Starting phenix.real_space_refine
on Fri Oct 10 11:14:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r4d_18886/10_2025/8r4d_18886.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r4d_18886/10_2025/8r4d_18886.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r4d_18886/10_2025/8r4d_18886.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r4d_18886/10_2025/8r4d_18886.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r4d_18886/10_2025/8r4d_18886.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r4d_18886/10_2025/8r4d_18886.cif"
  }
  resolution = 3.88
  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=   0.000 sd=   0.153
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      15      5.16       5
     C    2265      2.51       5
     N     608      2.21       5
     O     682      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3573
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2772
          Classifications: {'peptide': 371}
          Incomplete info: {'truncation_to_alanine': 65}
          Link IDs: {'PTRANS': 12, 'TRANS': 358}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 243
          Unresolved non-hydrogen angles: 294
          Unresolved non-hydrogen dihedrals: 204
          Unresolved non-hydrogen chiralities: 17
          Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 6, 'GLN:plan1': 2, 'ARG:plan': 6, 'ASP:plan': 3, 'TYR:plan': 2, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 114
    Chain: "B"
      Number of atoms: 769
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 769
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 3, 'TRANS': 103}
          Unresolved non-hydrogen bonds: 80
          Unresolved non-hydrogen angles: 103
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 2, 'ARG:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 48
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GSP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.12, per 1000 atoms: 0.31
  Number of scatterers: 3573
  At special positions: 0
  Unit cell: (61.8381, 74.7809, 97.7905, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      15     16.00
     P       3     15.00
     O     682      8.00
     N     608      7.00
     C    2265      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  99 " distance=2.03

  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: 0.32
  Conformation dependent library (CDL) restraints added in 164.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  898

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 5 sheets defined
      29.9% alpha, 17.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 465 through 470
    Processing helix  chain 'A' and resid 503 through 507
      removed outlier: 3.834A  pdb=" N   LEU A 506 " --> pdb=" O   ASP A 503 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LYS A 507 " --> pdb=" O   ASP A 504 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 503 through 507'
    Processing helix  chain 'A' and resid 541 through 545
      removed outlier: 3.631A  pdb=" N   ASP A 545 " --> pdb=" O   SER A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 558
      removed outlier: 3.626A  pdb=" N   LEU A 552 " --> pdb=" O   LYS A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 588
    Processing helix  chain 'A' and resid 608 through 618
      removed outlier: 3.512A  pdb=" N   LEU A 618 " --> pdb=" O   LYS A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 647
      removed outlier: 3.629A  pdb=" N   ILE A 633 " --> pdb=" O   ALA A 629 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ALA A 645 " --> pdb=" O   GLU A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 650 through 661
      removed outlier: 4.040A  pdb=" N   SER A 661 " --> pdb=" O   ILE A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 678
    Processing helix  chain 'A' and resid 697 through 710
      removed outlier: 3.550A  pdb=" N   THR A 702 " --> pdb=" O   PRO A 698 " (cutoff:3.500A)
      removed outlier: 4.928A  pdb=" N   ILE A 703 " --> pdb=" O   HIS A 699 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   VAL A 705 " --> pdb=" O   VAL A 701 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ASN A 710 " --> pdb=" O   TYR A 706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 728
      removed outlier: 3.687A  pdb=" N   ILE A 727 " --> pdb=" O   ALA A 723 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 749 through 763
    Processing helix  chain 'A' and resid 809 through 814
    Processing helix  chain 'A' and resid 872 through 881
    Processing sheet with id=AA1, first strand: chain 'A' and resid 490 through 493
      removed outlier: 8.611A  pdb=" N   VAL A 535 " --> pdb=" O   GLU A 452 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   LYS A 454 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   MET A 537 " --> pdb=" O   LYS A 454 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   HIS A 456 " --> pdb=" O   MET A 537 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   LEU A 539 " --> pdb=" O   HIS A 456 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ILE A 458 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
      removed outlier: 8.610A  pdb=" N   ILE A 565 " --> pdb=" O   SER A 534 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   TYR A 536 " --> pdb=" O   ILE A 565 " (cutoff:3.500A)
      removed outlier: 7.290A  pdb=" N   VAL A 567 " --> pdb=" O   TYR A 536 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   LEU A 538 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   HIS A 596 " --> pdb=" O   VAL A 566 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 830 through 834
      removed outlier: 3.622A  pdb=" N   LYS A 844 " --> pdb=" O   ALA A 857 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   MET A 800 " --> pdb=" O   ILE A 854 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 17 through 23
    Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.839A  pdb=" N   PHE B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   ARG B  38 " --> pdb=" O   PHE B  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ALA B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 54

    125 hydrogen bonds defined for protein.
    354 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: 0.51

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1169
        1.34 -     1.46: 786
        1.46 -     1.58: 1662
        1.58 -     1.69: 5
        1.69 -     1.81: 23
  Bond restraints: 3645
  Sorted by residual:
  bond pdb=" N   GLU A 769 "
       pdb=" CA  GLU A 769 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.016 1.29e-02 6.01e+03 1.54e+00
  bond pdb=" C   ALA B  40 "
       pdb=" N   PRO B  41 "
    ideal  model  delta    sigma   weight residual
    1.340  1.373 -0.033 2.76e-02 1.31e+03 1.43e+00
  bond pdb=" CB  PRO B  41 "
       pdb=" CG  PRO B  41 "
    ideal  model  delta    sigma   weight residual
    1.492  1.532 -0.040 5.00e-02 4.00e+02 6.56e-01
  bond pdb=" CB  GLU A 556 "
       pdb=" CG  GLU A 556 "
    ideal  model  delta    sigma   weight residual
    1.520  1.543 -0.023 3.00e-02 1.11e+03 5.95e-01
  bond pdb=" CG  GLU A 556 "
       pdb=" CD  GLU A 556 "
    ideal  model  delta    sigma   weight residual
    1.516  1.534 -0.018 2.50e-02 1.60e+03 5.28e-01
  ... (remaining 3640 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 4722
        1.31 -     2.62: 187
        2.62 -     3.93: 43
        3.93 -     5.24: 13
        5.24 -     6.55: 2
  Bond angle restraints: 4967
  Sorted by residual:
  angle pdb=" N   THR A 749 "
        pdb=" CA  THR A 749 "
        pdb=" C   THR A 749 "
      ideal   model   delta    sigma   weight residual
     108.34  111.98   -3.64 1.31e+00 5.83e-01 7.72e+00
  angle pdb=" CA  GLN A 818 "
        pdb=" C   GLN A 818 "
        pdb=" N   HIS A 819 "
      ideal   model   delta    sigma   weight residual
     118.27  114.10    4.17 1.59e+00 3.96e-01 6.88e+00
  angle pdb=" C   GLU A 769 "
        pdb=" CA  GLU A 769 "
        pdb=" CB  GLU A 769 "
      ideal   model   delta    sigma   weight residual
     110.42  115.51   -5.09 1.99e+00 2.53e-01 6.54e+00
  angle pdb=" C   LYS A 561 "
        pdb=" N   SER A 562 "
        pdb=" CA  SER A 562 "
      ideal   model   delta    sigma   weight residual
     120.68  124.52   -3.84 1.52e+00 4.33e-01 6.38e+00
  angle pdb=" C   MET A 760 "
        pdb=" N   LYS A 761 "
        pdb=" CA  LYS A 761 "
      ideal   model   delta    sigma   weight residual
     120.31  116.63    3.68 1.52e+00 4.33e-01 5.85e+00
  ... (remaining 4962 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.03: 1988
       22.03 -    44.06: 130
       44.06 -    66.09: 14
       66.09 -    88.12: 4
       88.12 -   110.15: 2
  Dihedral angle restraints: 2138
    sinusoidal: 751
      harmonic: 1387
  Sorted by residual:
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  99 "
           pdb=" CB  CYS B  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  141.70  -48.70     1      1.00e+01 1.00e-02 3.26e+01
  dihedral pdb=" O3B GSP A1201 "
           pdb=" O3A GSP A1201 "
           pdb=" PB  GSP A1201 "
           pdb=" PA  GSP A1201 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.55 -156.30 -110.15     1      2.00e+01 2.50e-03 3.23e+01
  dihedral pdb=" O3A GSP A1201 "
           pdb=" O3B GSP A1201 "
           pdb=" PB  GSP A1201 "
           pdb=" PG  GSP A1201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     195.33   97.50   97.83     1      2.00e+01 2.50e-03 2.73e+01
  ... (remaining 2135 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 339
       0.033 -    0.066: 160
       0.066 -    0.099: 52
       0.099 -    0.132: 17
       0.132 -    0.165: 2
  Chirality restraints: 570
  Sorted by residual:
  chirality pdb=" CA  ILE A 821 "
            pdb=" N   ILE A 821 "
            pdb=" C   ILE A 821 "
            pdb=" CB  ILE A 821 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.81e-01
  chirality pdb=" CA  ILE A 565 "
            pdb=" N   ILE A 565 "
            pdb=" C   ILE A 565 "
            pdb=" CB  ILE A 565 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 5.00e-01
  chirality pdb=" CA  ILE A 453 "
            pdb=" N   ILE A 453 "
            pdb=" C   ILE A 453 "
            pdb=" CB  ILE A 453 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 567 not shown)

  Planarity restraints: 631
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 803 "   -0.008 2.00e-02 2.50e+03   1.65e-02 2.73e+00
        pdb=" CG  ASP A 803 "    0.029 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 803 "   -0.010 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 803 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 810 "    0.023 5.00e-02 4.00e+02   3.49e-02 1.95e+00
        pdb=" N   PRO A 811 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 811 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 811 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 588 "    0.023 5.00e-02 4.00e+02   3.48e-02 1.94e+00
        pdb=" N   PRO A 589 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 589 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 589 "    0.019 5.00e-02 4.00e+02
  ... (remaining 628 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 968
        2.81 -     3.33: 3338
        3.33 -     3.86: 5640
        3.86 -     4.38: 6492
        4.38 -     4.90: 10914
  Nonbonded interactions: 27352
  Sorted by model distance:
  nonbonded pdb=" N   GLU A 686 "
            pdb=" OE1 GLU A 686 "
     model   vdw
     2.289 3.120
  nonbonded pdb=" O   SER A 711 "
            pdb=" OG  SER A 712 "
     model   vdw
     2.327 3.040
  nonbonded pdb=" OD1 ASP A 460 "
            pdb=" NE1 TRP A 551 "
     model   vdw
     2.328 3.120
  nonbonded pdb=" OG1 THR A 749 "
            pdb=" OE1 GLU A 752 "
     model   vdw
     2.360 3.040
  nonbonded pdb=" O   LEU A 639 "
            pdb=" OG1 THR A 643 "
     model   vdw
     2.439 3.040
  ... (remaining 27347 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             0.300
  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:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.460
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5774
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3646  Z= 0.127
  Angle     :  0.648   6.553   4969  Z= 0.348
  Chirality :  0.043   0.165    570
  Planarity :  0.004   0.035    631
  Dihedral  : 14.853 110.147   1237
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  9.57 %
    Favored  : 89.78 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  0.30 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.57 (0.37), residues: 460
  helix: -0.90 (0.43), residues: 138
  sheet: -0.49 (0.46), residues: 115
  loop : -3.05 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 824 
 TYR   0.010   0.001   TYR A 767 
 PHE   0.007   0.001   PHE A 588 
 TRP   0.009   0.001   TRP A 514 
 HIS   0.004   0.001   HIS A 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 3645)
  covalent geometry    : angle       0.64738 ( 4967)
  SS BOND              : bond        0.00039 (    1)
  SS BOND              : angle       0.90169 (    2)
  hydrogen bonds       : bond        0.17030 (  125)
  hydrogen bonds       : angle       7.26146 (  354)

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

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

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: A  515 ASP cc_start: 0.6318 (p0) cc_final: 0.6002 (p0)
REVERT: A  768 ASP cc_start: 0.5049 (p0) cc_final: 0.4820 (p0)
REVERT: B   86 MET cc_start: 0.7287 (mmm) cc_final: 0.6979 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 81
  average time/residue: 0.0685
  time to fit residues: 6.6844
Evaluate side-chains
  71 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  577 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    7.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 449 HIS
** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 578 ASN
** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.190713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.162466 restraints weight = 4690.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.164936 restraints weight = 3398.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.167136 restraints weight = 2758.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.168362 restraints weight = 2354.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.169537 restraints weight = 2118.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5934
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061   3646  Z= 0.311
  Angle     :  0.818   7.083   4969  Z= 0.432
  Chirality :  0.050   0.160    570
  Planarity :  0.006   0.043    631
  Dihedral  : 11.350 127.672    518
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 19.56
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  : 10.65 %
    Favored  : 88.70 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.99 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.19 (0.36), residues: 460
  helix: -1.68 (0.38), residues: 143
  sheet: -0.81 (0.47), residues: 111
  loop : -3.21 (0.39), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 651 
 TYR   0.020   0.003   TYR A 536 
 PHE   0.016   0.003   PHE A 588 
 TRP   0.022   0.003   TRP B  53 
 HIS   0.017   0.003   HIS A 523 

Details of bonding type rmsd
  covalent geometry    : bond        0.00711 ( 3645)
  covalent geometry    : angle       0.81741 ( 4967)
  SS BOND              : bond        0.00740 (    1)
  SS BOND              : angle       2.25282 (    2)
  hydrogen bonds       : bond        0.05448 (  125)
  hydrogen bonds       : angle       6.27201 (  354)

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

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

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  456 HIS cc_start: 0.6938 (m90) cc_final: 0.6690 (m90)
REVERT: A  515 ASP cc_start: 0.6515 (p0) cc_final: 0.6186 (p0)
REVERT: A  568 MET cc_start: 0.7553 (mtm) cc_final: 0.7219 (mtm)
  outliers start: 8
  outliers final: 6
  residues processed: 77
  average time/residue: 0.0798
  time to fit residues: 7.2971
Evaluate side-chains
  79 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  649 LEU
Chi-restraints excluded: chain A residue  650 ASN
Chi-restraints excluded: chain A residue  758 ASP
Chi-restraints excluded: chain A residue  815 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 753 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 = 0.4120 r_free = 0.4120 target = 0.194484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.168222 restraints weight = 4708.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.170598 restraints weight = 3562.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.172534 restraints weight = 2919.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.173657 restraints weight = 2530.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.174850 restraints weight = 2290.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5844
moved from start:          0.1632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3646  Z= 0.142
  Angle     :  0.614   6.315   4969  Z= 0.325
  Chirality :  0.043   0.149    570
  Planarity :  0.004   0.039    631
  Dihedral  : 10.528 127.219    518
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  : 10.65 %
    Favored  : 88.70 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 16.67 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.00 (0.36), residues: 460
  helix: -1.35 (0.40), residues: 143
  sheet: -0.84 (0.46), residues: 110
  loop : -3.15 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 824 
 TYR   0.022   0.002   TYR A 767 
 PHE   0.012   0.001   PHE A 588 
 TRP   0.012   0.001   TRP B  53 
 HIS   0.003   0.001   HIS A 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 3645)
  covalent geometry    : angle       0.61393 ( 4967)
  SS BOND              : bond        0.00211 (    1)
  SS BOND              : angle       0.94536 (    2)
  hydrogen bonds       : bond        0.03871 (  125)
  hydrogen bonds       : angle       5.56436 (  354)

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

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

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: A  581 GLN cc_start: 0.6608 (pp30) cc_final: 0.6102 (pp30)
REVERT: A  760 MET cc_start: 0.7044 (mtm) cc_final: 0.6709 (mtp)
  outliers start: 10
  outliers final: 9
  residues processed: 84
  average time/residue: 0.0742
  time to fit residues: 7.4218
Evaluate side-chains
  87 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 GLN
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  650 ASN
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  708 ILE
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   74 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 20 optimal weight:    0.1980
   chunk 0 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 753 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 = 0.4102 r_free = 0.4102 target = 0.192726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.166244 restraints weight = 4661.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.168745 restraints weight = 3504.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.170944 restraints weight = 2854.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.172104 restraints weight = 2451.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.172962 restraints weight = 2207.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5870
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3646  Z= 0.174
  Angle     :  0.640   6.264   4969  Z= 0.339
  Chirality :  0.044   0.148    570
  Planarity :  0.005   0.040    631
  Dihedral  : 10.648 126.256    518
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 15.44
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  : 11.09 %
    Favored  : 88.26 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 18.75 %
    Favored  : 77.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.02 (0.36), residues: 460
  helix: -1.37 (0.40), residues: 143
  sheet: -0.92 (0.46), residues: 112
  loop : -3.13 (0.40), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 651 
 TYR   0.014   0.002   TYR A 536 
 PHE   0.014   0.002   PHE A 588 
 TRP   0.014   0.002   TRP B  53 
 HIS   0.005   0.001   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 3645)
  covalent geometry    : angle       0.63942 ( 4967)
  SS BOND              : bond        0.00303 (    1)
  SS BOND              : angle       0.97553 (    2)
  hydrogen bonds       : bond        0.03970 (  125)
  hydrogen bonds       : angle       5.52462 (  354)

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

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

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: A  456 HIS cc_start: 0.7019 (m90) cc_final: 0.6656 (m-70)
REVERT: A  556 GLU cc_start: 0.6453 (tp30) cc_final: 0.6201 (tp30)
REVERT: A  582 LYS cc_start: 0.7198 (mptt) cc_final: 0.6511 (ttpp)
REVERT: A  760 MET cc_start: 0.7069 (mtm) cc_final: 0.6737 (mtp)
  outliers start: 13
  outliers final: 10
  residues processed: 84
  average time/residue: 0.0777
  time to fit residues: 7.9175
Evaluate side-chains
  83 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 GLN
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  523 HIS
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  650 ASN
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  708 ILE
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   74 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   chunk 41 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0970
   chunk 33 optimal weight:    0.0040
   chunk 1 optimal weight:    1.9990
   chunk 11 optimal weight:    0.4980
   overall best weight:    0.3790

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

Flipped N/Q/H residues before XYZ refinement:
A 578 ASN
** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.195537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.169402 restraints weight = 4627.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.171853 restraints weight = 3400.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.173601 restraints weight = 2756.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.175282 restraints weight = 2374.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.176101 restraints weight = 2113.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5795
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3646  Z= 0.113
  Angle     :  0.572   6.432   4969  Z= 0.299
  Chirality :  0.042   0.147    570
  Planarity :  0.004   0.037    631
  Dihedral  :  9.892 121.404    518
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  : 10.22 %
    Favored  : 89.13 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 20.54 %
    Favored  : 75.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.72 (0.37), residues: 460
  helix: -0.85 (0.43), residues: 137
  sheet: -0.83 (0.46), residues: 110
  loop : -3.05 (0.39), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 754 
 TYR   0.025   0.001   TYR A 767 
 PHE   0.009   0.001   PHE A 588 
 TRP   0.008   0.001   TRP B  53 
 HIS   0.004   0.001   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 3645)
  covalent geometry    : angle       0.57192 ( 4967)
  SS BOND              : bond        0.00096 (    1)
  SS BOND              : angle       0.49243 (    2)
  hydrogen bonds       : bond        0.03211 (  125)
  hydrogen bonds       : angle       5.10205 (  354)

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

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

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: A  582 LYS cc_start: 0.7015 (mptt) cc_final: 0.6463 (ttpp)
REVERT: A  760 MET cc_start: 0.7098 (mtm) cc_final: 0.6886 (mtp)
REVERT: A  824 ARG cc_start: 0.6675 (mmm-85) cc_final: 0.6009 (mmm-85)
REVERT: A  831 MET cc_start: 0.6080 (ptp) cc_final: 0.5663 (ptp)
  outliers start: 12
  outliers final: 9
  residues processed: 86
  average time/residue: 0.0770
  time to fit residues: 7.9310
Evaluate side-chains
  87 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 GLN
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  526 HIS
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  708 ILE
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain B residue   74 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0370
   chunk 36 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0980
   chunk 14 optimal weight:    0.3980
   chunk 15 optimal weight:    0.9990
   chunk 43 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.3458

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

Flipped N/Q/H residues before XYZ refinement:
A 578 ASN
** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 646 GLN
** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.196608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.170757 restraints weight = 4647.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.173397 restraints weight = 3441.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.175478 restraints weight = 2773.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.176590 restraints weight = 2367.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.177620 restraints weight = 2136.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5792
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3646  Z= 0.110
  Angle     :  0.585   7.426   4969  Z= 0.303
  Chirality :  0.043   0.147    570
  Planarity :  0.004   0.037    631
  Dihedral  :  9.565 115.647    518
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  : 10.43 %
    Favored  : 88.91 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 21.13 %
    Favored  : 75.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.52 (0.37), residues: 460
  helix: -0.64 (0.44), residues: 135
  sheet: -0.67 (0.46), residues: 111
  loop : -2.98 (0.39), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 651 
 TYR   0.010   0.001   TYR A 767 
 PHE   0.009   0.001   PHE A 588 
 TRP   0.008   0.001   TRP B  53 
 HIS   0.002   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 3645)
  covalent geometry    : angle       0.58549 ( 4967)
  SS BOND              : bond        0.00125 (    1)
  SS BOND              : angle       0.48107 (    2)
  hydrogen bonds       : bond        0.03119 (  125)
  hydrogen bonds       : angle       5.03572 (  354)

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

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

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: A  456 HIS cc_start: 0.6866 (m90) cc_final: 0.6652 (m90)
REVERT: A  567 VAL cc_start: 0.7106 (OUTLIER) cc_final: 0.6894 (p)
REVERT: A  582 LYS cc_start: 0.6940 (mptt) cc_final: 0.6431 (ttpp)
REVERT: A  824 ARG cc_start: 0.6626 (mmm-85) cc_final: 0.5956 (mmm-85)
  outliers start: 12
  outliers final: 8
  residues processed: 87
  average time/residue: 0.0829
  time to fit residues: 8.5745
Evaluate side-chains
  84 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 GLN
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  526 HIS
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  650 ASN
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  708 ILE
Chi-restraints excluded: chain A residue  815 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 28 optimal weight:    0.0570
   chunk 26 optimal weight:    0.7980
   chunk 45 optimal weight:    0.2980
   chunk 35 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 25 optimal weight:    0.3980
   chunk 39 optimal weight:    0.6980
   chunk 27 optimal weight:    0.3980
   overall best weight:    0.3698

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

Flipped N/Q/H residues before XYZ refinement:
A 578 ASN
** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.196868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.172644 restraints weight = 4708.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.173371 restraints weight = 3927.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.176052 restraints weight = 3295.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.176839 restraints weight = 2650.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.177142 restraints weight = 2161.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5784
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3646  Z= 0.115
  Angle     :  0.627  14.554   4969  Z= 0.313
  Chirality :  0.044   0.165    570
  Planarity :  0.004   0.035    631
  Dihedral  :  9.372 112.137    518
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  : 10.00 %
    Favored  : 89.35 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 19.94 %
    Favored  : 75.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.51 (0.37), residues: 460
  helix: -0.55 (0.45), residues: 135
  sheet: -0.69 (0.46), residues: 110
  loop : -3.01 (0.39), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 651 
 TYR   0.016   0.001   TYR A 767 
 PHE   0.009   0.001   PHE A 588 
 TRP   0.007   0.001   TRP B  53 
 HIS   0.002   0.001   HIS A 526 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 3645)
  covalent geometry    : angle       0.62668 ( 4967)
  SS BOND              : bond        0.00116 (    1)
  SS BOND              : angle       0.46713 (    2)
  hydrogen bonds       : bond        0.03139 (  125)
  hydrogen bonds       : angle       4.99128 (  354)

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

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

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: A  456 HIS cc_start: 0.6793 (m90) cc_final: 0.6591 (m90)
REVERT: A  567 VAL cc_start: 0.7077 (OUTLIER) cc_final: 0.6868 (p)
REVERT: A  582 LYS cc_start: 0.6907 (mptt) cc_final: 0.6443 (ttpp)
REVERT: A  824 ARG cc_start: 0.6572 (mmm-85) cc_final: 0.6105 (mmm-85)
REVERT: B   86 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6297 (mtp)
  outliers start: 15
  outliers final: 8
  residues processed: 86
  average time/residue: 0.0825
  time to fit residues: 8.3959
Evaluate side-chains
  87 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 GLN
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  526 HIS
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue   86 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 14 optimal weight:    0.4980
   chunk 34 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 578 ASN
** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.195133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.168413 restraints weight = 4805.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.171074 restraints weight = 3609.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.172792 restraints weight = 2951.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.174359 restraints weight = 2552.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.174857 restraints weight = 2293.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5832
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3646  Z= 0.144
  Angle     :  0.662  13.169   4969  Z= 0.338
  Chirality :  0.045   0.162    570
  Planarity :  0.004   0.036    631
  Dihedral  :  9.609 110.802    518
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  : 10.43 %
    Favored  : 88.91 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 22.02 %
    Favored  : 73.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.50 (0.37), residues: 460
  helix: -0.73 (0.43), residues: 135
  sheet: -0.47 (0.47), residues: 103
  loop : -2.93 (0.40), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 651 
 TYR   0.015   0.001   TYR A 767 
 PHE   0.011   0.001   PHE A 588 
 TRP   0.011   0.001   TRP B  53 
 HIS   0.004   0.001   HIS A 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 3645)
  covalent geometry    : angle       0.66242 ( 4967)
  SS BOND              : bond        0.00256 (    1)
  SS BOND              : angle       0.80528 (    2)
  hydrogen bonds       : bond        0.03453 (  125)
  hydrogen bonds       : angle       5.11658 (  354)

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

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

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: A  582 LYS cc_start: 0.6982 (mptt) cc_final: 0.6415 (tmmt)
REVERT: A  824 ARG cc_start: 0.6602 (mmm-85) cc_final: 0.6121 (mmm-85)
REVERT: B   86 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6306 (mtp)
  outliers start: 14
  outliers final: 10
  residues processed: 85
  average time/residue: 0.0768
  time to fit residues: 7.8601
Evaluate side-chains
  87 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 GLN
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  650 ASN
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  708 ILE
Chi-restraints excluded: chain A residue  768 ASP
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue   86 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 14 optimal weight:    0.0570
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0970
   chunk 27 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0970
   chunk 22 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.3094

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

Flipped N/Q/H residues before XYZ refinement:
A 578 ASN
** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.197751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.172657 restraints weight = 4718.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.173089 restraints weight = 4264.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.174929 restraints weight = 3748.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.176065 restraints weight = 2979.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.177864 restraints weight = 2417.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5770
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3646  Z= 0.113
  Angle     :  0.627  11.949   4969  Z= 0.318
  Chirality :  0.043   0.142    570
  Planarity :  0.004   0.034    631
  Dihedral  :  9.118 107.909    518
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  9.57 %
    Favored  : 89.78 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 22.32 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.41 (0.37), residues: 460
  helix: -0.51 (0.44), residues: 135
  sheet: -0.57 (0.46), residues: 111
  loop : -2.97 (0.39), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 651 
 TYR   0.017   0.001   TYR A 767 
 PHE   0.007   0.001   PHE A 588 
 TRP   0.008   0.001   TRP A 827 
 HIS   0.005   0.001   HIS A 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 3645)
  covalent geometry    : angle       0.62659 ( 4967)
  SS BOND              : bond        0.00097 (    1)
  SS BOND              : angle       0.51237 (    2)
  hydrogen bonds       : bond        0.03072 (  125)
  hydrogen bonds       : angle       4.94951 (  354)

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

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

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
REVERT: A  582 LYS cc_start: 0.6962 (mptt) cc_final: 0.6396 (tmmt)
REVERT: A  824 ARG cc_start: 0.6542 (mmm-85) cc_final: 0.6076 (mmm-85)
REVERT: B   86 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6315 (mtp)
  outliers start: 12
  outliers final: 9
  residues processed: 87
  average time/residue: 0.0774
  time to fit residues: 8.0441
Evaluate side-chains
  91 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 GLN
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  526 HIS
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  650 ASN
Chi-restraints excluded: chain A residue  708 ILE
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue   86 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 44 optimal weight:    0.4980
   chunk 9 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 17 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 13 optimal weight:    0.3980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 578 ASN
** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.193664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.168484 restraints weight = 4720.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.169109 restraints weight = 4055.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.171742 restraints weight = 3339.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.172551 restraints weight = 2692.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.172690 restraints weight = 2196.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5839
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3646  Z= 0.146
  Angle     :  0.661  11.891   4969  Z= 0.338
  Chirality :  0.044   0.149    570
  Planarity :  0.004   0.035    631
  Dihedral  :  9.411 108.029    518
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  : 10.22 %
    Favored  : 89.13 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 22.32 %
    Favored  : 73.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.44 (0.37), residues: 460
  helix: -0.71 (0.43), residues: 135
  sheet: -0.46 (0.47), residues: 103
  loop : -2.85 (0.40), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 651 
 TYR   0.017   0.001   TYR A 767 
 PHE   0.011   0.001   PHE A 588 
 TRP   0.011   0.001   TRP B  53 
 HIS   0.005   0.001   HIS A 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 3645)
  covalent geometry    : angle       0.66094 ( 4967)
  SS BOND              : bond        0.00267 (    1)
  SS BOND              : angle       0.87737 (    2)
  hydrogen bonds       : bond        0.03405 (  125)
  hydrogen bonds       : angle       5.12247 (  354)

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

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

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
REVERT: A  824 ARG cc_start: 0.6687 (mmm-85) cc_final: 0.6175 (mmm-85)
REVERT: B   86 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6526 (mtp)
  outliers start: 13
  outliers final: 10
  residues processed: 88
  average time/residue: 0.0762
  time to fit residues: 8.0465
Evaluate side-chains
  91 residues out of total 421 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  471 GLN
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  526 HIS
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  650 ASN
Chi-restraints excluded: chain A residue  708 ILE
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue   86 MET
Chi-restraints excluded: chain B residue   99 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0570
   chunk 29 optimal weight:    0.0770
   chunk 23 optimal weight:    0.3980
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.3656

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

Flipped N/Q/H residues before XYZ refinement:
A 578 ASN
A 581 GLN
** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.197040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.172074 restraints weight = 4610.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.172270 restraints weight = 4105.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.173901 restraints weight = 3632.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.175058 restraints weight = 2912.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.177326 restraints weight = 2417.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5791
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3646  Z= 0.118
  Angle     :  0.637  11.410   4969  Z= 0.324
  Chirality :  0.043   0.145    570
  Planarity :  0.004   0.034    631
  Dihedral  :  9.065 105.331    518
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  9.78 %
    Favored  : 89.57 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 23.21 %
    Favored  : 73.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.39 (0.37), residues: 460
  helix: -0.59 (0.44), residues: 135
  sheet: -0.58 (0.46), residues: 111
  loop : -2.88 (0.40), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 651 
 TYR   0.019   0.001   TYR A 767 
 PHE   0.007   0.001   PHE A 588 
 TRP   0.008   0.001   TRP A 827 
 HIS   0.004   0.001   HIS A 549 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 3645)
  covalent geometry    : angle       0.63701 ( 4967)
  SS BOND              : bond        0.00119 (    1)
  SS BOND              : angle       0.58356 (    2)
  hydrogen bonds       : bond        0.03111 (  125)
  hydrogen bonds       : angle       4.99359 (  354)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 762.75 seconds
wall clock time: 13 minutes 46.06 seconds (826.06 seconds total)