 (tpt90) cc_final: 0.6845 (tpm170)
REVERT: A  879 MET cc_start: 0.8509 (ttt) cc_final: 0.8019 (tpp)
REVERT: A  882 LEU cc_start: 0.8255 (mp) cc_final: 0.7535 (tt)
  outliers start: 3
  outliers final: 2
  residues processed: 69
  average time/residue: 0.3822
  time to fit residues: 36.8518
Evaluate side-chains
  67 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 HIS
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:   10.0000
   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:    0.3980
   chunk 15 optimal weight:    7.9990
   chunk 78 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.4146 r_free = 0.4146 target = 0.120164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.093123 restraints weight = 65369.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.096706 restraints weight = 32533.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.098858 restraints weight = 21142.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.4703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6899  Z= 0.097
  Angle     :  0.489   5.715   9356  Z= 0.254
  Chirality :  0.036   0.126   1044
  Planarity :  0.004   0.048   1219
  Dihedral  :  4.714  23.157    917
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  7.55 %
    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: -0.45 (0.29), residues: 846
  helix:  0.50 (0.25), residues: 444
  sheet: -0.31 (1.15), residues: 18
  loop : -1.23 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 796 
 HIS   0.003   0.001   HIS A 517 
 PHE   0.012   0.001   PHE A 331 
 TYR   0.011   0.001   TYR A 120 
 ARG   0.008   0.000   ARG A 514 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03305 (  259)
  hydrogen bonds       : angle       4.82945 (  720)
  covalent geometry    : bond        0.00215 ( 6899)
  covalent geometry    : angle       0.48901 ( 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: 2
    poor density    : 66
  time to evaluate  : 1.008 
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: 0.8913 (tp-100) cc_final: 0.8543 (tp-100)
REVERT: A  751 ARG cc_start: 0.7457 (tpt90) cc_final: 0.6781 (tpm170)
REVERT: A  879 MET cc_start: 0.8404 (ttt) cc_final: 0.8033 (tpp)
REVERT: A  882 LEU cc_start: 0.8268 (mp) cc_final: 0.7585 (tt)
  outliers start: 2
  outliers final: 1
  residues processed: 66
  average time/residue: 0.3652
  time to fit residues: 33.5944
Evaluate side-chains
  62 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 HIS
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:    8.9990
   chunk 29 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 12 optimal weight:    9.9990
   chunk 17 optimal weight:    0.6980
   chunk 58 optimal weight:    5.9990
   chunk 80 optimal weight:    5.9990
   chunk 53 optimal weight:    8.9990
   chunk 4 optimal weight:   20.0000
   overall best weight:    1.6584

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.118440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.091047 restraints weight = 64736.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.094529 restraints weight = 32527.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.096682 restraints weight = 21374.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.4906

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= 0.139
  Angle     :  0.518   5.356   9356  Z= 0.273
  Chirality :  0.036   0.125   1044
  Planarity :  0.004   0.048   1219
  Dihedral  :  4.713  22.140    917
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  7.68 %
    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: -0.52 (0.29), residues: 846
  helix:  0.44 (0.24), residues: 445
  sheet: -0.70 (1.00), residues: 29
  loop : -1.24 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 796 
 HIS   0.005   0.001   HIS A 517 
 PHE   0.013   0.001   PHE A 531 
 TYR   0.011   0.001   TYR A 120 
 ARG   0.001   0.000   ARG A 840 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03554 (  259)
  hydrogen bonds       : angle       4.97197 (  720)
  covalent geometry    : bond        0.00307 ( 6899)
  covalent geometry    : angle       0.51843 ( 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
  70 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.966 
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: 0.8850 (tp-100) cc_final: 0.8511 (tp-100)
REVERT: A  751 ARG cc_start: 0.7477 (tpt90) cc_final: 0.6801 (tpm170)
REVERT: A  879 MET cc_start: 0.8421 (ttt) cc_final: 0.8038 (tpp)
REVERT: A  882 LEU cc_start: 0.8392 (mp) cc_final: 0.7699 (tt)
  outliers start: 6
  outliers final: 4
  residues processed: 66
  average time/residue: 0.4000
  time to fit residues: 37.0350
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  : 0.999 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 64 optimal weight:    9.9990
   chunk 10 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 83 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   chunk 69 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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 = 0.4130 r_free = 0.4130 target = 0.119101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.091545 restraints weight = 65851.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.095165 restraints weight = 32631.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.097380 restraints weight = 21151.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.5098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6899  Z= 0.124
  Angle     :  0.498   5.081   9356  Z= 0.261
  Chirality :  0.036   0.128   1044
  Planarity :  0.004   0.048   1219
  Dihedral  :  4.661  23.200    917
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  7.68 %
    Favored  : 91.66 %
  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: -0.39 (0.30), residues: 846
  helix:  0.59 (0.25), residues: 445
  sheet: -0.90 (0.98), residues: 30
  loop : -1.21 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 796 
 HIS   0.004   0.001   HIS A 517 
 PHE   0.012   0.001   PHE A 531 
 TYR   0.009   0.001   TYR A 885 
 ARG   0.001   0.000   ARG A 559 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03398 (  259)
  hydrogen bonds       : angle       4.88004 (  720)
  covalent geometry    : bond        0.00274 ( 6899)
  covalent geometry    : angle       0.49763 ( 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
  70 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 1.107 
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: 0.8841 (tp-100) cc_final: 0.8501 (tp-100)
REVERT: A  751 ARG cc_start: 0.7503 (tpt90) cc_final: 0.6795 (tpm170)
REVERT: A  827 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7183 (mt-10)
REVERT: A  879 MET cc_start: 0.8498 (ttt) cc_final: 0.8087 (tpp)
REVERT: A  882 LEU cc_start: 0.8232 (mp) cc_final: 0.7652 (tp)
  outliers start: 5
  outliers final: 4
  residues processed: 66
  average time/residue: 0.4106
  time to fit residues: 37.0044
Evaluate side-chains
  69 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    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
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:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 64 optimal weight:    9.9990
   chunk 8 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 84 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0270
   chunk 39 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.9042

-------------------------------------------------------------------------------
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 = 0.4140 r_free = 0.4140 target = 0.119723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.092306 restraints weight = 64815.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.095940 restraints weight = 32012.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.098147 restraints weight = 20771.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.5239

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= 0.096
  Angle     :  0.484   5.427   9356  Z= 0.251
  Chirality :  0.036   0.126   1044
  Planarity :  0.004   0.047   1219
  Dihedral  :  4.539  22.213    917
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  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: -0.19 (0.30), residues: 846
  helix:  0.76 (0.25), residues: 450
  sheet: -0.81 (0.97), residues: 30
  loop : -1.16 (0.35), residues: 366

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   0.010   0.001   PHE A 531 
 TYR   0.011   0.001   TYR A 885 
 ARG   0.001   0.000   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03170 (  259)
  hydrogen bonds       : angle       4.68676 (  720)
  covalent geometry    : bond        0.00217 ( 6899)
  covalent geometry    : angle       0.48390 ( 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  : 1.003 
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: 0.8841 (tp-100) cc_final: 0.8498 (tp-100)
REVERT: A  827 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7089 (mt-10)
REVERT: A  879 MET cc_start: 0.8481 (ttt) cc_final: 0.8075 (tpp)
REVERT: A  882 LEU cc_start: 0.8306 (mp) cc_final: 0.7748 (tp)
  outliers start: 5
  outliers final: 4
  residues processed: 71
  average time/residue: 0.4026
  time to fit residues: 38.7140
Evaluate side-chains
  70 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 68 optimal weight:    0.4980
   chunk 69 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 35 optimal weight:    0.1980
   chunk 5 optimal weight:    9.9990
   chunk 52 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   chunk 65 optimal weight:    6.9990
   chunk 13 optimal weight:    4.9990
   chunk 64 optimal weight:    8.9990
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.4142 r_free = 0.4142 target = 0.119857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.092656 restraints weight = 65841.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.096269 restraints weight = 32757.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.098443 restraints weight = 21256.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.5396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6899  Z= 0.091
  Angle     :  0.483   5.931   9356  Z= 0.250
  Chirality :  0.036   0.134   1044
  Planarity :  0.004   0.047   1219
  Dihedral  :  4.445  22.275    917
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  8.87 %
    Favored  : 90.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.30), residues: 846
  helix:  0.88 (0.25), residues: 453
  sheet: -0.73 (0.97), residues: 30
  loop : -1.16 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 817 
 HIS   0.002   0.001   HIS A 517 
 PHE   0.009   0.001   PHE A 816 
 TYR   0.009   0.001   TYR A 885 
 ARG   0.001   0.000   ARG A 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03039 (  259)
  hydrogen bonds       : angle       4.57081 (  720)
  covalent geometry    : bond        0.00202 ( 6899)
  covalent geometry    : angle       0.48308 ( 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
  74 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.969 
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: 0.8846 (tp-100) cc_final: 0.8503 (tp-100)
REVERT: A  827 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7127 (mt-10)
REVERT: A  879 MET cc_start: 0.8461 (ttt) cc_final: 0.7999 (tpp)
REVERT: A  882 LEU cc_start: 0.8299 (mp) cc_final: 0.7761 (tp)
  outliers start: 5
  outliers final: 4
  residues processed: 71
  average time/residue: 0.4147
  time to fit residues: 39.5433
Evaluate side-chains
  70 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 35 optimal weight:    0.3980
   chunk 14 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0970
   chunk 10 optimal weight:    0.6980
   chunk 50 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    0.6378

-------------------------------------------------------------------------------
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 = 0.4126 r_free = 0.4126 target = 0.119277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.091734 restraints weight = 62334.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.094130 restraints weight = 29459.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.095292 restraints weight = 21504.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.5566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6899  Z= 0.091
  Angle     :  0.486   5.342   9356  Z= 0.251
  Chirality :  0.036   0.122   1044
  Planarity :  0.004   0.047   1219
  Dihedral  :  4.346  21.421    917
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  8.34 %
    Favored  : 90.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.30), residues: 846
  helix:  1.02 (0.25), residues: 454
  sheet: -0.65 (0.95), residues: 30
  loop : -1.14 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 817 
 HIS   0.004   0.001   HIS A  43 
 PHE   0.009   0.001   PHE A 816 
 TYR   0.007   0.001   TYR A 120 
 ARG   0.001   0.000   ARG A 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02967 (  259)
  hydrogen bonds       : angle       4.47129 (  720)
  covalent geometry    : bond        0.00207 ( 6899)
  covalent geometry    : angle       0.48603 ( 9356)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4566.84 seconds
wall clock time: 80 minutes 38.54 seconds (4838.54 seconds total)