Starting phenix.real_space_refine
on Tue Mar  3 14:56:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8a9b_15275/03_2026/8a9b_15275.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8a9b_15275/03_2026/8a9b_15275.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8a9b_15275/03_2026/8a9b_15275.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8a9b_15275/03_2026/8a9b_15275.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8a9b_15275/03_2026/8a9b_15275.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8a9b_15275/03_2026/8a9b_15275.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.093
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       8      5.16       5
     C    4120      2.51       5
     N    1027      2.21       5
     O    1231      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6386
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 6386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 809, 6386
          Classifications: {'peptide': 809}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 786}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 22
  Time building chain proxies: 1.57, per 1000 atoms: 0.25
  Number of scatterers: 6386
  At special positions: 0
  Unit cell: (91.41, 103.044, 149.58, 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       8     16.00
     O    1231      8.00
     N    1027      7.00
     C    4120      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: 0.55
  Conformation dependent library (CDL) restraints added in 276.6 milliseconds
  

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1530

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 6 sheets defined
      42.3% alpha, 10.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'B' and resid 95 through 106
      removed outlier: 3.572A  pdb=" N   GLY B  99 " --> pdb=" O   ASP B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 125
      removed outlier: 3.820A  pdb=" N   ALA B 113 " --> pdb=" O   LYS B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 256
      removed outlier: 3.742A  pdb=" N   ASN B 255 " --> pdb=" O   GLU B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 266
    Processing helix  chain 'B' and resid 268 through 297
      removed outlier: 3.936A  pdb=" N   GLY B 295 " --> pdb=" O   ALA B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 304
      removed outlier: 4.202A  pdb=" N   GLN B 304 " --> pdb=" O   GLU B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 311 through 316
    Processing helix  chain 'B' and resid 319 through 331
    Processing helix  chain 'B' and resid 334 through 344
    Processing helix  chain 'B' and resid 353 through 360
      removed outlier: 3.966A  pdb=" N   LEU B 357 " --> pdb=" O   THR B 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 370
    Processing helix  chain 'B' and resid 376 through 381
    Processing helix  chain 'B' and resid 383 through 389
    Processing helix  chain 'B' and resid 396 through 414
      removed outlier: 4.462A  pdb=" N   ASP B 406 " --> pdb=" O   GLN B 402 " (cutoff:3.500A)
      removed outlier: 5.022A  pdb=" N   LEU B 407 " --> pdb=" O   SER B 403 " (cutoff:3.500A)
      Proline residue:  B 410  - end of helix
    Processing helix  chain 'B' and resid 421 through 431
      removed outlier: 3.647A  pdb=" N   GLN B 431 " --> pdb=" O   GLU B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 462
    Processing helix  chain 'B' and resid 465 through 477
      removed outlier: 4.038A  pdb=" N   VAL B 469 " --> pdb=" O   MET B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 486
    Processing helix  chain 'B' and resid 489 through 499
    Processing helix  chain 'B' and resid 515 through 525
    Processing helix  chain 'B' and resid 532 through 539
    Processing helix  chain 'B' and resid 552 through 557
      removed outlier: 3.647A  pdb=" N   ALA B 557 " --> pdb=" O   ALA B 553 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 582
      removed outlier: 3.879A  pdb=" N   GLU B 569 " --> pdb=" O   ASP B 565 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   GLN B 570 " --> pdb=" O   TYR B 566 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ALA B 573 " --> pdb=" O   GLU B 569 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 592
    Processing helix  chain 'B' and resid 635 through 643
    Processing helix  chain 'B' and resid 649 through 659
      removed outlier: 4.131A  pdb=" N   THR B 653 " --> pdb=" O   ASP B 649 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 663 through 674
    Processing helix  chain 'B' and resid 685 through 689
    Processing helix  chain 'B' and resid 692 through 700
    Processing helix  chain 'B' and resid 706 through 717
    Processing helix  chain 'B' and resid 797 through 816
    Processing sheet with id=AA1, first strand: chain 'B' and resid 135 through 137
      removed outlier: 4.353A  pdb=" N   PHE B 157 " --> pdb=" O   TYR B 187 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   TYR B 187 " --> pdb=" O   PHE B 157 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 141 through 142
      removed outlier: 3.618A  pdb=" N   ASN B 142 " --> pdb=" O   ASP B 154 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   ASP B 154 " --> pdb=" O   ASN B 142 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 189 through 190
      removed outlier: 3.584A  pdb=" N   ASN B 190 " --> pdb=" O   THR B 218 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 607 through 609
      removed outlier: 3.987A  pdb=" N   LEU B 614 " --> pdb=" O   VAL B 747 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   LYS B 618 " --> pdb=" O   GLU B 743 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   GLU B 743 " --> pdb=" O   LYS B 618 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   ASP B 620 " --> pdb=" O   GLY B 741 " (cutoff:3.500A)
      removed outlier: 7.406A  pdb=" N   GLY B 741 " --> pdb=" O   ASP B 620 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   PHE B 736 " --> pdb=" O   VAL B 625 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 607 through 609
      removed outlier: 3.987A  pdb=" N   LEU B 614 " --> pdb=" O   VAL B 747 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   LYS B 618 " --> pdb=" O   GLU B 743 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   GLU B 743 " --> pdb=" O   LYS B 618 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   ASP B 620 " --> pdb=" O   GLY B 741 " (cutoff:3.500A)
      removed outlier: 7.406A  pdb=" N   GLY B 741 " --> pdb=" O   ASP B 620 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   THR B 769 " --> pdb=" O   LYS B 739 " (cutoff:3.500A)
      removed outlier: 5.562A  pdb=" N   GLU B 743 " --> pdb=" O   GLY B 765 " (cutoff:3.500A)
      removed outlier: 8.570A  pdb=" N   GLY B 765 " --> pdb=" O   GLU B 743 " (cutoff:3.500A)
      removed outlier: 8.211A  pdb=" N   LEU B 745 " --> pdb=" O   ILE B 763 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   ILE B 763 " --> pdb=" O   LEU B 745 " (cutoff:3.500A)
      removed outlier: 8.664A  pdb=" N   VAL B 747 " --> pdb=" O   TYR B 761 " (cutoff:3.500A)
      removed outlier: 8.741A  pdb=" N   TYR B 761 " --> pdb=" O   VAL B 747 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   GLN B 762 " --> pdb=" O   VAL B 829 " (cutoff:3.500A)
      removed outlier: 7.151A  pdb=" N   VAL B 829 " --> pdb=" O   GLN B 762 " (cutoff:3.500A)
      removed outlier: 5.622A  pdb=" N   ILE B 764 " --> pdb=" O   ILE B 827 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   ILE B 827 " --> pdb=" O   ILE B 764 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 630 through 632
      removed outlier: 3.843A  pdb=" N   PHE B 630 " --> pdb=" O   LEU B 732 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   GLU B 778 " --> pdb=" O   THR B 731 " (cutoff:3.500A)

    239 hydrogen bonds defined for protein.
    687 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: 0.89

  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:
        1.22 -     1.34: 2007
        1.34 -     1.45: 795
        1.45 -     1.57: 3677
        1.57 -     1.69: 0
        1.69 -     1.80: 16
  Bond restraints: 6495
  Sorted by residual:
  bond pdb=" CA  THR B 414 "
       pdb=" C   THR B 414 "
    ideal  model  delta    sigma   weight residual
    1.524  1.557 -0.033 1.59e-02 3.96e+03 4.39e+00
  bond pdb=" CG1 ILE B 289 "
       pdb=" CD1 ILE B 289 "
    ideal  model  delta    sigma   weight residual
    1.513  1.450  0.063 3.90e-02 6.57e+02 2.65e+00
  bond pdb=" CG  LEU B 797 "
       pdb=" CD1 LEU B 797 "
    ideal  model  delta    sigma   weight residual
    1.521  1.473  0.048 3.30e-02 9.18e+02 2.10e+00
  bond pdb=" CB  PRO B 375 "
       pdb=" CG  PRO B 375 "
    ideal  model  delta    sigma   weight residual
    1.506  1.458  0.048 3.90e-02 6.57e+02 1.54e+00
  bond pdb=" CG  PRO B 375 "
       pdb=" CD  PRO B 375 "
    ideal  model  delta    sigma   weight residual
    1.512  1.479  0.033 2.70e-02 1.37e+03 1.45e+00
  ... (remaining 6490 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.81: 8685
        3.81 -     7.62: 56
        7.62 -    11.44: 7
       11.44 -    15.25: 0
       15.25 -    19.06: 2
  Bond angle restraints: 8750
  Sorted by residual:
  angle pdb=" C   ILE B 374 "
        pdb=" N   PRO B 375 "
        pdb=" CD  PRO B 375 "
      ideal   model   delta    sigma   weight residual
     120.60  101.54   19.06 2.20e+00 2.07e-01 7.51e+01
  angle pdb=" N   PRO B  61 "
        pdb=" CA  PRO B  61 "
        pdb=" CB  PRO B  61 "
      ideal   model   delta    sigma   weight residual
     103.25  111.43   -8.18 1.05e+00 9.07e-01 6.07e+01
  angle pdb=" C   ILE B 374 "
        pdb=" N   PRO B 375 "
        pdb=" CA  PRO B 375 "
      ideal   model   delta    sigma   weight residual
     127.00  144.95  -17.95 2.40e+00 1.74e-01 5.59e+01
  angle pdb=" C   ILE B 374 "
        pdb=" CA  ILE B 374 "
        pdb=" CB  ILE B 374 "
      ideal   model   delta    sigma   weight residual
     111.36  120.22   -8.86 1.82e+00 3.02e-01 2.37e+01
  angle pdb=" C   PHE B 437 "
        pdb=" N   ASP B 438 "
        pdb=" CA  ASP B 438 "
      ideal   model   delta    sigma   weight residual
     121.54  129.80   -8.26 1.91e+00 2.74e-01 1.87e+01
  ... (remaining 8745 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.67: 3475
       16.67 -    33.35: 373
       33.35 -    50.02: 79
       50.02 -    66.70: 8
       66.70 -    83.37: 12
  Dihedral angle restraints: 3947
    sinusoidal: 1589
      harmonic: 2358
  Sorted by residual:
  dihedral pdb=" CA  ILE B 374 "
           pdb=" C   ILE B 374 "
           pdb=" N   PRO B 375 "
           pdb=" CA  PRO B 375 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -34.11   34.11     0      5.00e+00 4.00e-02 4.65e+01
  dihedral pdb=" CA  ILE B 632 "
           pdb=" C   ILE B 632 "
           pdb=" N   LYS B 633 "
           pdb=" CA  LYS B 633 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.44  -31.56     0      5.00e+00 4.00e-02 3.98e+01
  dihedral pdb=" CA  GLU B 416 "
           pdb=" C   GLU B 416 "
           pdb=" N   LYS B 417 "
           pdb=" CA  LYS B 417 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.22   26.78     0      5.00e+00 4.00e-02 2.87e+01
  ... (remaining 3944 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 937
       0.096 -    0.191: 57
       0.191 -    0.287: 4
       0.287 -    0.383: 0
       0.383 -    0.478: 1
  Chirality restraints: 999
  Sorted by residual:
  chirality pdb=" CB  ILE B 374 "
            pdb=" CA  ILE B 374 "
            pdb=" CG1 ILE B 374 "
            pdb=" CG2 ILE B 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.17    0.48 2.00e-01 2.50e+01 5.72e+00
  chirality pdb=" CB  ILE B 289 "
            pdb=" CA  ILE B 289 "
            pdb=" CG1 ILE B 289 "
            pdb=" CG2 ILE B 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CB  THR B 610 "
            pdb=" CA  THR B 610 "
            pdb=" OG1 THR B 610 "
            pdb=" CG2 THR B 610 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 996 not shown)

  Planarity restraints: 1119
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 686 "    0.044 5.00e-02 4.00e+02   6.76e-02 7.32e+00
        pdb=" N   PRO B 687 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO B 687 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 687 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 374 "    0.038 5.00e-02 4.00e+02   5.56e-02 4.95e+00
        pdb=" N   PRO B 375 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO B 375 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 375 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 852 "    0.029 5.00e-02 4.00e+02   4.43e-02 3.14e+00
        pdb=" N   PRO B 853 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 853 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 853 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1116 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 168
        2.67 -     3.23: 6610
        3.23 -     3.79: 9933
        3.79 -     4.34: 13463
        4.34 -     4.90: 20822
  Nonbonded interactions: 50996
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 470 "
            pdb=" OG1 THR B 473 "
     model   vdw
     2.113 3.040
  nonbonded pdb=" OG  SER B 311 "
            pdb=" O   LEU B 484 "
     model   vdw
     2.153 3.040
  nonbonded pdb=" OE1 GLU B 306 "
            pdb=" NZ  LYS B 575 "
     model   vdw
     2.190 3.120
  nonbonded pdb=" OE1 GLU B 758 "
            pdb=" OG  SER B 838 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OG1 THR B 768 "
            pdb=" O   PHE B 823 "
     model   vdw
     2.220 3.040
  ... (remaining 50991 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.250
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.670
  Find NCS groups from input model:        0.020
  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:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5803
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      :  0.004   0.063   6495  Z= 0.198
  Angle     :  0.877  19.061   8750  Z= 0.459
  Chirality :  0.051   0.478    999
  Planarity :  0.005   0.068   1119
  Dihedral  : 14.890  83.373   2417
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 20.52
  Ramachandran Plot:
    Outliers :  1.00 %
    Allowed  : 14.82 %
    Favored  : 84.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.17 (0.28), residues: 803
  helix: -0.88 (0.28), residues: 328
  sheet: -2.16 (0.78), residues: 50
  loop : -3.23 (0.27), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 140 
 TYR   0.029   0.002   TYR B 740 
 PHE   0.023   0.002   PHE B 578 
 TRP   0.004   0.001   TRP B 805 
 HIS   0.003   0.001   HIS B 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 6495)
  covalent geometry    : angle       0.87710 ( 8750)
  hydrogen bonds       : bond        0.18601 (  234)
  hydrogen bonds       : angle       8.02160 (  687)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  294 MET cc_start: 0.5566 (mtt) cc_final: 0.5230 (mmp)
REVERT: B  447 LEU cc_start: 0.7382 (mm) cc_final: 0.7135 (mm)
REVERT: B  633 LYS cc_start: 0.8057 (tptm) cc_final: 0.7845 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.0835
  time to fit residues: 8.4073
Evaluate side-chains
  46 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    0.0970
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0020
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    0.2980
   overall best weight:    0.2986

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 415 ASN ** 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 = 0.4724 r_free = 0.4724 target = 0.183166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.154108 restraints weight = 18192.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.155554 restraints weight = 13618.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.155363 restraints weight = 10429.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.155462 restraints weight = 11636.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.155661 restraints weight = 10797.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.4331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6136
moved from start:          0.1343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6495  Z= 0.149
  Angle     :  0.764  10.393   8750  Z= 0.394
  Chirality :  0.048   0.506    999
  Planarity :  0.004   0.051   1119
  Dihedral  :  6.092  35.325    838
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 16.31
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  : 13.45 %
    Favored  : 85.68 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  8.71 %
    Favored  : 90.71 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.96 (0.28), residues: 803
  helix: -0.89 (0.28), residues: 330
  sheet: -2.16 (0.88), residues: 42
  loop : -2.94 (0.27), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 331 
 TYR   0.018   0.001   TYR B 187 
 PHE   0.029   0.002   PHE B 854 
 TRP   0.005   0.001   TRP B 805 
 HIS   0.002   0.001   HIS B 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6495)
  covalent geometry    : angle       0.76435 ( 8750)
  hydrogen bonds       : bond        0.04737 (  234)
  hydrogen bonds       : angle       6.36275 (  687)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  185 PHE cc_start: 0.4951 (t80) cc_final: 0.4415 (t80)
REVERT: B  294 MET cc_start: 0.6377 (mtt) cc_final: 0.5996 (mtt)
REVERT: B  447 LEU cc_start: 0.7571 (mm) cc_final: 0.7349 (mm)
REVERT: B  465 MET cc_start: 0.5680 (mpp) cc_final: 0.5406 (ptp)
REVERT: B  640 MET cc_start: 0.7752 (ptm) cc_final: 0.7287 (ptm)
  outliers start: 4
  outliers final: 2
  residues processed: 62
  average time/residue: 0.0745
  time to fit residues: 6.4411
Evaluate side-chains
  48 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  785 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0570
   chunk 26 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.9502

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

Flipped N/Q/H residues before XYZ refinement:
B 125 GLN
** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 849 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.178057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.148960 restraints weight = 18187.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.149391 restraints weight = 15939.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.149304 restraints weight = 12811.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.149644 restraints weight = 12285.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.149775 restraints weight = 11403.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.4259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6300
moved from start:          0.1878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   6495  Z= 0.209
  Angle     :  0.817  10.094   8750  Z= 0.418
  Chirality :  0.049   0.498    999
  Planarity :  0.005   0.057   1119
  Dihedral  :  6.457  36.076    838
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 18.41
  Ramachandran Plot:
    Outliers :  0.75 %
    Allowed  : 14.20 %
    Favored  : 85.06 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 14.00 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.16 (0.28), residues: 803
  helix: -1.00 (0.27), residues: 330
  sheet: -2.38 (1.08), residues: 26
  loop : -3.09 (0.27), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 708 
 TYR   0.017   0.002   TYR B 187 
 PHE   0.025   0.002   PHE B 854 
 TRP   0.006   0.002   TRP B 121 
 HIS   0.002   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 6495)
  covalent geometry    : angle       0.81722 ( 8750)
  hydrogen bonds       : bond        0.04741 (  234)
  hydrogen bonds       : angle       6.19904 (  687)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  294 MET cc_start: 0.6324 (mtt) cc_final: 0.5942 (mmp)
REVERT: B  447 LEU cc_start: 0.7785 (mm) cc_final: 0.6964 (tp)
REVERT: B  578 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.7567 (m-80)
REVERT: B  640 MET cc_start: 0.8298 (ptm) cc_final: 0.7820 (ptm)
  outliers start: 10
  outliers final: 7
  residues processed: 58
  average time/residue: 0.0704
  time to fit residues: 5.9131
Evaluate side-chains
  51 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  474 GLU
Chi-restraints excluded: chain B residue  578 PHE
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  766 VAL
Chi-restraints excluded: chain B residue  785 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 35 optimal weight:   10.0000
   chunk 39 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0040
   chunk 0 optimal weight:    9.9990
   chunk 26 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 459 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.179876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.153552 restraints weight = 17979.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.152933 restraints weight = 14105.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.152568 restraints weight = 12820.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.152707 restraints weight = 13404.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.153001 restraints weight = 11761.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.4330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6192
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6495  Z= 0.152
  Angle     :  0.747  12.480   8750  Z= 0.377
  Chirality :  0.045   0.248    999
  Planarity :  0.004   0.062   1119
  Dihedral  :  6.047  27.445    838
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 16.23
  Ramachandran Plot:
    Outliers :  0.62 %
    Allowed  : 13.45 %
    Favored  : 85.93 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 16.43 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 are not related in a simple way.
  whole: -2.99 (0.28), residues: 803
  helix: -0.77 (0.28), residues: 326
  sheet: -2.22 (1.09), residues: 24
  loop : -3.05 (0.27), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 331 
 TYR   0.012   0.001   TYR B 187 
 PHE   0.036   0.002   PHE B 111 
 TRP   0.005   0.001   TRP B 805 
 HIS   0.002   0.001   HIS B 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6495)
  covalent geometry    : angle       0.74659 ( 8750)
  hydrogen bonds       : bond        0.04053 (  234)
  hydrogen bonds       : angle       6.00224 (  687)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  294 MET cc_start: 0.6528 (mtt) cc_final: 0.6072 (mtt)
REVERT: B  640 MET cc_start: 0.8068 (ptm) cc_final: 0.7678 (ptp)
  outliers start: 14
  outliers final: 9
  residues processed: 63
  average time/residue: 0.0612
  time to fit residues: 5.8246
Evaluate side-chains
  52 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  474 GLU
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  766 VAL
Chi-restraints excluded: chain B residue  768 THR
Chi-restraints excluded: chain B residue  785 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 69 optimal weight:    0.4980
   chunk 20 optimal weight:    0.2980
   chunk 27 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:   10.0000
   chunk 60 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 863 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4674 r_free = 0.4674 target = 0.178793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.150645 restraints weight = 18297.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.150643 restraints weight = 14956.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.150365 restraints weight = 12886.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.150485 restraints weight = 13145.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.150739 restraints weight = 11975.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.4274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6270
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6495  Z= 0.162
  Angle     :  0.744   9.829   8750  Z= 0.377
  Chirality :  0.046   0.233    999
  Planarity :  0.004   0.064   1119
  Dihedral  :  5.999  26.515    838
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 16.54
  Ramachandran Plot:
    Outliers :  0.62 %
    Allowed  : 14.07 %
    Favored  : 85.31 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 18.57 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 are not related in a simple way.
  whole: -2.93 (0.28), residues: 803
  helix: -0.76 (0.28), residues: 326
  sheet: -2.02 (1.12), residues: 24
  loop : -2.99 (0.27), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 708 
 TYR   0.012   0.001   TYR B 751 
 PHE   0.037   0.002   PHE B 111 
 TRP   0.005   0.001   TRP B 805 
 HIS   0.002   0.001   HIS B 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 6495)
  covalent geometry    : angle       0.74447 ( 8750)
  hydrogen bonds       : bond        0.04009 (  234)
  hydrogen bonds       : angle       5.99583 (  687)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   90 LYS cc_start: 0.6607 (OUTLIER) cc_final: 0.6335 (tptp)
REVERT: B  280 ILE cc_start: 0.7035 (mt) cc_final: 0.6770 (mt)
REVERT: B  294 MET cc_start: 0.6318 (mtt) cc_final: 0.6036 (mmp)
REVERT: B  465 MET cc_start: 0.4993 (mpp) cc_final: 0.4379 (mtm)
REVERT: B  669 ASP cc_start: 0.7559 (m-30) cc_final: 0.6822 (p0)
  outliers start: 15
  outliers final: 11
  residues processed: 62
  average time/residue: 0.0638
  time to fit residues: 5.9224
Evaluate side-chains
  55 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 LYS
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  474 GLU
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  766 VAL
Chi-restraints excluded: chain B residue  768 THR
Chi-restraints excluded: chain B residue  785 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0770
   chunk 51 optimal weight:    0.5980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 415 ASN ** 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 = 0.4667 r_free = 0.4667 target = 0.177979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.147664 restraints weight = 18262.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.149262 restraints weight = 13804.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.150179 restraints weight = 11408.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.151378 restraints weight = 10109.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.151800 restraints weight = 9244.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.4323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6236
moved from start:          0.2885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6495  Z= 0.159
  Angle     :  0.743  10.312   8750  Z= 0.374
  Chirality :  0.045   0.240    999
  Planarity :  0.004   0.065   1119
  Dihedral  :  5.959  25.504    838
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 16.15
  Ramachandran Plot:
    Outliers :  0.62 %
    Allowed  : 13.95 %
    Favored  : 85.43 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 19.57 %
    Favored  : 77.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 are not related in a simple way.
  whole: -3.01 (0.28), residues: 803
  helix: -0.87 (0.28), residues: 332
  sheet: -2.48 (0.94), residues: 30
  loop : -2.99 (0.27), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 140 
 TYR   0.011   0.001   TYR B 751 
 PHE   0.036   0.002   PHE B 111 
 TRP   0.005   0.001   TRP B 121 
 HIS   0.002   0.001   HIS B 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6495)
  covalent geometry    : angle       0.74316 ( 8750)
  hydrogen bonds       : bond        0.03941 (  234)
  hydrogen bonds       : angle       6.01878 (  687)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 50
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   90 LYS cc_start: 0.6507 (OUTLIER) cc_final: 0.6267 (tptp)
REVERT: B  431 GLN cc_start: 0.7411 (pm20) cc_final: 0.7198 (pm20)
REVERT: B  447 LEU cc_start: 0.7670 (mm) cc_final: 0.7397 (mm)
REVERT: B  465 MET cc_start: 0.4969 (mpp) cc_final: 0.4470 (mtm)
REVERT: B  640 MET cc_start: 0.7958 (ptm) cc_final: 0.7466 (ptm)
  outliers start: 19
  outliers final: 13
  residues processed: 67
  average time/residue: 0.0605
  time to fit residues: 6.1339
Evaluate side-chains
  58 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 LYS
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  216 HIS
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  474 GLU
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  766 VAL
Chi-restraints excluded: chain B residue  768 THR
Chi-restraints excluded: chain B residue  785 LYS
Chi-restraints excluded: chain B residue  817 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 24 optimal weight:    0.4980
   chunk 11 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0000
   chunk 50 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 16 optimal weight:    0.2980
   chunk 40 optimal weight:    0.0000
   overall best weight:    0.2988

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 415 ASN ** 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 = 0.4696 r_free = 0.4696 target = 0.180465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.153041 restraints weight = 18245.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.153073 restraints weight = 14437.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.153098 restraints weight = 12579.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.153177 restraints weight = 12129.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.153539 restraints weight = 11394.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.4316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6184
moved from start:          0.3075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6495  Z= 0.128
  Angle     :  0.720  11.760   8750  Z= 0.359
  Chirality :  0.044   0.222    999
  Planarity :  0.004   0.067   1119
  Dihedral  :  5.725  24.015    838
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 15.13
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 13.45 %
    Favored  : 86.05 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 20.29 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 are not related in a simple way.
  whole: -2.89 (0.28), residues: 803
  helix: -0.86 (0.28), residues: 333
  sheet: -1.92 (0.97), residues: 32
  loop : -2.90 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 708 
 TYR   0.010   0.001   TYR B 623 
 PHE   0.036   0.002   PHE B 111 
 TRP   0.005   0.001   TRP B 805 
 HIS   0.002   0.001   HIS B 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6495)
  covalent geometry    : angle       0.71951 ( 8750)
  hydrogen bonds       : bond        0.03682 (  234)
  hydrogen bonds       : angle       5.84838 (  687)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 50
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  280 ILE cc_start: 0.6986 (mt) cc_final: 0.6722 (mt)
REVERT: B  414 THR cc_start: 0.6554 (OUTLIER) cc_final: 0.6244 (p)
REVERT: B  447 LEU cc_start: 0.7621 (mm) cc_final: 0.7420 (mm)
REVERT: B  465 MET cc_start: 0.4894 (OUTLIER) cc_final: 0.4415 (mtm)
REVERT: B  640 MET cc_start: 0.8090 (ptm) cc_final: 0.7515 (ptm)
  outliers start: 18
  outliers final: 12
  residues processed: 65
  average time/residue: 0.0644
  time to fit residues: 6.2235
Evaluate side-chains
  56 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  414 THR
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain B residue  474 GLU
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  631 GLU
Chi-restraints excluded: chain B residue  633 LYS
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  766 VAL
Chi-restraints excluded: chain B residue  785 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 55 optimal weight:    0.2980
   chunk 40 optimal weight:    0.0370
   chunk 13 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 44 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.5260

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 415 ASN ** 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 = 0.4679 r_free = 0.4679 target = 0.178828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.151293 restraints weight = 18265.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.150942 restraints weight = 16058.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.151069 restraints weight = 13580.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.151128 restraints weight = 12826.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.151387 restraints weight = 12246.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.4284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6249
moved from start:          0.3251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6495  Z= 0.146
  Angle     :  0.727  10.734   8750  Z= 0.363
  Chirality :  0.045   0.228    999
  Planarity :  0.004   0.068   1119
  Dihedral  :  5.737  22.947    838
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 15.45
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 14.20 %
    Favored  : 85.31 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 20.71 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 are not related in a simple way.
  whole: -2.88 (0.28), residues: 803
  helix: -0.83 (0.28), residues: 333
  sheet: -1.91 (0.97), residues: 32
  loop : -2.91 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 708 
 TYR   0.013   0.001   TYR B 206 
 PHE   0.036   0.002   PHE B 111 
 TRP   0.006   0.001   TRP B 121 
 HIS   0.002   0.001   HIS B 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6495)
  covalent geometry    : angle       0.72666 ( 8750)
  hydrogen bonds       : bond        0.03715 (  234)
  hydrogen bonds       : angle       5.88661 (  687)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 44
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  280 ILE cc_start: 0.6872 (mt) cc_final: 0.6536 (mt)
REVERT: B  414 THR cc_start: 0.6549 (OUTLIER) cc_final: 0.6233 (p)
REVERT: B  465 MET cc_start: 0.4871 (OUTLIER) cc_final: 0.4433 (mtm)
REVERT: B  633 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8148 (mmmm)
REVERT: B  740 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.7269 (t80)
  outliers start: 20
  outliers final: 12
  residues processed: 61
  average time/residue: 0.0631
  time to fit residues: 5.8076
Evaluate side-chains
  58 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 42
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  414 THR
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain B residue  474 GLU
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  631 GLU
Chi-restraints excluded: chain B residue  633 LYS
Chi-restraints excluded: chain B residue  740 TYR
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  766 VAL
Chi-restraints excluded: chain B residue  785 LYS
Chi-restraints excluded: chain B residue  817 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 51 optimal weight:    0.5980
   chunk 63 optimal weight:    0.7980
   chunk 58 optimal weight:    0.2980
   chunk 64 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0970
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 415 ASN ** 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 = 0.4682 r_free = 0.4682 target = 0.178863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.151932 restraints weight = 18470.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.151581 restraints weight = 17742.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.151579 restraints weight = 15347.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.151598 restraints weight = 15321.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.151870 restraints weight = 13390.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.4294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6222
moved from start:          0.3526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6495  Z= 0.137
  Angle     :  0.713  11.244   8750  Z= 0.356
  Chirality :  0.044   0.241    999
  Planarity :  0.004   0.069   1119
  Dihedral  :  5.705  21.947    838
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 15.53
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 13.95 %
    Favored  : 85.55 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 21.57 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 are not related in a simple way.
  whole: -2.83 (0.28), residues: 803
  helix: -0.75 (0.28), residues: 333
  sheet: -1.92 (0.95), residues: 32
  loop : -2.92 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 708 
 TYR   0.013   0.001   TYR B 206 
 PHE   0.036   0.002   PHE B 111 
 TRP   0.005   0.001   TRP B 805 
 HIS   0.001   0.000   HIS B 580 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6495)
  covalent geometry    : angle       0.71261 ( 8750)
  hydrogen bonds       : bond        0.03631 (  234)
  hydrogen bonds       : angle       5.88690 (  687)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 48
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  280 ILE cc_start: 0.6836 (mt) cc_final: 0.6503 (mt)
REVERT: B  414 THR cc_start: 0.6512 (OUTLIER) cc_final: 0.6179 (p)
REVERT: B  483 ASP cc_start: 0.6731 (t0) cc_final: 0.6474 (t70)
REVERT: B  633 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7984 (mmmm)
REVERT: B  740 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.7239 (t80)
  outliers start: 18
  outliers final: 13
  residues processed: 63
  average time/residue: 0.0690
  time to fit residues: 6.3917
Evaluate side-chains
  61 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 45
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  414 THR
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  474 GLU
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  631 GLU
Chi-restraints excluded: chain B residue  633 LYS
Chi-restraints excluded: chain B residue  740 TYR
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  766 VAL
Chi-restraints excluded: chain B residue  785 LYS
Chi-restraints excluded: chain B residue  817 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 24 optimal weight:    0.0980
   chunk 13 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 70 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 283 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 = 0.4665 r_free = 0.4665 target = 0.177644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.147966 restraints weight = 18112.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.149675 restraints weight = 13697.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.150551 restraints weight = 11276.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.151583 restraints weight = 10015.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.151802 restraints weight = 9178.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.4294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6243
moved from start:          0.3661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6495  Z= 0.149
  Angle     :  0.734  11.093   8750  Z= 0.366
  Chirality :  0.045   0.212    999
  Planarity :  0.004   0.066   1119
  Dihedral  :  5.759  21.945    838
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 14.20 %
    Favored  : 85.31 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 21.86 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 are not related in a simple way.
  whole: -2.86 (0.28), residues: 803
  helix: -0.77 (0.28), residues: 333
  sheet: -1.97 (0.94), residues: 32
  loop : -2.93 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 400 
 TYR   0.017   0.001   TYR B 206 
 PHE   0.037   0.002   PHE B 111 
 TRP   0.006   0.001   TRP B 121 
 HIS   0.001   0.000   HIS B 580 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6495)
  covalent geometry    : angle       0.73439 ( 8750)
  hydrogen bonds       : bond        0.03720 (  234)
  hydrogen bonds       : angle       5.89887 (  687)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  280 ILE cc_start: 0.7003 (mt) cc_final: 0.6667 (mt)
REVERT: B  414 THR cc_start: 0.6589 (OUTLIER) cc_final: 0.6246 (p)
REVERT: B  633 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8246 (mmmm)
REVERT: B  740 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.7300 (t80)
  outliers start: 18
  outliers final: 14
  residues processed: 61
  average time/residue: 0.0576
  time to fit residues: 5.2573
Evaluate side-chains
  61 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 44
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  414 THR
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain B residue  474 GLU
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  631 GLU
Chi-restraints excluded: chain B residue  633 LYS
Chi-restraints excluded: chain B residue  740 TYR
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  766 VAL
Chi-restraints excluded: chain B residue  785 LYS
Chi-restraints excluded: chain B residue  817 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 8 optimal weight:    0.3980
   chunk 62 optimal weight:    0.0980
   chunk 12 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0870
   chunk 7 optimal weight:    0.2980
   chunk 11 optimal weight:    0.0170
   chunk 40 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.1796

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

Flipped N/Q/H residues before XYZ refinement:
** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 GLN
B 580 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4703 r_free = 0.4703 target = 0.180742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.152822 restraints weight = 18273.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.153445 restraints weight = 14596.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.153730 restraints weight = 12823.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.154008 restraints weight = 11639.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.154197 restraints weight = 11386.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.4324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6176
moved from start:          0.3876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6495  Z= 0.117
  Angle     :  0.701  11.179   8750  Z= 0.349
  Chirality :  0.044   0.224    999
  Planarity :  0.004   0.066   1119
  Dihedral  :  5.500  20.680    838
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 12.83 %
    Favored  : 86.80 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 22.43 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 are not related in a simple way.
  whole: -2.62 (0.28), residues: 803
  helix: -0.52 (0.29), residues: 327
  sheet: -1.75 (0.95), residues: 32
  loop : -2.83 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 400 
 TYR   0.014   0.001   TYR B 206 
 PHE   0.035   0.002   PHE B 111 
 TRP   0.006   0.001   TRP B 805 
 HIS   0.001   0.000   HIS B 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 6495)
  covalent geometry    : angle       0.70124 ( 8750)
  hydrogen bonds       : bond        0.03406 (  234)
  hydrogen bonds       : angle       5.75912 (  687)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1230.68 seconds
wall clock time: 21 minutes 58.49 seconds (1318.49 seconds total)