Starting phenix.real_space_refine
on Fri Aug 22 19:05:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gcn_29936/08_2025/8gcn_29936.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gcn_29936/08_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_29936/08_2025/8gcn_29936.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gcn_29936/08_2025/8gcn_29936.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gcn_29936/08_2025/8gcn_29936.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gcn_29936/08_2025/8gcn_29936.cif"
  }
  resolution = 3.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.07, per 1000 atoms: 0.29
  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: 0.56
  Conformation dependent library (CDL) restraints added in 321.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.17
  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: 1.10

  Time building geometry restraints manager: 0.73 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:             0.540
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.890
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.900
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.005   0.000   ARG B  39 
 TYR   0.031   0.001   TYR A 482 
 PHE   0.014   0.001   PHE A 577 
 TRP   0.021   0.002   TRP A  80 
 HIS   0.002   0.001   HIS A 706 

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

*********************** 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  : 0.382 
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: 0.0688
  time to fit residues: 7.4447
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  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:   30.0000
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0270
   overall best weight:    1.6046

-------------------------------------------------------------------------------
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 759 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.055604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.040619 restraints weight = 50835.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.041978 restraints weight = 32753.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.042983 restraints weight = 24236.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.043678 restraints weight = 19437.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.044217 restraints weight = 16574.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7285  Z= 0.143
  Angle     :  0.676  10.670   9875  Z= 0.333
  Chirality :  0.040   0.133   1148
  Planarity :  0.004   0.064   1291
  Dihedral  :  4.177  22.060    982
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 26.71 %
    Favored  : 70.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.29), residues: 915
  helix:  0.67 (0.20), residues: 713
  sheet:  None (None), residues: 0
  loop : -0.51 (0.48), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  39 
 TYR   0.015   0.001   TYR A 482 
 PHE   0.015   0.001   PHE A 577 
 TRP   0.008   0.002   TRP A 472 
 HIS   0.002   0.000   HIS A 844 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 7285)
  covalent geometry    : angle       0.67600 ( 9875)
  hydrogen bonds       : bond        0.04424 (  497)
  hydrogen bonds       : angle       4.79576 ( 1443)

*********************** 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
  109 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: A  472 TRP cc_start: 0.9244 (OUTLIER) cc_final: 0.8565 (m-90)
REVERT: A  482 TYR cc_start: 0.9175 (OUTLIER) cc_final: 0.8964 (m-80)
REVERT: B   30 ARG cc_start: 0.9512 (mtp85) cc_final: 0.9095 (mtp85)
  outliers start: 22
  outliers final: 10
  residues processed: 102
  average time/residue: 0.0744
  time to fit residues: 10.6088
Evaluate side-chains
  90 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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 0 optimal weight:   40.0000
   chunk 31 optimal weight:    9.9990
   chunk 67 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   chunk 12 optimal weight:    7.9990
   chunk 52 optimal weight:    3.9990
   chunk 16 optimal weight:    0.2980
   chunk 61 optimal weight:    7.9990
   overall best weight:    3.0586

-------------------------------------------------------------------------------
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 = 0.3350 r_free = 0.3350 target = 0.054931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.039983 restraints weight = 51674.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.041353 restraints weight = 33147.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.042319 restraints weight = 24460.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.042972 restraints weight = 19660.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.043443 restraints weight = 16812.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.1587

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= 0.156
  Angle     :  0.682  10.695   9875  Z= 0.335
  Chirality :  0.040   0.175   1148
  Planarity :  0.004   0.065   1291
  Dihedral  :  4.137  22.337    982
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 26.96 %
    Favored  : 69.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.28), residues: 915
  helix:  0.74 (0.20), residues: 716
  sheet:  None (None), residues: 0
  loop : -0.54 (0.49), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  50 
 TYR   0.019   0.001   TYR A 482 
 PHE   0.014   0.001   PHE A 577 
 TRP   0.010   0.002   TRP A 472 
 HIS   0.003   0.001   HIS A 706 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 7285)
  covalent geometry    : angle       0.68165 ( 9875)
  hydrogen bonds       : bond        0.03999 (  497)
  hydrogen bonds       : angle       4.72983 ( 1443)

*********************** 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
  110 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 81
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  472 TRP cc_start: 0.9287 (OUTLIER) cc_final: 0.8642 (m-90)
REVERT: A  482 TYR cc_start: 0.9172 (OUTLIER) cc_final: 0.8934 (m-80)
REVERT: A  551 THR cc_start: 0.9639 (m) cc_final: 0.9391 (p)
REVERT: A  589 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8485 (pp30)
REVERT: A  608 MET cc_start: 0.9031 (tmm) cc_final: 0.8789 (ppp)
REVERT: A  614 MET cc_start: 0.9221 (ppp) cc_final: 0.9007 (ppp)
REVERT: B   20 LYS cc_start: 0.8935 (mmmm) cc_final: 0.8618 (mmtt)
REVERT: B   30 ARG cc_start: 0.9508 (mtp85) cc_final: 0.9056 (mtp85)
  outliers start: 29
  outliers final: 13
  residues processed: 100
  average time/residue: 0.0741
  time to fit residues: 10.6133
Evaluate side-chains
  94 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
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  439 LEU
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  552 LEU
Chi-restraints excluded: chain A residue  589 GLN
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 B residue   53 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 11 optimal weight:    8.9990
   chunk 68 optimal weight:    7.9990
   chunk 3 optimal weight:   20.0000
   chunk 75 optimal weight:    5.9990
   chunk 37 optimal weight:    0.8980
   chunk 83 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 12 optimal weight:    0.1980
   chunk 57 optimal weight:   10.0000
   overall best weight:    2.6186

-------------------------------------------------------------------------------
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 = 0.3353 r_free = 0.3353 target = 0.055035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.040316 restraints weight = 52076.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.041699 restraints weight = 32806.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.042657 restraints weight = 23991.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.043366 restraints weight = 19197.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.043865 restraints weight = 16289.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.1863

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= 0.142
  Angle     :  0.680  10.934   9875  Z= 0.330
  Chirality :  0.041   0.278   1148
  Planarity :  0.004   0.062   1291
  Dihedral  :  4.127  22.313    982
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 26.20 %
    Favored  : 69.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.28), residues: 915
  helix:  0.81 (0.20), residues: 716
  sheet:  None (None), residues: 0
  loop : -0.60 (0.48), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  39 
 TYR   0.019   0.001   TYR A 482 
 PHE   0.014   0.001   PHE A 577 
 TRP   0.009   0.002   TRP A  80 
 HIS   0.003   0.001   HIS A 706 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7285)
  covalent geometry    : angle       0.68043 ( 9875)
  hydrogen bonds       : bond        0.03694 (  497)
  hydrogen bonds       : angle       4.60231 ( 1443)

*********************** 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
  116 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 80
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 LEU cc_start: 0.9498 (tt) cc_final: 0.9228 (pp)
REVERT: A  472 TRP cc_start: 0.9268 (OUTLIER) cc_final: 0.8634 (m-90)
REVERT: A  482 TYR cc_start: 0.9172 (OUTLIER) cc_final: 0.8918 (m-80)
REVERT: B   20 LYS cc_start: 0.8892 (mmmm) cc_final: 0.8524 (mtmm)
REVERT: B   30 ARG cc_start: 0.9524 (mtp85) cc_final: 0.9076 (mtp85)
  outliers start: 36
  outliers final: 21
  residues processed: 102
  average time/residue: 0.0815
  time to fit residues: 11.4385
Evaluate side-chains
  101 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  254 THR
Chi-restraints excluded: chain A residue  353 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  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  552 LEU
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  761 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 30 optimal weight:   20.0000
   chunk 31 optimal weight:    6.9990
   chunk 44 optimal weight:   10.0000
   chunk 55 optimal weight:    0.0470
   chunk 7 optimal weight:    6.9990
   chunk 88 optimal weight:   10.0000
   chunk 78 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 0 optimal weight:   40.0000
   chunk 11 optimal weight:    3.9990
   chunk 74 optimal weight:    0.5980
   overall best weight:    3.3284

-------------------------------------------------------------------------------
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 = 0.3345 r_free = 0.3345 target = 0.054751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.040163 restraints weight = 51556.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.041525 restraints weight = 32844.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.042462 restraints weight = 24144.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.043162 restraints weight = 19366.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.043631 restraints weight = 16477.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.2091

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= 0.163
  Angle     :  0.718  11.581   9875  Z= 0.351
  Chirality :  0.042   0.308   1148
  Planarity :  0.004   0.063   1291
  Dihedral  :  4.147  22.574    982
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 14.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 27.97 %
    Favored  : 67.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.29), residues: 915
  helix:  0.91 (0.20), residues: 714
  sheet:  None (None), residues: 0
  loop : -0.38 (0.47), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  39 
 TYR   0.020   0.001   TYR A 482 
 PHE   0.014   0.002   PHE A 577 
 TRP   0.010   0.002   TRP A 472 
 HIS   0.004   0.001   HIS A 706 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 7285)
  covalent geometry    : angle       0.71799 ( 9875)
  hydrogen bonds       : bond        0.03640 (  497)
  hydrogen bonds       : angle       4.62538 ( 1443)

*********************** 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: 33
    poor density    : 81
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.9000 (mm) cc_final: 0.8704 (mm)
REVERT: A  198 LEU cc_start: 0.9492 (tt) cc_final: 0.9239 (pp)
REVERT: A  408 GLN cc_start: 0.9397 (OUTLIER) cc_final: 0.9156 (pt0)
REVERT: A  472 TRP cc_start: 0.9297 (OUTLIER) cc_final: 0.8671 (m-90)
REVERT: A  482 TYR cc_start: 0.9168 (OUTLIER) cc_final: 0.8914 (m-80)
REVERT: A  533 MET cc_start: 0.9163 (mmt) cc_final: 0.8823 (mmt)
REVERT: A  589 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8477 (pp30)
REVERT: B   20 LYS cc_start: 0.8931 (mmmm) cc_final: 0.8525 (mtmm)
REVERT: B   30 ARG cc_start: 0.9494 (mtp85) cc_final: 0.9047 (mtp85)
  outliers start: 33
  outliers final: 21
  residues processed: 102
  average time/residue: 0.0797
  time to fit residues: 11.4291
Evaluate side-chains
  102 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
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  181 MET
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  408 GLN
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  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  548 GLN
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  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 33 optimal weight:    4.9990
   chunk 30 optimal weight:   10.0000
   chunk 90 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 59 optimal weight:    6.9990
   chunk 32 optimal weight:    0.2980
   chunk 35 optimal weight:    0.9980
   chunk 79 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 22 optimal weight:    1.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    2.0586

-------------------------------------------------------------------------------
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 = 0.3357 r_free = 0.3357 target = 0.055287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.040574 restraints weight = 51191.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.041947 restraints weight = 32421.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.042938 restraints weight = 23857.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.043620 restraints weight = 19052.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.044123 restraints weight = 16180.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7285  Z= 0.132
  Angle     :  0.706  11.102   9875  Z= 0.340
  Chirality :  0.042   0.297   1148
  Planarity :  0.004   0.061   1291
  Dihedral  :  4.101  22.593    982
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 29.11 %
    Favored  : 66.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.28), residues: 915
  helix:  0.97 (0.20), residues: 711
  sheet:  None (None), residues: 0
  loop : -0.43 (0.47), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  39 
 TYR   0.020   0.001   TYR A 482 
 PHE   0.013   0.001   PHE A 577 
 TRP   0.007   0.002   TRP A  80 
 HIS   0.003   0.001   HIS A 706 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 7285)
  covalent geometry    : angle       0.70579 ( 9875)
  hydrogen bonds       : bond        0.03479 (  497)
  hydrogen bonds       : angle       4.48703 ( 1443)

*********************** 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
  116 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 83
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.8963 (mm) cc_final: 0.8665 (mm)
REVERT: A  198 LEU cc_start: 0.9468 (tt) cc_final: 0.9224 (pp)
REVERT: A  472 TRP cc_start: 0.9262 (OUTLIER) cc_final: 0.8689 (m-90)
REVERT: A  482 TYR cc_start: 0.9183 (OUTLIER) cc_final: 0.8906 (m-80)
REVERT: B   20 LYS cc_start: 0.8913 (mmmm) cc_final: 0.8450 (mtmm)
REVERT: B   30 ARG cc_start: 0.9504 (mtp85) cc_final: 0.9065 (mtp85)
  outliers start: 33
  outliers final: 26
  residues processed: 103
  average time/residue: 0.0795
  time to fit residues: 11.4823
Evaluate side-chains
  105 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 77
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
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  254 THR
Chi-restraints excluded: chain A residue  353 MET
Chi-restraints excluded: chain A residue  408 GLN
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  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  548 GLN
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  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 85 optimal weight:    7.9990
   chunk 89 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 12 optimal weight:    7.9990
   chunk 18 optimal weight:    6.9990
   chunk 81 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 682 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 = 0.3368 r_free = 0.3368 target = 0.055878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.041097 restraints weight = 51705.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.042519 restraints weight = 32553.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.043532 restraints weight = 23705.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.044209 restraints weight = 18950.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.044629 restraints weight = 16106.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7285  Z= 0.126
  Angle     :  0.745  15.990   9875  Z= 0.352
  Chirality :  0.042   0.323   1148
  Planarity :  0.004   0.061   1291
  Dihedral  :  4.023  22.918    982
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 29.75 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.29), residues: 915
  helix:  1.01 (0.20), residues: 712
  sheet:  None (None), residues: 0
  loop : -0.47 (0.46), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 762 
 TYR   0.018   0.001   TYR A 482 
 PHE   0.012   0.001   PHE A 577 
 TRP   0.014   0.002   TRP A  80 
 HIS   0.002   0.000   HIS A 706 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7285)
  covalent geometry    : angle       0.74473 ( 9875)
  hydrogen bonds       : bond        0.03365 (  497)
  hydrogen bonds       : angle       4.41530 ( 1443)

*********************** 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
  110 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 81
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.8965 (mm) cc_final: 0.8669 (mm)
REVERT: A  198 LEU cc_start: 0.9449 (tt) cc_final: 0.9205 (pp)
REVERT: A  290 GLU cc_start: 0.9334 (OUTLIER) cc_final: 0.9116 (mm-30)
REVERT: A  408 GLN cc_start: 0.9393 (OUTLIER) cc_final: 0.9157 (pt0)
REVERT: A  446 ASP cc_start: 0.9083 (t0) cc_final: 0.8668 (p0)
REVERT: A  472 TRP cc_start: 0.9247 (OUTLIER) cc_final: 0.8735 (m-90)
REVERT: A  482 TYR cc_start: 0.9181 (OUTLIER) cc_final: 0.8911 (m-80)
REVERT: A  533 MET cc_start: 0.9224 (mmt) cc_final: 0.8928 (mmt)
REVERT: B   20 LYS cc_start: 0.8876 (mmmm) cc_final: 0.8431 (mtmm)
REVERT: B   30 ARG cc_start: 0.9523 (mtp85) cc_final: 0.9092 (mtp85)
  outliers start: 29
  outliers final: 20
  residues processed: 101
  average time/residue: 0.0802
  time to fit residues: 11.3029
Evaluate side-chains
  104 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 80
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
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  254 THR
Chi-restraints excluded: chain A residue  290 GLU
Chi-restraints excluded: chain A residue  408 GLN
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  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  554 ILE
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  854 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 90 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 76 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 34 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.7584

-------------------------------------------------------------------------------
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 = 0.3357 r_free = 0.3357 target = 0.055427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.040710 restraints weight = 51757.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.042113 restraints weight = 32671.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.043154 restraints weight = 23879.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.043857 restraints weight = 18992.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.044401 restraints weight = 16089.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7285  Z= 0.129
  Angle     :  0.738  14.902   9875  Z= 0.348
  Chirality :  0.042   0.353   1148
  Planarity :  0.004   0.061   1291
  Dihedral  :  3.946  22.282    982
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 29.49 %
    Favored  : 66.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.28), residues: 915
  helix:  1.06 (0.20), residues: 714
  sheet:  None (None), residues: 0
  loop : -0.46 (0.46), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  39 
 TYR   0.017   0.001   TYR A 482 
 PHE   0.013   0.001   PHE A 577 
 TRP   0.013   0.002   TRP A  80 
 HIS   0.002   0.001   HIS A 706 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7285)
  covalent geometry    : angle       0.73773 ( 9875)
  hydrogen bonds       : bond        0.03305 (  497)
  hydrogen bonds       : angle       4.36465 ( 1443)

*********************** 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
  114 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 85
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.8947 (mm) cc_final: 0.8646 (mm)
REVERT: A  198 LEU cc_start: 0.9440 (tt) cc_final: 0.9202 (pp)
REVERT: A  290 GLU cc_start: 0.9327 (OUTLIER) cc_final: 0.9104 (mm-30)
REVERT: A  408 GLN cc_start: 0.9385 (OUTLIER) cc_final: 0.9165 (pt0)
REVERT: A  446 ASP cc_start: 0.9026 (t0) cc_final: 0.8627 (p0)
REVERT: A  472 TRP cc_start: 0.9256 (OUTLIER) cc_final: 0.8814 (m-90)
REVERT: A  482 TYR cc_start: 0.9188 (OUTLIER) cc_final: 0.8639 (m-80)
REVERT: A  533 MET cc_start: 0.9211 (mmt) cc_final: 0.8884 (mmt)
REVERT: B   20 LYS cc_start: 0.8884 (mmmm) cc_final: 0.8414 (mtmm)
REVERT: B   30 ARG cc_start: 0.9521 (mtp85) cc_final: 0.9102 (mtp85)
  outliers start: 29
  outliers final: 21
  residues processed: 103
  average time/residue: 0.0833
  time to fit residues: 11.8786
Evaluate side-chains
  105 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
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  254 THR
Chi-restraints excluded: chain A residue  290 GLU
Chi-restraints excluded: chain A residue  408 GLN
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  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  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  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 79 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 84 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 86 optimal weight:    9.9990
   chunk 28 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 73 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    1.1188

-------------------------------------------------------------------------------
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 = 0.3370 r_free = 0.3370 target = 0.055959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.041301 restraints weight = 50974.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.042738 restraints weight = 32098.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.043777 restraints weight = 23408.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.044484 restraints weight = 18577.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.045027 restraints weight = 15766.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.2636

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= 0.125
  Angle     :  0.758  15.488   9875  Z= 0.354
  Chirality :  0.042   0.346   1148
  Planarity :  0.004   0.060   1291
  Dihedral  :  3.940  21.891    982
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 30.25 %
    Favored  : 66.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.29), residues: 915
  helix:  1.14 (0.20), residues: 707
  sheet:  None (None), residues: 0
  loop : -0.42 (0.45), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  31 
 TYR   0.012   0.001   TYR A 482 
 PHE   0.011   0.001   PHE A 577 
 TRP   0.016   0.001   TRP A  80 
 HIS   0.002   0.000   HIS A 706 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 7285)
  covalent geometry    : angle       0.75814 ( 9875)
  hydrogen bonds       : bond        0.03290 (  497)
  hydrogen bonds       : angle       4.33339 ( 1443)

*********************** 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
  107 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 83
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.8940 (mm) cc_final: 0.8645 (mm)
REVERT: A  198 LEU cc_start: 0.9406 (tt) cc_final: 0.9186 (pp)
REVERT: A  408 GLN cc_start: 0.9383 (OUTLIER) cc_final: 0.9164 (pt0)
REVERT: A  446 ASP cc_start: 0.8931 (t0) cc_final: 0.8537 (p0)
REVERT: A  472 TRP cc_start: 0.9263 (OUTLIER) cc_final: 0.8874 (m-90)
REVERT: A  482 TYR cc_start: 0.9194 (OUTLIER) cc_final: 0.8883 (m-80)
REVERT: B   20 LYS cc_start: 0.8835 (mmmm) cc_final: 0.8236 (mtmm)
REVERT: B   30 ARG cc_start: 0.9531 (mtp85) cc_final: 0.9116 (mtp85)
  outliers start: 24
  outliers final: 17
  residues processed: 99
  average time/residue: 0.0801
  time to fit residues: 11.1139
Evaluate side-chains
  100 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
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  254 THR
Chi-restraints excluded: chain A residue  408 GLN
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  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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 18 optimal weight:    0.3980
   chunk 1 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 81 optimal weight:    6.9990
   chunk 49 optimal weight:    8.9990
   chunk 22 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 85 optimal weight:   10.0000
   overall best weight:    1.8788

-------------------------------------------------------------------------------
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 = 0.3364 r_free = 0.3364 target = 0.055549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.040887 restraints weight = 51554.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.042290 restraints weight = 32372.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.043310 restraints weight = 23602.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.043983 restraints weight = 18781.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.044522 restraints weight = 15950.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7285  Z= 0.134
  Angle     :  0.777  15.309   9875  Z= 0.364
  Chirality :  0.042   0.348   1148
  Planarity :  0.004   0.061   1291
  Dihedral  :  3.974  22.131    982
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.50 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 30.76 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.28), residues: 915
  helix:  1.13 (0.20), residues: 707
  sheet:  None (None), residues: 0
  loop : -0.44 (0.45), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  39 
 TYR   0.015   0.001   TYR A 482 
 PHE   0.011   0.001   PHE A 577 
 TRP   0.015   0.002   TRP A  80 
 HIS   0.003   0.000   HIS A 706 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 7285)
  covalent geometry    : angle       0.77733 ( 9875)
  hydrogen bonds       : bond        0.03375 (  497)
  hydrogen bonds       : angle       4.38348 ( 1443)

********************** 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
  105 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ILE cc_start: 0.8963 (mm) cc_final: 0.8678 (mm)
REVERT: A  198 LEU cc_start: 0.9392 (tt) cc_final: 0.9179 (pp)
REVERT: A  252 MET cc_start: 0.9200 (mmt) cc_final: 0.8905 (mmp)
REVERT: A  408 GLN cc_start: 0.9386 (OUTLIER) cc_final: 0.9170 (pt0)
REVERT: A  446 ASP cc_start: 0.8935 (t0) cc_final: 0.8559 (p0)
REVERT: A  472 TRP cc_start: 0.9277 (OUTLIER) cc_final: 0.8899 (m-90)
REVERT: A  482 TYR cc_start: 0.9172 (OUTLIER) cc_final: 0.8878 (m-80)
REVERT: A  533 MET cc_start: 0.9249 (mmt) cc_final: 0.8743 (mmm)
REVERT: A  589 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8307 (pp30)
REVERT: B   20 LYS cc_start: 0.8872 (mmmm) cc_final: 0.8250 (mtmm)
REVERT: B   30 ARG cc_start: 0.9517 (mtp85) cc_final: 0.9108 (mtp85)
  outliers start: 22
  outliers final: 17
  residues processed: 97
  average time/residue: 0.0788
  time to fit residues: 10.7944
Evaluate side-chains
  101 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
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  254 THR
Chi-restraints excluded: chain A residue  408 GLN
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  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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 81 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   chunk 29 optimal weight:    8.9990
   chunk 57 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 77 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 85 optimal weight:    9.9990
   chunk 27 optimal weight:    0.0370
   overall best weight:    1.8066

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

Flipped N/Q/H residues before XYZ refinement:
A 625 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.055567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.040887 restraints weight = 51271.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.042301 restraints weight = 32376.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.043331 restraints weight = 23652.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.044046 restraints weight = 18809.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.044513 restraints weight = 15952.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7285  Z= 0.133
  Angle     :  0.768  15.529   9875  Z= 0.360
  Chirality :  0.043   0.359   1148
  Planarity :  0.004   0.060   1291
  Dihedral  :  3.945  21.751    982
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.50 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 30.63 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.28), residues: 915
  helix:  1.11 (0.20), residues: 707
  sheet:  None (None), residues: 0
  loop : -0.46 (0.45), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  39 
 TYR   0.015   0.001   TYR A 482 
 PHE   0.011   0.001   PHE A  36 
 TRP   0.018   0.002   TRP A  80 
 HIS   0.002   0.000   HIS A 706 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7285)
  covalent geometry    : angle       0.76766 ( 9875)
  hydrogen bonds       : bond        0.03362 (  497)
  hydrogen bonds       : angle       4.38007 ( 1443)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1372.18 seconds
wall clock time: 24 minutes 27.59 seconds (1467.59 seconds total)