Starting phenix.real_space_refine
on Sat May 10 23:41:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gcn_29936/05_2025/8gcn_29936.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gcn_29936/05_2025/8gcn_29936.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gcn_29936/05_2025/8gcn_29936.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gcn_29936/05_2025/8gcn_29936.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gcn_29936/05_2025/8gcn_29936.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gcn_29936/05_2025/8gcn_29936.cif"
  }
  resolution = 3.95
  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=   0.002 sd=   0.014
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: 4
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    4507      2.51       5
     N    1224      2.21       5
     O    1393      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7173
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 876, 6805
          Classifications: {'peptide': 876}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 37, 'TRANS': 838}
    Chain: "B"
      Number of atoms: 368
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 368
          Classifications: {'peptide': 43}
          Link IDs: {'TRANS': 42}
  Time building chain proxies: 4.33, per 1000 atoms: 0.60
  Number of scatterers: 7173
  At special positions: 0
  Unit cell: (81.096, 91.56, 112.488, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      49     16.00
     O    1393      8.00
     N    1224      7.00
     C    4507      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.68
  Conformation dependent library (CDL) restraints added in 912.2 milliseconds
  

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1760

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 0 sheets defined
      85.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 10
    Processing helix  chain 'A' and resid 14 through 32
    Processing helix  chain 'A' and resid 32 through 46
      removed outlier: 3.524A  pdb=" N   ASN A  46 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 66
    Processing helix  chain 'A' and resid 69 through 82
      removed outlier: 3.662A  pdb=" N   ALA A  82 " --> pdb=" O   GLN A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 99
      removed outlier: 3.646A  pdb=" N   LEU A  99 " --> pdb=" O   VAL A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 124
      removed outlier: 4.250A  pdb=" N   GLN A 111 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   CYS A 112 " --> pdb=" O   SER A 108 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   ALA A 119 " --> pdb=" O   GLY A 115 " (cutoff:3.500A)
      Proline residue:  A 122  - end of helix
    Processing helix  chain 'A' and resid 128 through 139
    Processing helix  chain 'A' and resid 143 through 161
    Processing helix  chain 'A' and resid 162 through 167
    Processing helix  chain 'A' and resid 169 through 181
      removed outlier: 4.007A  pdb=" N   ILE A 173 " --> pdb=" O   LYS A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 202
      removed outlier: 3.788A  pdb=" N   LYS A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 210
      removed outlier: 3.894A  pdb=" N   ASP A 210 " --> pdb=" O   LYS A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 226
    Processing helix  chain 'A' and resid 230 through 248
    Processing helix  chain 'A' and resid 251 through 255
    Processing helix  chain 'A' and resid 259 through 270
    Processing helix  chain 'A' and resid 272 through 304
    Processing helix  chain 'A' and resid 313 through 330
      removed outlier: 5.536A  pdb=" N   GLN A 320 " --> pdb=" O   LYS A 316 " (cutoff:3.500A)
      removed outlier: 5.659A  pdb=" N   TYR A 321 " --> pdb=" O   GLY A 317 " (cutoff:3.500A)
      Proline residue:  A 324  - end of helix
    Processing helix  chain 'A' and resid 343 through 360
    Processing helix  chain 'A' and resid 363 through 375
      Proline residue:  A 369  - end of helix
    Processing helix  chain 'A' and resid 379 through 393
      removed outlier: 3.690A  pdb=" N   ARG A 383 " --> pdb=" O   ASP A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 418
      removed outlier: 3.582A  pdb=" N   LEU A 402 " --> pdb=" O   GLU A 398 " (cutoff:3.500A)
      Proline residue:  A 404  - end of helix
      Proline residue:  A 411  - end of helix
      removed outlier: 3.987A  pdb=" N   LYS A 418 " --> pdb=" O   ILE A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 439
    Processing helix  chain 'A' and resid 439 through 444
      removed outlier: 4.068A  pdb=" N   ALA A 443 " --> pdb=" O   LEU A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 460
      removed outlier: 4.210A  pdb=" N   ALA A 450 " --> pdb=" O   ASP A 446 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
    Processing helix  chain 'A' and resid 463 through 486
      removed outlier: 4.676A  pdb=" N   ASN A 469 " --> pdb=" O   ARG A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 501
    Processing helix  chain 'A' and resid 502 through 515
      removed outlier: 3.900A  pdb=" N   GLN A 508 " --> pdb=" O   GLU A 504 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LYS A 509 " --> pdb=" O   LEU A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 523
      removed outlier: 4.483A  pdb=" N   HIS A 520 " --> pdb=" O   PRO A 517 " (cutoff:3.500A)
      removed outlier: 5.042A  pdb=" N   ASN A 522 " --> pdb=" O   GLY A 519 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ASN A 523 " --> pdb=" O   HIS A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 538
      removed outlier: 3.871A  pdb=" N   TYR A 529 " --> pdb=" O   ARG A 525 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLU A 530 " --> pdb=" O   SER A 526 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLU A 534 " --> pdb=" O   GLU A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 542
      No H-bonds generated for 'chain 'A' and resid 540 through 542'
    Processing helix  chain 'A' and resid 543 through 562
      removed outlier: 3.744A  pdb=" N   MET A 555 " --> pdb=" O   THR A 551 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   GLU A 556 " --> pdb=" O   LEU A 552 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG A 557 " --> pdb=" O   VAL A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 593
      removed outlier: 3.865A  pdb=" N   GLN A 589 " --> pdb=" O   CYS A 585 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ARG A 593 " --> pdb=" O   GLN A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 618
      removed outlier: 3.972A  pdb=" N   GLN A 602 " --> pdb=" O   GLN A 598 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   ILE A 603 " --> pdb=" O   ASP A 599 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ASP A 605 " --> pdb=" O   LEU A 601 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   VAL A 606 " --> pdb=" O   GLN A 602 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   PHE A 615 " --> pdb=" O   LEU A 611 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   GLN A 616 " --> pdb=" O   LEU A 612 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   THR A 618 " --> pdb=" O   MET A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 640
      removed outlier: 4.129A  pdb=" N   GLN A 625 " --> pdb=" O   SER A 621 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ASP A 627 " --> pdb=" O   GLY A 623 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   LEU A 629 " --> pdb=" O   GLN A 625 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   MET A 630 " --> pdb=" O   GLU A 626 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU A 635 " --> pdb=" O   ALA A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 649
      removed outlier: 4.753A  pdb=" N   LEU A 644 " --> pdb=" O   GLY A 641 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   LYS A 645 " --> pdb=" O   GLU A 642 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   MET A 647 " --> pdb=" O   LEU A 644 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   GLU A 648 " --> pdb=" O   LYS A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 650 through 659
    Processing helix  chain 'A' and resid 663 through 682
      removed outlier: 3.984A  pdb=" N   CYS A 667 " --> pdb=" O   GLU A 663 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ARG A 679 " --> pdb=" O   GLY A 675 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 685 through 702
      removed outlier: 4.063A  pdb=" N   ASP A 690 " --> pdb=" O   ILE A 686 " (cutoff:3.500A)
      removed outlier: 5.030A  pdb=" N   GLU A 691 " --> pdb=" O   PRO A 687 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL A 692 " --> pdb=" O   PHE A 688 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLU A 698 " --> pdb=" O   GLN A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 725
      removed outlier: 3.566A  pdb=" N   LEU A 714 " --> pdb=" O   LYS A 710 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLY A 718 " --> pdb=" O   LEU A 714 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ASP A 719 " --> pdb=" O   SER A 715 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ALA A 721 " --> pdb=" O   PHE A 717 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LEU A 722 " --> pdb=" O   GLY A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 745
      removed outlier: 4.371A  pdb=" N   GLU A 733 " --> pdb=" O   LYS A 729 " (cutoff:3.500A)
      removed outlier: 5.470A  pdb=" N   VAL A 734 " --> pdb=" O   LYS A 730 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   VAL A 735 " --> pdb=" O   TYR A 731 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LEU A 736 " --> pdb=" O   LEU A 732 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ASN A 737 " --> pdb=" O   GLU A 733 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLN A 741 " --> pdb=" O   ASN A 737 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ALA A 742 " --> pdb=" O   THR A 738 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 751 through 778
    Processing helix  chain 'A' and resid 784 through 792
      removed outlier: 3.937A  pdb=" N   LEU A 789 " --> pdb=" O   ASP A 786 " (cutoff:3.500A)
      Proline residue:  A 792  - end of helix
    Processing helix  chain 'A' and resid 793 through 807
    Processing helix  chain 'A' and resid 811 through 829
      removed outlier: 3.546A  pdb=" N   GLY A 820 " --> pdb=" O   ALA A 816 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   LEU A 821 " --> pdb=" O   CYS A 817 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   ILE A 822 " --> pdb=" O   ALA A 818 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 839
      removed outlier: 4.021A  pdb=" N   LYS A 835 " --> pdb=" O   LYS A 831 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   LEU A 836 " --> pdb=" O   ASP A 832 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 853
      removed outlier: 4.046A  pdb=" N   GLU A 845 " --> pdb=" O   PRO A 841 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   THR A 848 " --> pdb=" O   HIS A 844 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLU A 849 " --> pdb=" O   GLU A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 874
      removed outlier: 3.650A  pdb=" N   GLU A 868 " --> pdb=" O   TRP A 864 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LYS A 871 " --> pdb=" O   LYS A 867 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 13 through 17
    Processing helix  chain 'B' and resid 23 through 52

    497 hydrogen bonds defined for protein.
    1443 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.21

  Time building geometry restraints manager: 1.98 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1858
        1.33 -     1.45: 1169
        1.45 -     1.57: 4183
        1.57 -     1.70: 0
        1.70 -     1.82: 75
  Bond restraints: 7285
  Sorted by residual:
  bond pdb=" N   GLU A 493 "
       pdb=" CA  GLU A 493 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.029 1.04e-02 9.25e+03 7.99e+00
  bond pdb=" N   GLU A 492 "
       pdb=" CA  GLU A 492 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.21e-02 6.83e+03 6.15e+00
  bond pdb=" N   GLN A 491 "
       pdb=" CA  GLN A 491 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.17e-02 7.31e+03 5.97e+00
  bond pdb=" C   PRO A 494 "
       pdb=" O   PRO A 494 "
    ideal  model  delta    sigma   weight residual
    1.233  1.212  0.021 1.10e-02 8.26e+03 3.58e+00
  bond pdb=" CA  GLN A 491 "
       pdb=" C   GLN A 491 "
    ideal  model  delta    sigma   weight residual
    1.519  1.536 -0.016 1.01e-02 9.80e+03 2.60e+00
  ... (remaining 7280 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.91: 9757
        2.91 -     5.82: 86
        5.82 -     8.74: 22
        8.74 -    11.65: 8
       11.65 -    14.56: 2
  Bond angle restraints: 9875
  Sorted by residual:
  angle pdb=" CA  LEU A 198 "
        pdb=" CB  LEU A 198 "
        pdb=" CG  LEU A 198 "
      ideal   model   delta    sigma   weight residual
     116.30  130.86  -14.56 3.50e+00 8.16e-02 1.73e+01
  angle pdb=" CA  LEU A 416 "
        pdb=" CB  LEU A 416 "
        pdb=" CG  LEU A 416 "
      ideal   model   delta    sigma   weight residual
     116.30  130.51  -14.21 3.50e+00 8.16e-02 1.65e+01
  angle pdb=" CB  LYS B  18 "
        pdb=" CG  LYS B  18 "
        pdb=" CD  LYS B  18 "
      ideal   model   delta    sigma   weight residual
     111.30  120.14   -8.84 2.30e+00 1.89e-01 1.48e+01
  angle pdb=" CB  MET A 555 "
        pdb=" CG  MET A 555 "
        pdb=" SD  MET A 555 "
      ideal   model   delta    sigma   weight residual
     112.70  123.54  -10.84 3.00e+00 1.11e-01 1.31e+01
  angle pdb=" CB  MET B  47 "
        pdb=" CG  MET B  47 "
        pdb=" SD  MET B  47 "
      ideal   model   delta    sigma   weight residual
     112.70  123.40  -10.70 3.00e+00 1.11e-01 1.27e+01
  ... (remaining 9870 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.01: 3786
       18.01 -    36.01: 533
       36.01 -    54.02: 139
       54.02 -    72.03: 31
       72.03 -    90.03: 21
  Dihedral angle restraints: 4510
    sinusoidal: 1810
      harmonic: 2700
  Sorted by residual:
  dihedral pdb=" CA  LEU A 562 "
           pdb=" C   LEU A 562 "
           pdb=" N   GLN A 563 "
           pdb=" CA  GLN A 563 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.64  -24.36     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" CA  GLN A 563 "
           pdb=" C   GLN A 563 "
           pdb=" N   MET A 564 "
           pdb=" CA  MET A 564 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.57   22.43     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" CA  ALA A 259 "
           pdb=" C   ALA A 259 "
           pdb=" N   LEU A 260 "
           pdb=" CA  LEU A 260 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.44  -18.56     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 4507 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1000
       0.059 -    0.118: 143
       0.118 -    0.177: 4
       0.177 -    0.236: 0
       0.236 -    0.295: 1
  Chirality restraints: 1148
  Sorted by residual:
  chirality pdb=" CG  LEU A 202 "
            pdb=" CB  LEU A 202 "
            pdb=" CD1 LEU A 202 "
            pdb=" CD2 LEU A 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.88    0.30 2.00e-01 2.50e+01 2.18e+00
  chirality pdb=" CB  THR A 863 "
            pdb=" CA  THR A 863 "
            pdb=" OG1 THR A 863 "
            pdb=" CG2 THR A 863 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.72   -0.17 2.00e-01 2.50e+01 7.09e-01
  chirality pdb=" CA  GLU A 493 "
            pdb=" N   GLU A 493 "
            pdb=" C   GLU A 493 "
            pdb=" CB  GLU A 493 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.80e-01
  ... (remaining 1145 not shown)

  Planarity restraints: 1291
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 396 "   -0.043 5.00e-02 4.00e+02   6.45e-02 6.66e+00
        pdb=" N   PRO A 397 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A 397 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 397 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 490 "    0.013 2.00e-02 2.50e+03   2.58e-02 6.65e+00
        pdb=" C   ASP A 490 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   ASP A 490 "    0.017 2.00e-02 2.50e+03
        pdb=" N   GLN A 491 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 479 "   -0.010 2.00e-02 2.50e+03   2.07e-02 4.29e+00
        pdb=" CD  GLU A 479 "    0.036 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 479 "   -0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 479 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1288 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 169
        2.67 -     3.23: 8007
        3.23 -     3.79: 12435
        3.79 -     4.34: 15526
        4.34 -     4.90: 23268
  Nonbonded interactions: 59405
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 547 "
            pdb=" OG1 THR A 551 "
     model   vdw
     2.118 3.040
  nonbonded pdb=" OG1 THR A 827 "
            pdb=" OE2 GLU A 868 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" OD1 ASP A 690 "
            pdb=" OH  TYR A 731 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" O   LEU A 847 "
            pdb=" NH1 ARG A 851 "
     model   vdw
     2.190 3.120
  nonbonded pdb=" OE2 GLU A 398 "
            pdb=" OG  SER A 400 "
     model   vdw
     2.204 3.040
  ... (remaining 59400 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             0.660
  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:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.850
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7285  Z= 0.157
  Angle     :  0.777  14.562   9875  Z= 0.369
  Chirality :  0.041   0.295   1148
  Planarity :  0.004   0.065   1291
  Dihedral  : 18.905  90.034   2750
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 19.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  : 33.42 %
    Favored  : 66.46 %
  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:  0.47 (0.29), residues: 915
  helix:  0.66 (0.20), residues: 692
  sheet:  None (None), residues: 0
  loop : -0.49 (0.46), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  80 
 HIS   0.002   0.001   HIS A 706 
 PHE   0.014   0.001   PHE A 577 
 TYR   0.031   0.001   TYR A 482 
 ARG   0.005   0.000   ARG B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19539 (  497)
  hydrogen bonds       : angle       6.47846 ( 1443)
  covalent geometry    : bond        0.00322 ( 7285)
  covalent geometry    : angle       0.77653 ( 9875)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 MET cc_start: 0.9580 (mmm) cc_final: 0.9291 (mmm)
REVERT: B   20 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8237 (mmmm)
REVERT: B   30 ARG cc_start: 0.9475 (mtp85) cc_final: 0.8980 (mtp85)
  outliers start: 1
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1824
  time to fit residues: 19.3427
Evaluate side-chains
  72 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 82 optimal weight:    8.9990
   overall best weight:    2.7188

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

Flipped N/Q/H residues before XYZ refinement:
A 522 ASN
A 569 GLN
A 576 GLN
A 660 ASN
A 684 ASN
A 712 GLN
A 737 ASN
A 759 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.054961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.040123 restraints weight = 50733.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.041485 restraints weight = 32878.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.042444 restraints weight = 24353.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.1254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7285  Z= 0.158
  Angle     :  0.677  10.358   9875  Z= 0.338
  Chirality :  0.040   0.132   1148
  Planarity :  0.004   0.064   1291
  Dihedral  :  4.205  21.869    982
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 27.22 %
    Favored  : 69.75 %
  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:  0.53 (0.29), residues: 915
  helix:  0.66 (0.20), residues: 710
  sheet:  None (None), residues: 0
  loop : -0.40 (0.49), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 472 
 HIS   0.002   0.001   HIS A 706 
 PHE   0.015   0.001   PHE A 577 
 TYR   0.016   0.001   TYR A 482 
 ARG   0.003   0.001   ARG B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04633 (  497)
  hydrogen bonds       : angle       4.90142 ( 1443)
  covalent geometry    : bond        0.00340 ( 7285)
  covalent geometry    : angle       0.67684 ( 9875)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 0.857 
Fit side-chains
   revert: symmetry clash
REVERT: A  472 TRP cc_start: 0.9292 (OUTLIER) cc_final: 0.8655 (m-90)
REVERT: A  482 TYR cc_start: 0.9204 (OUTLIER) cc_final: 0.8992 (m-80)
REVERT: B   30 ARG cc_start: 0.9498 (mtp85) cc_final: 0.9071 (mtp85)
  outliers start: 24
  outliers final: 12
  residues processed: 100
  average time/residue: 0.1666
  time to fit residues: 23.5040
Evaluate side-chains
  90 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  458 GLU
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  474 PHE
Chi-restraints excluded: chain A residue  482 TYR
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  678 CYS
Chi-restraints excluded: chain A residue  739 LEU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain B residue   53 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 84 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   chunk 56 optimal weight:    0.5980
   chunk 88 optimal weight:    5.9990
   chunk 5 optimal weight:   20.0000
   chunk 78 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   chunk 83 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 3 optimal weight:   20.0000
   overall best weight:    5.3188

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

Flipped N/Q/H residues before XYZ refinement:
A 521 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.053402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.038753 restraints weight = 52862.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.040075 restraints weight = 34064.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.040996 restraints weight = 25191.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7285  Z= 0.227
  Angle     :  0.711   9.245   9875  Z= 0.363
  Chirality :  0.042   0.148   1148
  Planarity :  0.004   0.065   1291
  Dihedral  :  4.332  23.286    982
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 19.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 27.09 %
    Favored  : 67.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.28), residues: 915
  helix:  0.55 (0.19), residues: 717
  sheet:  None (None), residues: 0
  loop : -0.45 (0.50), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 472 
 HIS   0.005   0.001   HIS A 706 
 PHE   0.016   0.002   PHE A 577 
 TYR   0.021   0.002   TYR A 482 
 ARG   0.005   0.001   ARG A 613 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04252 (  497)
  hydrogen bonds       : angle       5.01711 ( 1443)
  covalent geometry    : bond        0.00474 ( 7285)
  covalent geometry    : angle       0.71136 ( 9875)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 77
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.9038 (mm) cc_final: 0.8745 (mm)
REVERT: A  472 TRP cc_start: 0.9338 (OUTLIER) cc_final: 0.8664 (m-90)
REVERT: A  482 TYR cc_start: 0.9181 (OUTLIER) cc_final: 0.8975 (m-80)
REVERT: A  551 THR cc_start: 0.9640 (m) cc_final: 0.9418 (p)
REVERT: A  589 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8566 (pp30)
REVERT: A  608 MET cc_start: 0.9073 (tmm) cc_final: 0.8818 (ppp)
REVERT: B   30 ARG cc_start: 0.9468 (mtp85) cc_final: 0.8868 (mtp85)
  outliers start: 41
  outliers final: 21
  residues processed: 105
  average time/residue: 0.1796
  time to fit residues: 26.3292
Evaluate side-chains
  97 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 73
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  474 PHE
Chi-restraints excluded: chain A residue  482 TYR
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  589 GLN
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  678 CYS
Chi-restraints excluded: chain A residue  730 LYS
Chi-restraints excluded: chain A residue  739 LEU
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  854 LYS
Chi-restraints excluded: chain B residue   53 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 51 optimal weight:    8.9990
   chunk 25 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 70 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 57 optimal weight:    6.9990
   chunk 2 optimal weight:   30.0000
   chunk 82 optimal weight:    3.9990
   chunk 87 optimal weight:    0.0050
   chunk 81 optimal weight:    1.9990
   chunk 72 optimal weight:   10.0000
   overall best weight:    2.8002

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

Flipped N/Q/H residues before XYZ refinement:
A 741 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.054489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.039713 restraints weight = 52379.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.041058 restraints weight = 33053.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.042028 restraints weight = 24328.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7285  Z= 0.147
  Angle     :  0.696  10.689   9875  Z= 0.341
  Chirality :  0.042   0.282   1148
  Planarity :  0.004   0.062   1291
  Dihedral  :  4.190  22.224    982
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 15.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 28.48 %
    Favored  : 67.34 %
  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:  0.64 (0.28), residues: 915
  helix:  0.75 (0.19), residues: 715
  sheet:  None (None), residues: 0
  loop : -0.45 (0.49), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 472 
 HIS   0.003   0.001   HIS A 706 
 PHE   0.015   0.001   PHE A 577 
 TYR   0.021   0.001   TYR A 482 
 ARG   0.005   0.000   ARG B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03759 (  497)
  hydrogen bonds       : angle       4.69973 ( 1443)
  covalent geometry    : bond        0.00321 ( 7285)
  covalent geometry    : angle       0.69612 ( 9875)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 79
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.8997 (mm) cc_final: 0.8693 (mm)
REVERT: A  198 LEU cc_start: 0.9502 (tt) cc_final: 0.9237 (pp)
REVERT: A  252 MET cc_start: 0.9585 (mmm) cc_final: 0.9286 (mmp)
REVERT: A  472 TRP cc_start: 0.9266 (OUTLIER) cc_final: 0.8638 (m-90)
REVERT: A  482 TYR cc_start: 0.9241 (OUTLIER) cc_final: 0.8976 (m-80)
REVERT: A  589 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8458 (pp30)
REVERT: A  608 MET cc_start: 0.9091 (tmm) cc_final: 0.8853 (ppp)
REVERT: A  614 MET cc_start: 0.9265 (ppp) cc_final: 0.9012 (ppp)
REVERT: B   30 ARG cc_start: 0.9496 (mtp85) cc_final: 0.9069 (mtp85)
  outliers start: 33
  outliers final: 21
  residues processed: 99
  average time/residue: 0.1989
  time to fit residues: 27.5458
Evaluate side-chains
  98 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 74
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  474 PHE
Chi-restraints excluded: chain A residue  482 TYR
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  589 GLN
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  678 CYS
Chi-restraints excluded: chain A residue  739 LEU
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  854 LYS
Chi-restraints excluded: chain B residue   53 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 2 optimal weight:   30.0000
   chunk 3 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 70 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 67 optimal weight:    7.9990
   chunk 11 optimal weight:    9.9990
   chunk 79 optimal weight:   10.0000
   chunk 69 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   chunk 1 optimal weight:   40.0000
   overall best weight:    3.5788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.054025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.039344 restraints weight = 52636.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.040675 restraints weight = 33482.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.041654 restraints weight = 24654.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7285  Z= 0.168
  Angle     :  0.706  10.705   9875  Z= 0.350
  Chirality :  0.042   0.305   1148
  Planarity :  0.004   0.063   1291
  Dihedral  :  4.173  20.503    982
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 16.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 28.35 %
    Favored  : 67.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.28), residues: 915
  helix:  0.87 (0.20), residues: 711
  sheet:  None (None), residues: 0
  loop : -0.46 (0.48), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 472 
 HIS   0.004   0.001   HIS A 706 
 PHE   0.015   0.001   PHE A 577 
 TYR   0.021   0.002   TYR A 482 
 ARG   0.003   0.000   ARG B  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03657 (  497)
  hydrogen bonds       : angle       4.70251 ( 1443)
  covalent geometry    : bond        0.00366 ( 7285)
  covalent geometry    : angle       0.70553 ( 9875)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 78
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.8995 (mm) cc_final: 0.8693 (mm)
REVERT: A  198 LEU cc_start: 0.9506 (tt) cc_final: 0.9262 (pp)
REVERT: A  472 TRP cc_start: 0.9310 (OUTLIER) cc_final: 0.8698 (m-90)
REVERT: A  482 TYR cc_start: 0.9228 (OUTLIER) cc_final: 0.8970 (m-80)
REVERT: A  589 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8451 (pp30)
REVERT: A  614 MET cc_start: 0.9285 (ppp) cc_final: 0.9085 (ppp)
REVERT: B   30 ARG cc_start: 0.9475 (mtp85) cc_final: 0.9021 (mtp85)
  outliers start: 36
  outliers final: 22
  residues processed: 102
  average time/residue: 0.1831
  time to fit residues: 26.4009
Evaluate side-chains
  101 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 76
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  474 PHE
Chi-restraints excluded: chain A residue  482 TYR
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  589 GLN
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  678 CYS
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  854 LYS
Chi-restraints excluded: chain B residue   53 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 84 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 74 optimal weight:   20.0000
   chunk 57 optimal weight:    5.9990
   chunk 2 optimal weight:   20.0000
   chunk 5 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 454 GLN
** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.053998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.039595 restraints weight = 50900.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.040993 restraints weight = 31990.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.041978 restraints weight = 23271.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7285  Z= 0.153
  Angle     :  0.717  11.231   9875  Z= 0.351
  Chirality :  0.042   0.267   1148
  Planarity :  0.004   0.061   1291
  Dihedral  :  4.116  20.493    982
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 15.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 29.24 %
    Favored  : 66.58 %
  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:  0.78 (0.28), residues: 915
  helix:  0.88 (0.20), residues: 713
  sheet:  None (None), residues: 0
  loop : -0.47 (0.47), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  80 
 HIS   0.003   0.001   HIS A 706 
 PHE   0.016   0.001   PHE A 577 
 TYR   0.021   0.001   TYR A 482 
 ARG   0.004   0.000   ARG B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03516 (  497)
  hydrogen bonds       : angle       4.63225 ( 1443)
  covalent geometry    : bond        0.00338 ( 7285)
  covalent geometry    : angle       0.71697 ( 9875)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 77
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.9011 (mm) cc_final: 0.8711 (mm)
REVERT: A  198 LEU cc_start: 0.9487 (tt) cc_final: 0.9232 (pp)
REVERT: A  290 GLU cc_start: 0.9368 (OUTLIER) cc_final: 0.9128 (mm-30)
REVERT: A  472 TRP cc_start: 0.9278 (OUTLIER) cc_final: 0.8680 (m-90)
REVERT: A  482 TYR cc_start: 0.9217 (OUTLIER) cc_final: 0.8941 (m-80)
REVERT: B   30 ARG cc_start: 0.9492 (mtp85) cc_final: 0.9063 (mtp85)
  outliers start: 33
  outliers final: 24
  residues processed: 99
  average time/residue: 0.1707
  time to fit residues: 23.5727
Evaluate side-chains
  103 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 76
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  290 GLU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  474 PHE
Chi-restraints excluded: chain A residue  482 TYR
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  589 GLN
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  678 CYS
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  854 LYS
Chi-restraints excluded: chain B residue   53 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 42 optimal weight:    8.9990
   chunk 53 optimal weight:    3.9990
   chunk 21 optimal weight:   10.0000
   chunk 86 optimal weight:    9.9990
   chunk 25 optimal weight:    0.7980
   chunk 2 optimal weight:   20.0000
   chunk 14 optimal weight:    2.9990
   chunk 55 optimal weight:    9.9990
   chunk 6 optimal weight:    7.9990
   chunk 76 optimal weight:   20.0000
   overall best weight:    4.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.053055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.038848 restraints weight = 51815.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.040241 restraints weight = 32639.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.041130 restraints weight = 23675.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7285  Z= 0.207
  Angle     :  0.775  13.765   9875  Z= 0.378
  Chirality :  0.044   0.315   1148
  Planarity :  0.004   0.062   1291
  Dihedral  :  4.218  19.932    982
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 18.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 29.11 %
    Favored  : 66.33 %
  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:  0.71 (0.28), residues: 915
  helix:  0.81 (0.20), residues: 719
  sheet:  None (None), residues: 0
  loop : -0.47 (0.48), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  80 
 HIS   0.005   0.001   HIS A 706 
 PHE   0.016   0.002   PHE A 577 
 TYR   0.022   0.002   TYR A 482 
 ARG   0.007   0.001   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03683 (  497)
  hydrogen bonds       : angle       4.82536 ( 1443)
  covalent geometry    : bond        0.00446 ( 7285)
  covalent geometry    : angle       0.77468 ( 9875)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 78
  time to evaluate  : 0.857 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 LEU cc_start: 0.9475 (tt) cc_final: 0.9254 (pp)
REVERT: A  252 MET cc_start: 0.9257 (mmt) cc_final: 0.8991 (mmm)
REVERT: A  290 GLU cc_start: 0.9381 (OUTLIER) cc_final: 0.9148 (mm-30)
REVERT: A  472 TRP cc_start: 0.9322 (OUTLIER) cc_final: 0.8773 (m-90)
REVERT: A  482 TYR cc_start: 0.9207 (OUTLIER) cc_final: 0.8194 (m-80)
REVERT: A  533 MET cc_start: 0.9213 (mmt) cc_final: 0.8864 (mmt)
REVERT: A  589 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8422 (pp30)
REVERT: B   30 ARG cc_start: 0.9478 (mtp85) cc_final: 0.9044 (mtp85)
REVERT: B   33 GLU cc_start: 0.9157 (pp20) cc_final: 0.8800 (pp20)
  outliers start: 36
  outliers final: 26
  residues processed: 102
  average time/residue: 0.1757
  time to fit residues: 25.0312
Evaluate side-chains
  100 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 70
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  290 GLU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  474 PHE
Chi-restraints excluded: chain A residue  482 TYR
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  589 GLN
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  678 CYS
Chi-restraints excluded: chain A residue  739 LEU
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  836 LEU
Chi-restraints excluded: chain A residue  854 LYS
Chi-restraints excluded: chain B residue   53 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 83 optimal weight:    9.9990
   chunk 20 optimal weight:    0.3980
   chunk 69 optimal weight:    9.9990
   chunk 17 optimal weight:    6.9990
   chunk 86 optimal weight:    9.9990
   chunk 41 optimal weight:    6.9990
   chunk 76 optimal weight:    1.9990
   chunk 4 optimal weight:   30.0000
   chunk 6 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    3.4786

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.053609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.039403 restraints weight = 51647.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.040797 restraints weight = 32559.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.041751 restraints weight = 23722.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.2724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7285  Z= 0.173
  Angle     :  0.768  13.244   9875  Z= 0.377
  Chirality :  0.044   0.320   1148
  Planarity :  0.004   0.060   1291
  Dihedral  :  4.219  20.189    982
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 17.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 30.38 %
    Favored  : 65.57 %
  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:  0.66 (0.28), residues: 915
  helix:  0.78 (0.19), residues: 716
  sheet:  None (None), residues: 0
  loop : -0.49 (0.48), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  80 
 HIS   0.004   0.001   HIS A 706 
 PHE   0.015   0.001   PHE A 577 
 TYR   0.025   0.002   TYR A 482 
 ARG   0.006   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03645 (  497)
  hydrogen bonds       : angle       4.72692 ( 1443)
  covalent geometry    : bond        0.00383 ( 7285)
  covalent geometry    : angle       0.76782 ( 9875)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 77
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 LEU cc_start: 0.9472 (tt) cc_final: 0.9260 (pp)
REVERT: A  252 MET cc_start: 0.9180 (mmt) cc_final: 0.8914 (mmp)
REVERT: A  290 GLU cc_start: 0.9377 (OUTLIER) cc_final: 0.9146 (mm-30)
REVERT: A  472 TRP cc_start: 0.9331 (OUTLIER) cc_final: 0.8898 (m-90)
REVERT: A  482 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.8670 (m-80)
REVERT: A  533 MET cc_start: 0.9199 (mmt) cc_final: 0.8812 (mmt)
REVERT: A  589 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8376 (pp30)
REVERT: B   30 ARG cc_start: 0.9474 (mtp85) cc_final: 0.9051 (mtp85)
  outliers start: 32
  outliers final: 25
  residues processed: 98
  average time/residue: 0.1725
  time to fit residues: 23.7478
Evaluate side-chains
  100 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 71
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  146 MET
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  290 GLU
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  474 PHE
Chi-restraints excluded: chain A residue  482 TYR
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  589 GLN
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  678 CYS
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  854 LYS
Chi-restraints excluded: chain B residue   53 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 70 optimal weight:    0.0770
   chunk 0 optimal weight:   30.0000
   chunk 88 optimal weight:    3.9990
   chunk 29 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 90 optimal weight:    5.9990
   chunk 74 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 81 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.8144

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.054790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.040066 restraints weight = 51709.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.041546 restraints weight = 32350.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.042560 restraints weight = 23436.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7285  Z= 0.140
  Angle     :  0.781  13.701   9875  Z= 0.377
  Chirality :  0.044   0.327   1148
  Planarity :  0.004   0.061   1291
  Dihedral  :  4.216  21.809    982
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 31.90 %
    Favored  : 64.30 %
  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:  0.77 (0.29), residues: 915
  helix:  0.87 (0.20), residues: 719
  sheet:  None (None), residues: 0
  loop : -0.49 (0.48), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  80 
 HIS   0.002   0.000   HIS A 706 
 PHE   0.013   0.001   PHE A 577 
 TYR   0.010   0.001   TYR A 482 
 ARG   0.006   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03529 (  497)
  hydrogen bonds       : angle       4.64465 ( 1443)
  covalent geometry    : bond        0.00315 ( 7285)
  covalent geometry    : angle       0.78121 ( 9875)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 79
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.9027 (mm) cc_final: 0.8719 (mm)
REVERT: A  198 LEU cc_start: 0.9449 (tt) cc_final: 0.9231 (pp)
REVERT: A  290 GLU cc_start: 0.9392 (OUTLIER) cc_final: 0.9169 (mm-30)
REVERT: A  472 TRP cc_start: 0.9266 (OUTLIER) cc_final: 0.8827 (m-90)
REVERT: A  482 TYR cc_start: 0.9310 (OUTLIER) cc_final: 0.9008 (m-80)
REVERT: A  859 LYS cc_start: 0.9574 (OUTLIER) cc_final: 0.9290 (ptpp)
REVERT: B   30 ARG cc_start: 0.9469 (mtp85) cc_final: 0.9069 (mtp85)
  outliers start: 30
  outliers final: 21
  residues processed: 99
  average time/residue: 0.1778
  time to fit residues: 24.4105
Evaluate side-chains
  104 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 79
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  146 MET
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  290 GLU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  474 PHE
Chi-restraints excluded: chain A residue  482 TYR
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  678 CYS
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  854 LYS
Chi-restraints excluded: chain A residue  859 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 70 optimal weight:    6.9990
   chunk 54 optimal weight:    0.8980
   chunk 5 optimal weight:    7.9990
   chunk 81 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9980
   chunk 80 optimal weight:    9.9990
   chunk 77 optimal weight:    8.9990
   chunk 46 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   chunk 79 optimal weight:    4.9990
   chunk 60 optimal weight:    9.9990
   overall best weight:    3.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.054049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.039660 restraints weight = 51750.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.041077 restraints weight = 32298.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.042096 restraints weight = 23411.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.2896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7285  Z= 0.171
  Angle     :  0.815  14.592   9875  Z= 0.398
  Chirality :  0.045   0.310   1148
  Planarity :  0.004   0.061   1291
  Dihedral  :  4.240  20.433    982
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 17.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 32.03 %
    Favored  : 64.43 %
  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:  0.67 (0.28), residues: 915
  helix:  0.78 (0.19), residues: 716
  sheet:  None (None), residues: 0
  loop : -0.48 (0.49), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 430 
 HIS   0.004   0.001   HIS A 706 
 PHE   0.013   0.001   PHE A 577 
 TYR   0.009   0.001   TYR A 382 
 ARG   0.005   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03601 (  497)
  hydrogen bonds       : angle       4.74296 ( 1443)
  covalent geometry    : bond        0.00379 ( 7285)
  covalent geometry    : angle       0.81478 ( 9875)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 78
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.9005 (mm) cc_final: 0.8701 (mm)
REVERT: A  198 LEU cc_start: 0.9448 (tt) cc_final: 0.9237 (pp)
REVERT: A  472 TRP cc_start: 0.9334 (OUTLIER) cc_final: 0.8945 (m-90)
REVERT: A  479 GLU cc_start: 0.9023 (pp20) cc_final: 0.8802 (pm20)
REVERT: A  482 TYR cc_start: 0.9293 (OUTLIER) cc_final: 0.8998 (m-80)
REVERT: A  533 MET cc_start: 0.9266 (mmt) cc_final: 0.8819 (mmm)
REVERT: A  589 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8265 (pp30)
REVERT: A  859 LYS cc_start: 0.9584 (OUTLIER) cc_final: 0.9379 (mtmt)
REVERT: B   30 ARG cc_start: 0.9474 (mtp85) cc_final: 0.8981 (mtp85)
  outliers start: 28
  outliers final: 22
  residues processed: 96
  average time/residue: 0.1831
  time to fit residues: 24.3998
Evaluate side-chains
  100 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 74
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  146 MET
Chi-restraints excluded: chain A residue  169 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  474 PHE
Chi-restraints excluded: chain A residue  482 TYR
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  589 GLN
Chi-restraints excluded: chain A residue  597 HIS
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  678 CYS
Chi-restraints excluded: chain A residue  833 VAL
Chi-restraints excluded: chain A residue  854 LYS
Chi-restraints excluded: chain A residue  859 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 56 optimal weight:   20.0000
   chunk 44 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 88 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 74 optimal weight:    9.9990
   chunk 52 optimal weight:    9.9990
   chunk 0 optimal weight:   30.0000
   chunk 72 optimal weight:    8.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    3.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.053754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.039386 restraints weight = 51418.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.040759 restraints weight = 32396.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.041759 restraints weight = 23639.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7285  Z= 0.174
  Angle     :  0.828  15.106   9875  Z= 0.402
  Chirality :  0.046   0.321   1148
  Planarity :  0.004   0.061   1291
  Dihedral  :  4.235  21.343    982
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 17.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 32.15 %
    Favored  : 64.43 %
  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:  0.67 (0.28), residues: 915
  helix:  0.78 (0.19), residues: 718
  sheet:  None (None), residues: 0
  loop : -0.50 (0.49), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  80 
 HIS   0.003   0.001   HIS A 706 
 PHE   0.014   0.001   PHE A 577 
 TYR   0.008   0.001   TYR A 497 
 ARG   0.005   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03624 (  497)
  hydrogen bonds       : angle       4.78806 ( 1443)
  covalent geometry    : bond        0.00386 ( 7285)
  covalent geometry    : angle       0.82846 ( 9875)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2428.00 seconds
wall clock time: 43 minutes 21.05 seconds (2601.05 seconds total)