Starting phenix.real_space_refine
on Sun May 11 01:25:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t1j_40969/05_2025/8t1j_40969.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t1j_40969/05_2025/8t1j_40969.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t1j_40969/05_2025/8t1j_40969.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t1j_40969/05_2025/8t1j_40969.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t1j_40969/05_2025/8t1j_40969.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t1j_40969/05_2025/8t1j_40969.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.121
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: 6
    Type Number    sf(0)   Gaussians
     Fe      2      7.16       5
     Zn      1      6.06       5
     S      42      5.16       5
     C    4460      2.51       5
     N    1202      2.21       5
     O    1266      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6973
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 419, 3414
          Classifications: {'peptide': 419}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 396}
    Chain: "B"
      Number of atoms: 3414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 419, 3414
          Classifications: {'peptide': 419}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 396}
    Chain: "A"
      Number of atoms: 73
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 73
          Unusual residues: {' ZN': 1, 'H4B': 1, 'HEM': 1}
          Inner-chain residues flagged as termini: ['pdbres="ARG A1502 "']
          Classifications: {'peptide': 1, 'undetermined': 3}
          Modifications used: {'COO': 1}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "B"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 60
          Unusual residues: {'H4B': 1, 'HEM': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    234  SG  CYS A 326      33.487  54.832  48.590  1.00  0.00           S
  ATOM    274  SG  CYS A 331      33.594  52.036  51.805  1.00  0.00           S
  ATOM   3648  SG  CYS B 326      36.099  54.944  52.568  1.00  0.00           S
  ATOM   3688  SG  CYS B 331      36.316  52.165  49.106  1.00  0.00           S
  ATOM    965  SG  CYS A 415      42.977  42.732  34.962  1.00  0.00           S
  ATOM   4379  SG  CYS B 415      28.567  40.706  65.373  1.00  0.00           S

  Time building chain proxies: 4.93, per 1000 atoms: 0.71
  Number of scatterers: 6973
  At special positions: 0
  Unit cell: (74.13, 83.661, 101.664, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     Fe      2     26.01
     S      42     16.00
     O    1266      8.00
     N    1202      7.00
     C    4460      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.48
  Conformation dependent library (CDL) restraints added in 794.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1501 "
        pdb="ZN    ZN A1501 " - pdb=" SG  CYS A 331 "
        pdb="ZN    ZN A1501 " - pdb=" SG  CYS B 331 "
        pdb="ZN    ZN A1501 " - pdb=" SG  CYS A 326 "
        pdb="ZN    ZN A1501 " - pdb=" SG  CYS B 326 "
      Number of angles added : 6


  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1584

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 16 sheets defined
      44.8% alpha, 9.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 315 through 320
    Processing helix  chain 'A' and resid 350 through 369
      Proline residue:  A 356  - end of helix
    Processing helix  chain 'A' and resid 374 through 392
    Processing helix  chain 'A' and resid 397 through 411
    Processing helix  chain 'A' and resid 417 through 421
    Processing helix  chain 'A' and resid 434 through 451
    Processing helix  chain 'A' and resid 452 through 454
      No H-bonds generated for 'chain 'A' and resid 452 through 454'
    Processing helix  chain 'A' and resid 498 through 507
    Processing helix  chain 'A' and resid 537 through 541
    Processing helix  chain 'A' and resid 553 through 558
    Processing helix  chain 'A' and resid 590 through 595
    Processing helix  chain 'A' and resid 606 through 614
    Processing helix  chain 'A' and resid 620 through 623
    Processing helix  chain 'A' and resid 624 through 644
    Processing helix  chain 'A' and resid 650 through 669
    Processing helix  chain 'A' and resid 675 through 680
    Processing helix  chain 'A' and resid 684 through 693
      Proline residue:  A 689  - end of helix
      removed outlier: 3.627A  pdb=" N   HIS A 692 " --> pdb=" O   PRO A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 713
    Processing helix  chain 'B' and resid 315 through 320
    Processing helix  chain 'B' and resid 350 through 369
      Proline residue:  B 356  - end of helix
    Processing helix  chain 'B' and resid 374 through 392
    Processing helix  chain 'B' and resid 397 through 411
    Processing helix  chain 'B' and resid 417 through 421
    Processing helix  chain 'B' and resid 434 through 451
    Processing helix  chain 'B' and resid 452 through 454
      No H-bonds generated for 'chain 'B' and resid 452 through 454'
    Processing helix  chain 'B' and resid 498 through 507
    Processing helix  chain 'B' and resid 537 through 541
    Processing helix  chain 'B' and resid 553 through 558
    Processing helix  chain 'B' and resid 590 through 595
    Processing helix  chain 'B' and resid 606 through 614
    Processing helix  chain 'B' and resid 620 through 623
    Processing helix  chain 'B' and resid 624 through 644
    Processing helix  chain 'B' and resid 650 through 669
    Processing helix  chain 'B' and resid 675 through 680
    Processing helix  chain 'B' and resid 684 through 693
      removed outlier: 3.508A  pdb=" N   ILE B 687 " --> pdb=" O   SER B 684 " (cutoff:3.500A)
      Proline residue:  B 689  - end of helix
    Processing helix  chain 'B' and resid 709 through 713
    Processing sheet with id=AA1, first strand: chain 'A' and resid 301 through 304
    Processing sheet with id=AA2, first strand: chain 'A' and resid 330 through 331
    Processing sheet with id=AA3, first strand: chain 'A' and resid 425 through 428
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'A' and resid 484 through 486
    Processing sheet with id=AA6, first strand: chain 'A' and resid 543 through 545
    Processing sheet with id=AA7, first strand: chain 'A' and resid 577 through 579
    Processing sheet with id=AA8, first strand: chain 'A' and resid 588 through 589
      removed outlier: 6.470A  pdb=" N   TYR A 588 " --> pdb=" O   VAL A 649 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 697 through 698
    Processing sheet with id=AB1, first strand: chain 'B' and resid 301 through 304
    Processing sheet with id=AB2, first strand: chain 'B' and resid 425 through 428
    Processing sheet with id=AB3, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AB4, first strand: chain 'B' and resid 484 through 486
    Processing sheet with id=AB5, first strand: chain 'B' and resid 543 through 545
    Processing sheet with id=AB6, first strand: chain 'B' and resid 577 through 579
    Processing sheet with id=AB7, first strand: chain 'B' and resid 588 through 589
      removed outlier: 6.526A  pdb=" N   TYR B 588 " --> pdb=" O   VAL B 649 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7

    296 hydrogen bonds defined for protein.
    732 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.02

  Time building geometry restraints manager: 1.74 seconds

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

  Histogram of bond lengths:
        1.21 -     1.40: 2923
        1.40 -     1.59: 4185
        1.59 -     1.78: 2
        1.78 -     1.98: 65
        1.98 -     2.17: 5
  Bond restraints: 7180
  Sorted by residual:
  bond pdb=" C3B HEM B1503 "
       pdb=" CAB HEM B1503 "
    ideal  model  delta    sigma   weight residual
    1.544  1.391  0.153 2.00e-02 2.50e+03 5.81e+01
  bond pdb=" C3B HEM A1504 "
       pdb=" CAB HEM A1504 "
    ideal  model  delta    sigma   weight residual
    1.544  1.394  0.150 2.00e-02 2.50e+03 5.60e+01
  bond pdb=" C3C HEM B1503 "
       pdb=" CAC HEM B1503 "
    ideal  model  delta    sigma   weight residual
    1.544  1.402  0.142 2.00e-02 2.50e+03 5.03e+01
  bond pdb=" C3C HEM A1504 "
       pdb=" CAC HEM A1504 "
    ideal  model  delta    sigma   weight residual
    1.544  1.409  0.135 2.00e-02 2.50e+03 4.57e+01
  bond pdb=" C4A H4B A1503 "
       pdb=" N5  H4B A1503 "
    ideal  model  delta    sigma   weight residual
    1.368  1.465 -0.097 1.60e-02 3.91e+03 3.68e+01
  ... (remaining 7175 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.38: 9692
        5.38 -    10.76: 74
       10.76 -    16.15: 2
       16.15 -    21.53: 0
       21.53 -    26.91: 2
  Bond angle restraints: 9770
  Sorted by residual:
  angle pdb=" N   LEU A 354 "
        pdb=" CA  LEU A 354 "
        pdb=" C   LEU A 354 "
      ideal   model   delta    sigma   weight residual
     111.36  119.13   -7.77 1.09e+00 8.42e-01 5.08e+01
  angle pdb=" N   LEU B 354 "
        pdb=" CA  LEU B 354 "
        pdb=" C   LEU B 354 "
      ideal   model   delta    sigma   weight residual
     111.36  119.12   -7.76 1.09e+00 8.42e-01 5.07e+01
  angle pdb=" N   VAL B 499 "
        pdb=" CA  VAL B 499 "
        pdb=" C   VAL B 499 "
      ideal   model   delta    sigma   weight residual
     110.42  116.18   -5.76 9.60e-01 1.09e+00 3.59e+01
  angle pdb=" N1  H4B B1502 "
        pdb=" C2  H4B B1502 "
        pdb=" N3  H4B B1502 "
      ideal   model   delta    sigma   weight residual
     123.14  117.15    5.99 1.00e+00 1.00e+00 3.59e+01
  angle pdb=" N   ASN A 712 "
        pdb=" CA  ASN A 712 "
        pdb=" C   ASN A 712 "
      ideal   model   delta    sigma   weight residual
     113.17  105.66    7.51 1.26e+00 6.30e-01 3.55e+01
  ... (remaining 9765 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.64: 4088
       21.64 -    43.28: 95
       43.28 -    64.92: 29
       64.92 -    86.56: 10
       86.56 -   108.20: 8
  Dihedral angle restraints: 4230
    sinusoidal: 1778
      harmonic: 2452
  Sorted by residual:
  dihedral pdb=" C2B HEM A1504 "
           pdb=" C3B HEM A1504 "
           pdb=" CAB HEM A1504 "
           pdb=" CBB HEM A1504 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -101.42  -78.58     2      1.00e+01 1.00e-02 4.61e+01
  dihedral pdb=" C2B HEM B1503 "
           pdb=" C3B HEM B1503 "
           pdb=" CAB HEM B1503 "
           pdb=" CBB HEM B1503 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -118.80  -61.20     2      1.00e+01 1.00e-02 3.69e+01
  dihedral pdb=" CA  TYR A 588 "
           pdb=" C   TYR A 588 "
           pdb=" N   MET A 589 "
           pdb=" CA  MET A 589 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.45   28.55     0      5.00e+00 4.00e-02 3.26e+01
  ... (remaining 4227 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 676
       0.070 -    0.139: 265
       0.139 -    0.209: 56
       0.209 -    0.278: 15
       0.278 -    0.348: 2
  Chirality restraints: 1014
  Sorted by residual:
  chirality pdb=" CA  VAL B 474 "
            pdb=" N   VAL B 474 "
            pdb=" C   VAL B 474 "
            pdb=" CB  VAL B 474 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.79   -0.35 2.00e-01 2.50e+01 3.02e+00
  chirality pdb=" CA  ASP B 471 "
            pdb=" N   ASP B 471 "
            pdb=" C   ASP B 471 "
            pdb=" CB  ASP B 471 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.78e+00
  chirality pdb=" CA  ASP B 347 "
            pdb=" N   ASP B 347 "
            pdb=" C   ASP B 347 "
            pdb=" CB  ASP B 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.26 2.00e-01 2.50e+01 1.63e+00
  ... (remaining 1011 not shown)

  Planarity restraints: 1240
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1A HEM A1504 "    0.015 2.00e-02 2.50e+03   1.26e-01 3.55e+02
        pdb=" C2A HEM A1504 "    0.038 2.00e-02 2.50e+03
        pdb=" C3A HEM A1504 "    0.104 2.00e-02 2.50e+03
        pdb=" C4A HEM A1504 "    0.015 2.00e-02 2.50e+03
        pdb=" CAA HEM A1504 "   -0.251 2.00e-02 2.50e+03
        pdb=" CHA HEM A1504 "    0.100 2.00e-02 2.50e+03
        pdb=" CHB HEM A1504 "   -0.174 2.00e-02 2.50e+03
        pdb=" CMA HEM A1504 "    0.162 2.00e-02 2.50e+03
        pdb=" NA  HEM A1504 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" ND  HEM B1503 "   -0.136 2.00e-02 2.50e+03   1.08e-01 2.62e+02
        pdb=" C1D HEM B1503 "   -0.147 2.00e-02 2.50e+03
        pdb=" C2D HEM B1503 "   -0.080 2.00e-02 2.50e+03
        pdb=" C3D HEM B1503 "   -0.024 2.00e-02 2.50e+03
        pdb=" C4D HEM B1503 "   -0.002 2.00e-02 2.50e+03
        pdb=" CAD HEM B1503 "   -0.003 2.00e-02 2.50e+03
        pdb=" CHA HEM B1503 "    0.145 2.00e-02 2.50e+03
        pdb=" CHD HEM B1503 "    0.179 2.00e-02 2.50e+03
        pdb=" CMD HEM B1503 "    0.068 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" NB  HEM A1504 "    0.164 2.00e-02 2.50e+03   1.01e-01 2.28e+02
        pdb=" C1B HEM A1504 "    0.019 2.00e-02 2.50e+03
        pdb=" C2B HEM A1504 "   -0.013 2.00e-02 2.50e+03
        pdb=" C3B HEM A1504 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4B HEM A1504 "    0.071 2.00e-02 2.50e+03
        pdb=" CAB HEM A1504 "   -0.092 2.00e-02 2.50e+03
        pdb=" CHB HEM A1504 "   -0.181 2.00e-02 2.50e+03
        pdb=" CHC HEM A1504 "   -0.074 2.00e-02 2.50e+03
        pdb=" CMB HEM A1504 "    0.108 2.00e-02 2.50e+03
  ... (remaining 1237 not shown)

  Histogram of nonbonded interaction distances:
        2.50 -     2.98: 3409
        2.98 -     3.46: 6712
        3.46 -     3.94: 12102
        3.94 -     4.42: 14631
        4.42 -     4.90: 22157
  Nonbonded interactions: 59011
  Sorted by model distance:
  nonbonded pdb=" N   ASN B 712 "
            pdb=" N   THR B 713 "
     model   vdw
     2.502 2.560
  nonbonded pdb=" N   ASN A 712 "
            pdb=" N   THR A 713 "
     model   vdw
     2.502 2.560
  nonbonded pdb=" O   THR B 433 "
            pdb=" ND2 ASN B 527 "
     model   vdw
     2.525 3.120
  nonbonded pdb=" OE1 GLN B 478 "
            pdb=" NH1 ARG B 481 "
     model   vdw
     2.526 3.120
  nonbonded pdb=" O   THR A 433 "
            pdb=" ND2 ASN A 527 "
     model   vdw
     2.531 3.120
  ... (remaining 59006 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 298 through 716 or resid 1502 through 1504))
  selection = chain 'B'
}

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 individual isotropic
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:             1.490
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.190
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
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      :  0.015   0.461   7186  Z= 0.717
  Angle     :  1.479  26.910   9776  Z= 0.970
  Chirality :  0.075   0.348   1014
  Planarity :  0.011   0.126   1240
  Dihedral  : 12.837 108.198   2646
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 0.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.26), residues: 834
  helix: -0.01 (0.26), residues: 296
  sheet:  0.14 (0.56), residues: 78
  loop :  0.33 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.065   0.006   TRP B 711 
 HIS   0.009   0.001   HIS B 714 
 PHE   0.035   0.003   PHE B 554 
 TYR   0.100   0.016   TYR A 604 
 ARG   0.008   0.001   ARG B 414 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21465 (  296)
  hydrogen bonds       : angle       7.16934 (  732)
  metal coordination   : bond        0.26405 (    4)
  metal coordination   : angle      12.43868 (    6)
  covalent geometry    : bond        0.01174 ( 7180)
  covalent geometry    : angle       1.44695 ( 9770)
  Misc. bond           : bond        0.45764 (    2)

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

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

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.805 
Fit side-chains
REVERT: B  369 ILE cc_start: 0.7254 (pt) cc_final: 0.7049 (pt)
REVERT: B  695 MET cc_start: 0.8951 (mtt) cc_final: 0.8687 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 1.6533
  time to fit residues: 247.4100
Evaluate side-chains
  84 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 525 GLN
A 535 GLN
B 353 GLN
B 385 ASN
** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 642 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.125851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.098773 restraints weight = 8469.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 1.99
r_work: 0.3128 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7186  Z= 0.152
  Angle     :  0.654  17.444   9776  Z= 0.309
  Chirality :  0.043   0.136   1014
  Planarity :  0.004   0.035   1240
  Dihedral  : 11.526 100.924    962
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  :  8.24 %
    Favored  : 89.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.29), residues: 834
  helix:  1.34 (0.30), residues: 314
  sheet:  0.10 (0.62), residues: 76
  loop :  0.85 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 711 
 HIS   0.017   0.001   HIS B 714 
 PHE   0.015   0.002   PHE B 300 
 TYR   0.012   0.002   TYR A 366 
 ARG   0.005   0.001   ARG A 414 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04970 (  296)
  hydrogen bonds       : angle       4.73349 (  732)
  metal coordination   : bond        0.01020 (    4)
  metal coordination   : angle       3.63794 (    6)
  covalent geometry    : bond        0.00365 ( 7180)
  covalent geometry    : angle       0.64779 ( 9770)
  Misc. bond           : bond        0.01982 (    2)

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

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

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
REVERT: A  355 PHE cc_start: 0.7494 (m-80) cc_final: 0.7267 (m-80)
REVERT: A  452 LYS cc_start: 0.8776 (mttt) cc_final: 0.8265 (mtmp)
REVERT: A  550 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7247 (tppt)
REVERT: A  601 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8166 (m-40)
REVERT: B  351 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7140 (mttp)
REVERT: B  527 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8232 (t0)
REVERT: B  573 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7213 (tt0)
REVERT: B  614 MET cc_start: 0.8375 (mtp) cc_final: 0.8127 (mtp)
REVERT: B  620 LYS cc_start: 0.7904 (mmtt) cc_final: 0.7212 (ptmm)
REVERT: B  695 MET cc_start: 0.9044 (mtt) cc_final: 0.8817 (mtt)
  outliers start: 18
  outliers final: 8
  residues processed: 101
  average time/residue: 1.5958
  time to fit residues: 168.0070
Evaluate side-chains
  91 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  507 GLN
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain A residue  550 LYS
Chi-restraints excluded: chain A residue  601 ASN
Chi-restraints excluded: chain A residue  615 ASP
Chi-restraints excluded: chain B residue  351 LYS
Chi-restraints excluded: chain B residue  371 ARG
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain B residue  527 ASN
Chi-restraints excluded: chain B residue  573 GLU
Chi-restraints excluded: chain B residue  668 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 65 optimal weight:    0.3980
   chunk 16 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0980
   chunk 17 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 364 GLN
A 605 ASN
A 712 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.124841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.097512 restraints weight = 8624.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 2.01
r_work: 0.3099 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7186  Z= 0.145
  Angle     :  0.625  17.347   9776  Z= 0.285
  Chirality :  0.042   0.137   1014
  Planarity :  0.004   0.039   1240
  Dihedral  : 11.143  98.749    962
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  :  9.57 %
    Favored  : 87.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.29), residues: 834
  helix:  1.48 (0.30), residues: 310
  sheet:  0.41 (0.56), residues: 96
  loop :  0.73 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 587 
 HIS   0.012   0.001   HIS B 714 
 PHE   0.016   0.002   PHE B 355 
 TYR   0.010   0.001   TYR A 366 
 ARG   0.003   0.000   ARG A 414 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04620 (  296)
  hydrogen bonds       : angle       4.56281 (  732)
  metal coordination   : bond        0.00562 (    4)
  metal coordination   : angle       3.83874 (    6)
  covalent geometry    : bond        0.00358 ( 7180)
  covalent geometry    : angle       0.61752 ( 9770)
  Misc. bond           : bond        0.01918 (    2)

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

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

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.763 
Fit side-chains
REVERT: A  452 LYS cc_start: 0.8781 (mttt) cc_final: 0.8432 (mtmt)
REVERT: A  601 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8303 (m-40)
REVERT: A  656 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7795 (mp0)
REVERT: B  351 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6736 (mttp)
REVERT: B  491 SER cc_start: 0.8398 (OUTLIER) cc_final: 0.7998 (m)
REVERT: B  527 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8249 (t0)
REVERT: B  573 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7200 (tm-30)
REVERT: B  614 MET cc_start: 0.8374 (mtp) cc_final: 0.8085 (mtp)
REVERT: B  620 LYS cc_start: 0.7959 (mmtt) cc_final: 0.7228 (ptmm)
  outliers start: 20
  outliers final: 10
  residues processed: 95
  average time/residue: 1.6713
  time to fit residues: 165.4413
Evaluate side-chains
  94 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  368 SER
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  507 GLN
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain A residue  601 ASN
Chi-restraints excluded: chain A residue  612 LYS
Chi-restraints excluded: chain A residue  615 ASP
Chi-restraints excluded: chain B residue  351 LYS
Chi-restraints excluded: chain B residue  368 SER
Chi-restraints excluded: chain B residue  491 SER
Chi-restraints excluded: chain B residue  527 ASN
Chi-restraints excluded: chain B residue  573 GLU
Chi-restraints excluded: chain B residue  602 SER
Chi-restraints excluded: chain B residue  612 LYS
Chi-restraints excluded: chain B residue  668 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0040
   chunk 15 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 25 optimal weight:    7.9990
   chunk 81 optimal weight:    0.6980
   chunk 24 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:
A 445 HIS
A 605 ASN
A 712 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.125316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.098081 restraints weight = 8551.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 2.01
r_work: 0.3114 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7186  Z= 0.128
  Angle     :  0.579  14.746   9776  Z= 0.270
  Chirality :  0.042   0.137   1014
  Planarity :  0.004   0.041   1240
  Dihedral  : 10.763  96.281    962
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 10.77 %
    Favored  : 86.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.30), residues: 834
  helix:  1.44 (0.30), residues: 310
  sheet:  0.40 (0.56), residues: 96
  loop :  0.71 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 587 
 HIS   0.010   0.001   HIS B 714 
 PHE   0.038   0.002   PHE B 355 
 TYR   0.010   0.001   TYR B 366 
 ARG   0.003   0.000   ARG A 414 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04202 (  296)
  hydrogen bonds       : angle       4.48640 (  732)
  metal coordination   : bond        0.00477 (    4)
  metal coordination   : angle       3.33556 (    6)
  covalent geometry    : bond        0.00322 ( 7180)
  covalent geometry    : angle       0.57286 ( 9770)
  Misc. bond           : bond        0.01523 (    2)

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

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

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.748 
Fit side-chains
REVERT: A  371 ARG cc_start: 0.7706 (mmt-90) cc_final: 0.7153 (tpp80)
REVERT: A  452 LYS cc_start: 0.8866 (mttt) cc_final: 0.8512 (mtmt)
REVERT: A  573 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7537 (tp30)
REVERT: A  656 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7750 (mp0)
REVERT: B  491 SER cc_start: 0.8347 (OUTLIER) cc_final: 0.7962 (m)
REVERT: B  573 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7295 (tm-30)
REVERT: B  614 MET cc_start: 0.8326 (mtp) cc_final: 0.8089 (mtp)
REVERT: B  620 LYS cc_start: 0.7962 (mmtt) cc_final: 0.7151 (ptmm)
  outliers start: 20
  outliers final: 9
  residues processed: 96
  average time/residue: 1.6165
  time to fit residues: 161.7071
Evaluate side-chains
  90 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  507 GLN
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain A residue  612 LYS
Chi-restraints excluded: chain A residue  615 ASP
Chi-restraints excluded: chain B residue  368 SER
Chi-restraints excluded: chain B residue  371 ARG
Chi-restraints excluded: chain B residue  491 SER
Chi-restraints excluded: chain B residue  573 GLU
Chi-restraints excluded: chain B residue  602 SER
Chi-restraints excluded: chain B residue  668 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 25 optimal weight:    9.9990
   chunk 15 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 601 ASN
A 605 ASN
A 692 HIS
A 712 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.123746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.096345 restraints weight = 8578.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 2.00
r_work: 0.3082 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.3117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   7186  Z= 0.170
  Angle     :  0.623  15.794   9776  Z= 0.288
  Chirality :  0.043   0.141   1014
  Planarity :  0.004   0.041   1240
  Dihedral  : 11.192 101.727    962
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 11.57 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.29), residues: 834
  helix:  1.24 (0.29), residues: 314
  sheet:  0.33 (0.56), residues: 96
  loop :  0.63 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 587 
 HIS   0.009   0.001   HIS B 714 
 PHE   0.036   0.002   PHE B 355 
 TYR   0.010   0.001   TYR A 366 
 ARG   0.003   0.000   ARG B 481 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04669 (  296)
  hydrogen bonds       : angle       4.59404 (  732)
  metal coordination   : bond        0.00488 (    4)
  metal coordination   : angle       3.39416 (    6)
  covalent geometry    : bond        0.00431 ( 7180)
  covalent geometry    : angle       0.61726 ( 9770)
  Misc. bond           : bond        0.01471 (    2)

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

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

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.775 
Fit side-chains
REVERT: A  355 PHE cc_start: 0.7697 (m-80) cc_final: 0.7472 (m-80)
REVERT: A  371 ARG cc_start: 0.7763 (mmt-90) cc_final: 0.7232 (tpp80)
REVERT: A  656 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7731 (mp0)
REVERT: B  438 MET cc_start: 0.8810 (mtp) cc_final: 0.8479 (mtp)
REVERT: B  491 SER cc_start: 0.8341 (OUTLIER) cc_final: 0.7963 (m)
REVERT: B  573 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7211 (tm-30)
REVERT: B  614 MET cc_start: 0.8438 (mtp) cc_final: 0.8137 (mtp)
REVERT: B  620 LYS cc_start: 0.8030 (mmtt) cc_final: 0.7203 (ptmm)
  outliers start: 17
  outliers final: 13
  residues processed: 92
  average time/residue: 1.5968
  time to fit residues: 153.2861
Evaluate side-chains
  91 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  368 SER
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  507 GLN
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain A residue  552 ASP
Chi-restraints excluded: chain A residue  612 LYS
Chi-restraints excluded: chain A residue  615 ASP
Chi-restraints excluded: chain B residue  368 SER
Chi-restraints excluded: chain B residue  371 ARG
Chi-restraints excluded: chain B residue  491 SER
Chi-restraints excluded: chain B residue  573 GLU
Chi-restraints excluded: chain B residue  602 SER
Chi-restraints excluded: chain B residue  622 SER
Chi-restraints excluded: chain B residue  668 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 601 ASN
A 605 ASN
A 712 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.123534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.096166 restraints weight = 8638.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 2.01
r_work: 0.3104 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.3209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7186  Z= 0.166
  Angle     :  0.609  14.750   9776  Z= 0.284
  Chirality :  0.043   0.140   1014
  Planarity :  0.004   0.042   1240
  Dihedral  : 11.156 101.168    962
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 11.30 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.29), residues: 834
  helix:  1.15 (0.29), residues: 318
  sheet:  0.28 (0.56), residues: 96
  loop :  0.58 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 587 
 HIS   0.009   0.001   HIS B 714 
 PHE   0.038   0.002   PHE B 355 
 TYR   0.009   0.001   TYR A 366 
 ARG   0.003   0.000   ARG B 481 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04607 (  296)
  hydrogen bonds       : angle       4.58025 (  732)
  metal coordination   : bond        0.00418 (    4)
  metal coordination   : angle       3.48014 (    6)
  covalent geometry    : bond        0.00421 ( 7180)
  covalent geometry    : angle       0.60294 ( 9770)
  Misc. bond           : bond        0.01175 (    2)

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

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

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 78
  time to evaluate  : 0.829 
Fit side-chains
REVERT: A  355 PHE cc_start: 0.7790 (m-80) cc_final: 0.7484 (m-80)
REVERT: A  371 ARG cc_start: 0.7751 (mmt-90) cc_final: 0.7211 (tpp80)
REVERT: A  550 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7361 (tppt)
REVERT: A  573 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7766 (tt0)
REVERT: A  656 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7690 (mp0)
REVERT: B  299 ARG cc_start: 0.5750 (mmp80) cc_final: 0.5114 (tpp-160)
REVERT: B  491 SER cc_start: 0.8309 (OUTLIER) cc_final: 0.7931 (m)
REVERT: B  573 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7165 (tm-30)
REVERT: B  614 MET cc_start: 0.8396 (mtp) cc_final: 0.8109 (mtp)
REVERT: B  620 LYS cc_start: 0.8007 (mmtt) cc_final: 0.7151 (ptmm)
  outliers start: 21
  outliers final: 13
  residues processed: 93
  average time/residue: 1.6175
  time to fit residues: 156.8512
Evaluate side-chains
  97 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  368 SER
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  507 GLN
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain A residue  550 LYS
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  612 LYS
Chi-restraints excluded: chain A residue  615 ASP
Chi-restraints excluded: chain B residue  368 SER
Chi-restraints excluded: chain B residue  371 ARG
Chi-restraints excluded: chain B residue  491 SER
Chi-restraints excluded: chain B residue  573 GLU
Chi-restraints excluded: chain B residue  602 SER
Chi-restraints excluded: chain B residue  622 SER
Chi-restraints excluded: chain B residue  668 CYS
Chi-restraints excluded: chain B residue  686 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   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 470 HIS
A 601 ASN
A 605 ASN
A 712 ASN
B 535 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.123508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.096139 restraints weight = 8461.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 2.00
r_work: 0.3094 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.3281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   7186  Z= 0.176
  Angle     :  0.620  14.782   9776  Z= 0.292
  Chirality :  0.044   0.146   1014
  Planarity :  0.004   0.042   1240
  Dihedral  : 11.243 101.637    962
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 11.30 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.29), residues: 834
  helix:  1.12 (0.29), residues: 318
  sheet:  0.26 (0.55), residues: 96
  loop :  0.48 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 587 
 HIS   0.009   0.001   HIS B 714 
 PHE   0.037   0.002   PHE B 355 
 TYR   0.009   0.001   TYR A 366 
 ARG   0.003   0.000   ARG B 481 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04699 (  296)
  hydrogen bonds       : angle       4.59398 (  732)
  metal coordination   : bond        0.00492 (    4)
  metal coordination   : angle       3.67327 (    6)
  covalent geometry    : bond        0.00444 ( 7180)
  covalent geometry    : angle       0.61369 ( 9770)
  Misc. bond           : bond        0.01076 (    2)

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

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

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.835 
Fit side-chains
REVERT: A  300 PHE cc_start: 0.7157 (m-80) cc_final: 0.6766 (p90)
REVERT: A  355 PHE cc_start: 0.7864 (m-80) cc_final: 0.7461 (m-80)
REVERT: A  371 ARG cc_start: 0.7735 (mmt-90) cc_final: 0.7231 (tpp80)
REVERT: A  391 THR cc_start: 0.7813 (OUTLIER) cc_final: 0.7591 (p)
REVERT: A  573 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7822 (tt0)
REVERT: A  656 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7591 (mp0)
REVERT: B  299 ARG cc_start: 0.5768 (mmp80) cc_final: 0.5099 (tpp-160)
REVERT: B  438 MET cc_start: 0.8757 (mtp) cc_final: 0.8390 (mtp)
REVERT: B  491 SER cc_start: 0.8291 (OUTLIER) cc_final: 0.7918 (m)
REVERT: B  573 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7134 (tm-30)
REVERT: B  614 MET cc_start: 0.8475 (mtp) cc_final: 0.8194 (mtp)
  outliers start: 19
  outliers final: 13
  residues processed: 94
  average time/residue: 1.5747
  time to fit residues: 155.2960
Evaluate side-chains
  96 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  368 SER
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  507 GLN
Chi-restraints excluded: chain A residue  539 GLU
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  612 LYS
Chi-restraints excluded: chain A residue  615 ASP
Chi-restraints excluded: chain B residue  368 SER
Chi-restraints excluded: chain B residue  371 ARG
Chi-restraints excluded: chain B residue  491 SER
Chi-restraints excluded: chain B residue  573 GLU
Chi-restraints excluded: chain B residue  602 SER
Chi-restraints excluded: chain B residue  622 SER
Chi-restraints excluded: chain B residue  668 CYS
Chi-restraints excluded: chain B residue  686 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 56 optimal weight:    0.3980
   chunk 44 optimal weight:    4.9990
   chunk 63 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 38 optimal weight:    0.4980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 605 ASN
A 712 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.124330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.097250 restraints weight = 8541.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.99
r_work: 0.3086 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7186  Z= 0.142
  Angle     :  0.583  13.423   9776  Z= 0.277
  Chirality :  0.042   0.136   1014
  Planarity :  0.004   0.043   1240
  Dihedral  : 10.966  99.087    962
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 11.84 %
    Favored  : 85.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.29), residues: 834
  helix:  1.26 (0.29), residues: 314
  sheet:  0.29 (0.55), residues: 96
  loop :  0.49 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 587 
 HIS   0.009   0.001   HIS B 714 
 PHE   0.040   0.002   PHE B 355 
 TYR   0.009   0.001   TYR B 366 
 ARG   0.008   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04300 (  296)
  hydrogen bonds       : angle       4.48359 (  732)
  metal coordination   : bond        0.00360 (    4)
  metal coordination   : angle       3.61140 (    6)
  covalent geometry    : bond        0.00361 ( 7180)
  covalent geometry    : angle       0.57597 ( 9770)
  Misc. bond           : bond        0.01041 (    2)

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

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

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.830 
Fit side-chains
REVERT: A  300 PHE cc_start: 0.7137 (m-80) cc_final: 0.6784 (p90)
REVERT: A  355 PHE cc_start: 0.7907 (m-80) cc_final: 0.7563 (m-80)
REVERT: A  371 ARG cc_start: 0.7742 (mmt-90) cc_final: 0.7252 (tpp80)
REVERT: A  573 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7796 (tt0)
REVERT: A  656 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7715 (mp0)
REVERT: B  299 ARG cc_start: 0.5718 (mmp80) cc_final: 0.5098 (tpp-160)
REVERT: B  438 MET cc_start: 0.8787 (mtp) cc_final: 0.8442 (mtp)
REVERT: B  491 SER cc_start: 0.8319 (OUTLIER) cc_final: 0.7972 (m)
REVERT: B  573 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7196 (tm-30)
REVERT: B  614 MET cc_start: 0.8392 (mtp) cc_final: 0.8138 (mtp)
  outliers start: 18
  outliers final: 14
  residues processed: 91
  average time/residue: 1.5652
  time to fit residues: 148.8159
Evaluate side-chains
  94 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  368 SER
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  489 ASP
Chi-restraints excluded: chain A residue  507 GLN
Chi-restraints excluded: chain A residue  552 ASP
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  612 LYS
Chi-restraints excluded: chain A residue  615 ASP
Chi-restraints excluded: chain B residue  368 SER
Chi-restraints excluded: chain B residue  371 ARG
Chi-restraints excluded: chain B residue  491 SER
Chi-restraints excluded: chain B residue  573 GLU
Chi-restraints excluded: chain B residue  602 SER
Chi-restraints excluded: chain B residue  622 SER
Chi-restraints excluded: chain B residue  668 CYS
Chi-restraints excluded: chain B residue  686 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 16 optimal weight:    0.3980
   chunk 35 optimal weight:    1.9990
   chunk 1 optimal weight:    0.1980
   chunk 58 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 54 optimal weight:    0.5980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 605 ASN
A 712 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.124726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.097603 restraints weight = 8572.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 1.99
r_work: 0.3128 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3014 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.3376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7186  Z= 0.127
  Angle     :  0.565  12.584   9776  Z= 0.270
  Chirality :  0.042   0.135   1014
  Planarity :  0.004   0.043   1240
  Dihedral  : 10.771  97.580    962
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 12.10 %
    Favored  : 85.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.29), residues: 834
  helix:  1.33 (0.29), residues: 314
  sheet:  0.30 (0.55), residues: 96
  loop :  0.55 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 587 
 HIS   0.009   0.001   HIS B 714 
 PHE   0.045   0.002   PHE B 355 
 TYR   0.010   0.001   TYR B 366 
 ARG   0.007   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04105 (  296)
  hydrogen bonds       : angle       4.43476 (  732)
  metal coordination   : bond        0.00346 (    4)
  metal coordination   : angle       3.63958 (    6)
  covalent geometry    : bond        0.00321 ( 7180)
  covalent geometry    : angle       0.55753 ( 9770)
  Misc. bond           : bond        0.01134 (    2)

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

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

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.743 
Fit side-chains
REVERT: A  300 PHE cc_start: 0.7099 (m-80) cc_final: 0.6758 (p90)
REVERT: A  355 PHE cc_start: 0.7827 (m-80) cc_final: 0.7474 (m-80)
REVERT: A  371 ARG cc_start: 0.7694 (mmt-90) cc_final: 0.7167 (tpp80)
REVERT: A  469 LYS cc_start: 0.8062 (tptt) cc_final: 0.7849 (mmtt)
REVERT: A  573 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7753 (tt0)
REVERT: A  656 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7606 (mp0)
REVERT: B  299 ARG cc_start: 0.5668 (mmp80) cc_final: 0.5093 (tpp-160)
REVERT: B  438 MET cc_start: 0.8729 (mtp) cc_final: 0.8347 (mtp)
REVERT: B  491 SER cc_start: 0.8295 (OUTLIER) cc_final: 0.7954 (m)
REVERT: B  573 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7155 (tm-30)
REVERT: B  614 MET cc_start: 0.8386 (mtp) cc_final: 0.8137 (mtp)
  outliers start: 16
  outliers final: 12
  residues processed: 88
  average time/residue: 1.6557
  time to fit residues: 151.7348
Evaluate side-chains
  92 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  368 SER
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  507 GLN
Chi-restraints excluded: chain A residue  552 ASP
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  612 LYS
Chi-restraints excluded: chain A residue  615 ASP
Chi-restraints excluded: chain B residue  368 SER
Chi-restraints excluded: chain B residue  371 ARG
Chi-restraints excluded: chain B residue  491 SER
Chi-restraints excluded: chain B residue  573 GLU
Chi-restraints excluded: chain B residue  602 SER
Chi-restraints excluded: chain B residue  622 SER
Chi-restraints excluded: chain B residue  668 CYS
Chi-restraints excluded: chain B residue  686 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 42 optimal weight:    0.3980
   chunk 36 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 72 optimal weight:    0.1980
   chunk 68 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 4 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
A 470 HIS
A 605 ASN
A 712 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.124416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.097275 restraints weight = 8631.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 2.00
r_work: 0.3123 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.3410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7186  Z= 0.135
  Angle     :  0.575  13.106   9776  Z= 0.274
  Chirality :  0.042   0.142   1014
  Planarity :  0.004   0.043   1240
  Dihedral  : 10.796  98.158    962
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 12.77 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.29), residues: 834
  helix:  1.32 (0.29), residues: 314
  sheet:  0.35 (0.55), residues: 96
  loop :  0.54 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 587 
 HIS   0.009   0.001   HIS B 714 
 PHE   0.045   0.002   PHE B 355 
 TYR   0.010   0.001   TYR B 366 
 ARG   0.007   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04176 (  296)
  hydrogen bonds       : angle       4.42247 (  732)
  metal coordination   : bond        0.00350 (    4)
  metal coordination   : angle       3.53682 (    6)
  covalent geometry    : bond        0.00343 ( 7180)
  covalent geometry    : angle       0.56835 ( 9770)
  Misc. bond           : bond        0.01069 (    2)

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

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

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 1.030 
Fit side-chains
REVERT: A  300 PHE cc_start: 0.7133 (m-80) cc_final: 0.6798 (p90)
REVERT: A  371 ARG cc_start: 0.7704 (mmt-90) cc_final: 0.7178 (tpp80)
REVERT: A  573 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7746 (tt0)
REVERT: A  656 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7607 (mp0)
REVERT: B  299 ARG cc_start: 0.5472 (mmp80) cc_final: 0.5058 (mmp-170)
REVERT: B  438 MET cc_start: 0.8733 (mtp) cc_final: 0.8354 (mtp)
REVERT: B  491 SER cc_start: 0.8296 (OUTLIER) cc_final: 0.7946 (m)
REVERT: B  573 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7174 (tm-30)
REVERT: B  614 MET cc_start: 0.8361 (mtp) cc_final: 0.8108 (mtp)
  outliers start: 14
  outliers final: 12
  residues processed: 86
  average time/residue: 1.8192
  time to fit residues: 164.4251
Evaluate side-chains
  92 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  368 SER
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  507 GLN
Chi-restraints excluded: chain A residue  552 ASP
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  612 LYS
Chi-restraints excluded: chain A residue  615 ASP
Chi-restraints excluded: chain B residue  368 SER
Chi-restraints excluded: chain B residue  371 ARG
Chi-restraints excluded: chain B residue  491 SER
Chi-restraints excluded: chain B residue  573 GLU
Chi-restraints excluded: chain B residue  602 SER
Chi-restraints excluded: chain B residue  622 SER
Chi-restraints excluded: chain B residue  668 CYS
Chi-restraints excluded: chain B residue  686 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 53 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0000
   chunk 18 optimal weight:    0.3980
   chunk 25 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 470 HIS
A 605 ASN
A 712 ASN
B 642 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.125235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.098110 restraints weight = 8594.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 2.00
r_work: 0.3107 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.3437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7186  Z= 0.123
  Angle     :  0.557  12.236   9776  Z= 0.266
  Chirality :  0.042   0.146   1014
  Planarity :  0.004   0.043   1240
  Dihedral  : 10.608  96.017    962
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 12.63 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.29), residues: 834
  helix:  1.38 (0.29), residues: 314
  sheet:  0.38 (0.55), residues: 96
  loop :  0.57 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 587 
 HIS   0.009   0.001   HIS B 714 
 PHE   0.046   0.002   PHE B 355 
 TYR   0.010   0.001   TYR B 366 
 ARG   0.007   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03989 (  296)
  hydrogen bonds       : angle       4.36385 (  732)
  metal coordination   : bond        0.00317 (    4)
  metal coordination   : angle       3.61671 (    6)
  covalent geometry    : bond        0.00314 ( 7180)
  covalent geometry    : angle       0.54941 ( 9770)
  Misc. bond           : bond        0.01080 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5481.42 seconds
wall clock time: 95 minutes 2.35 seconds (5702.35 seconds total)