Starting phenix.real_space_refine
on Tue Mar  3 14:16:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6t6v_10387/03_2026/6t6v_10387.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6t6v_10387/03_2026/6t6v_10387.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6t6v_10387/03_2026/6t6v_10387.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6t6v_10387/03_2026/6t6v_10387.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6t6v_10387/03_2026/6t6v_10387.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6t6v_10387/03_2026/6t6v_10387.map"
  }
  resolution = 4.5
  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=   0.005
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
     Ca      1      9.91       5
     Fe      2      7.16       5
     S      22      5.16       5
     C    3881      2.51       5
     N     977      2.21       5
     O     985      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5868
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5781
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 742, 5777
          Classifications: {'peptide': 742}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 35, 'TRANS': 706}
          Unresolved non-hydrogen bonds: 84
          Unresolved non-hydrogen angles: 103
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 44
      Conformer: "B"
        Number of residues, atoms: 742, 5777
          Classifications: {'peptide': 742}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 35, 'TRANS': 706}
          Unresolved non-hydrogen bonds: 84
          Unresolved non-hydrogen angles: 103
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 44
          bond proxies already assigned to first conformer: 5963
    Chain: "A"
      Number of atoms: 87
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 87
          Unusual residues: {' CA': 1, 'HEM': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AGLY A   2 " occ=0.50
      ... (6 atoms not shown)
      pdb=" O  BGLY A   2 " occ=0.50
  Time building chain proxies: 2.25, per 1000 atoms: 0.38
  Number of scatterers: 5868
  At special positions: 0
  Unit cell: (79.268, 71.967, 105.343, 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)
     Fe      2     26.01
     Ca      1     19.99
     S      22     16.00
     O     985      8.00
     N     977      7.00
     C    3881      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=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 311.8 milliseconds
  

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1340

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 2 sheets defined
      69.4% alpha, 0.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 10
      removed outlier: 3.539A  pdb=" N   PHE A   9 " --> pdb=" O   ARG A   5 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 10 through 30
      removed outlier: 3.799A  pdb=" N   VAL A  14 " --> pdb=" O   THR A  10 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 64
    Processing helix  chain 'A' and resid 65 through 69
      removed outlier: 3.533A  pdb=" N   LEU A  69 " --> pdb=" O   GLY A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 102
      removed outlier: 3.817A  pdb=" N   LEU A  88 " --> pdb=" O   THR A  84 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ASP A 102 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 127
    Processing helix  chain 'A' and resid 142 through 159
      removed outlier: 3.921A  pdb=" N   ALA A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   TYR A 155 " --> pdb=" O   GLN A 151 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   TYR A 156 " --> pdb=" O   THR A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 165
      No H-bonds generated for 'chain 'A' and resid 163 through 165'
    Processing helix  chain 'A' and resid 166 through 171
      removed outlier: 4.007A  pdb=" N   GLU A 171 " --> pdb=" O   HIS A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 199
    Processing helix  chain 'A' and resid 226 through 253
      removed outlier: 3.679A  pdb=" N   VAL A 230 " --> pdb=" O   SER A 226 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   LEU A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 281
    Processing helix  chain 'A' and resid 282 through 309
    Processing helix  chain 'A' and resid 323 through 355
      removed outlier: 3.551A  pdb=" N   PHE A 343 " --> pdb=" O   ILE A 339 " (cutoff:3.500A)
      Proline residue:  A 352  - end of helix
      removed outlier: 3.785A  pdb=" N   ASN A 355 " --> pdb=" O   ALA A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 390
      removed outlier: 3.745A  pdb=" N   GLY A 366 " --> pdb=" O   TYR A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 435
    Processing helix  chain 'A' and resid 436 through 438
      No H-bonds generated for 'chain 'A' and resid 436 through 438'
    Processing helix  chain 'A' and resid 444 through 461
      removed outlier: 4.277A  pdb=" N   LEU A 448 " --> pdb=" O   ASP A 444 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ALA A 449 " --> pdb=" O   LYS A 445 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   LEU A 450 " --> pdb=" O   ASN A 446 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   GLY A 459 " --> pdb=" O   VAL A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 466
    Processing helix  chain 'A' and resid 473 through 485
    Processing helix  chain 'A' and resid 493 through 508
    Processing helix  chain 'A' and resid 514 through 529
      removed outlier: 3.945A  pdb=" N   PHE A 527 " --> pdb=" O   SER A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 538
    Processing helix  chain 'A' and resid 545 through 555
      removed outlier: 3.740A  pdb=" N   SER A 554 " --> pdb=" O   ALA A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 560
      removed outlier: 4.191A  pdb=" N   GLU A 559 " --> pdb=" O   SER A 556 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   VAL A 560 " --> pdb=" O   ALA A 557 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 556 through 560'
    Processing helix  chain 'A' and resid 573 through 577
    Processing helix  chain 'A' and resid 580 through 585
    Processing helix  chain 'A' and resid 586 through 601
      removed outlier: 3.834A  pdb=" N   LEU A 590 " --> pdb=" O   LEU A 586 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ALA A 597 " --> pdb=" O   PHE A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 611
      removed outlier: 3.739A  pdb=" N   ILE A 611 " --> pdb=" O   PHE A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 613 through 619
      removed outlier: 4.280A  pdb=" N   TYR A 619 " --> pdb=" O   VAL A 615 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 637
    Processing helix  chain 'A' and resid 637 through 651
      removed outlier: 4.090A  pdb=" N   LEU A 643 " --> pdb=" O   GLY A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 670
    Processing helix  chain 'A' and resid 670 through 681
    Processing helix  chain 'A' and resid 682 through 697
      removed outlier: 3.509A  pdb=" N   ILE A 686 " --> pdb=" O   SER A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 698 through 703
      removed outlier: 3.843A  pdb=" N   ARG A 703 " --> pdb=" O   MET A 699 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 704 through 709
    Processing helix  chain 'A' and resid 712 through 719
    Processing helix  chain 'A' and resid 720 through 742
      removed outlier: 3.590A  pdb=" N   ASP A 724 " --> pdb=" O   ARG A 720 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   VAL A 726 " --> pdb=" O   PHE A 722 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41
      removed outlier: 5.036A  pdb=" N   PHE A  49 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72
      removed outlier: 4.233A  pdb=" N   ILE A  72 " --> pdb=" O   HIS A  75 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   HIS A  75 " --> pdb=" O   ILE A  72 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2

    334 hydrogen bonds defined for protein.
    972 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: 0.80

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.22 -     1.40: 2618
        1.40 -     1.57: 3403
        1.57 -     1.75: 0
        1.75 -     1.93: 44
        1.93 -     2.10: 6
  Bond restraints: 6071
  Sorted by residual:
  bond pdb=" C3B HEM A 802 "
       pdb=" CAB HEM A 802 "
    ideal  model  delta    sigma   weight residual
    1.544  1.473  0.071 2.00e-02 2.50e+03 1.26e+01
  bond pdb=" C3B HEM A 801 "
       pdb=" CAB HEM A 801 "
    ideal  model  delta    sigma   weight residual
    1.544  1.474  0.070 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" C3C HEM A 801 "
       pdb=" CAC HEM A 801 "
    ideal  model  delta    sigma   weight residual
    1.544  1.474  0.070 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" C3C HEM A 802 "
       pdb=" CAC HEM A 802 "
    ideal  model  delta    sigma   weight residual
    1.544  1.474  0.070 2.00e-02 2.50e+03 1.22e+01
  bond pdb=" CA  LEU A 521 "
       pdb=" C   LEU A 521 "
    ideal  model  delta    sigma   weight residual
    1.523  1.564 -0.041 1.30e-02 5.92e+03 9.88e+00
  ... (remaining 6066 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 7568
        2.10 -     4.19: 583
        4.19 -     6.29: 125
        6.29 -     8.39: 35
        8.39 -    10.48: 15
  Bond angle restraints: 8326
  Sorted by residual:
  angle pdb=" C   VAL A 560 "
        pdb=" N   VAL A 561 "
        pdb=" CA  VAL A 561 "
      ideal   model   delta    sigma   weight residual
     120.24  125.28   -5.04 6.30e-01 2.52e+00 6.41e+01
  angle pdb=" N   GLN A  32 "
        pdb=" CA  GLN A  32 "
        pdb=" C   GLN A  32 "
      ideal   model   delta    sigma   weight residual
     113.17  103.47    9.70 1.26e+00 6.30e-01 5.93e+01
  angle pdb=" C   VAL A 561 "
        pdb=" CA  VAL A 561 "
        pdb=" CB  VAL A 561 "
      ideal   model   delta    sigma   weight residual
     114.35  107.17    7.18 1.06e+00 8.90e-01 4.59e+01
  angle pdb=" N   VAL A 561 "
        pdb=" CA  VAL A 561 "
        pdb=" C   VAL A 561 "
      ideal   model   delta    sigma   weight residual
     112.61  122.40   -9.79 1.45e+00 4.76e-01 4.56e+01
  angle pdb=" N   GLY A 405 "
        pdb=" CA  GLY A 405 "
        pdb=" C   GLY A 405 "
      ideal   model   delta    sigma   weight residual
     115.64  124.51   -8.87 1.46e+00 4.69e-01 3.69e+01
  ... (remaining 8321 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 2986
       17.44 -    34.87: 282
       34.87 -    52.31: 66
       52.31 -    69.74: 14
       69.74 -    87.18: 10
  Dihedral angle restraints: 3358
    sinusoidal: 1248
      harmonic: 2110
  Sorted by residual:
  dihedral pdb=" C2B HEM A 802 "
           pdb=" C3B HEM A 802 "
           pdb=" CAB HEM A 802 "
           pdb=" CBB HEM A 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00   99.38   80.62     2      1.00e+01 1.00e-02 4.67e+01
  dihedral pdb=" C2C HEM A 801 "
           pdb=" C3C HEM A 801 "
           pdb=" CAC HEM A 801 "
           pdb=" CBC HEM A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -61.73   61.73     2      1.00e+01 1.00e-02 3.72e+01
  dihedral pdb=" C2B HEM A 801 "
           pdb=" C3B HEM A 801 "
           pdb=" CAB HEM A 801 "
           pdb=" CBB HEM A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.41   59.59     2      1.00e+01 1.00e-02 3.57e+01
  ... (remaining 3355 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 678
       0.077 -    0.154: 156
       0.154 -    0.231: 35
       0.231 -    0.308: 9
       0.308 -    0.386: 5
  Chirality restraints: 883
  Sorted by residual:
  chirality pdb=" CB  THR A 546 "
            pdb=" CA  THR A 546 "
            pdb=" OG1 THR A 546 "
            pdb=" CG2 THR A 546 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.17    0.39 2.00e-01 2.50e+01 3.72e+00
  chirality pdb=" CA  THR A 578 "
            pdb=" N   THR A 578 "
            pdb=" C   THR A 578 "
            pdb=" CB  THR A 578 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.14    0.39 2.00e-01 2.50e+01 3.71e+00
  chirality pdb=" CB  THR A 646 "
            pdb=" CA  THR A 646 "
            pdb=" OG1 THR A 646 "
            pdb=" CG2 THR A 646 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.21    0.34 2.00e-01 2.50e+01 2.90e+00
  ... (remaining 880 not shown)

  Planarity restraints: 1040
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 187 "   -0.025 2.00e-02 2.50e+03   4.97e-02 2.47e+01
        pdb=" C   ARG A 187 "    0.086 2.00e-02 2.50e+03
        pdb=" O   ARG A 187 "   -0.032 2.00e-02 2.50e+03
        pdb=" N   GLN A 188 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 599 "   -0.024 2.00e-02 2.50e+03   4.73e-02 2.23e+01
        pdb=" C   TRP A 599 "    0.082 2.00e-02 2.50e+03
        pdb=" O   TRP A 599 "   -0.030 2.00e-02 2.50e+03
        pdb=" N   ASN A 600 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 286 "    0.023 2.00e-02 2.50e+03   4.61e-02 2.13e+01
        pdb=" C   LEU A 286 "   -0.080 2.00e-02 2.50e+03
        pdb=" O   LEU A 286 "    0.030 2.00e-02 2.50e+03
        pdb=" N   PHE A 287 "    0.027 2.00e-02 2.50e+03
  ... (remaining 1037 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.54: 63
        2.54 -     3.13: 4456
        3.13 -     3.72: 10124
        3.72 -     4.31: 12944
        4.31 -     4.90: 20611
  Nonbonded interactions: 48198
  Sorted by model distance:
  nonbonded pdb=" O   GLU A  28 "
            pdb=" CG  GLN A  32 "
     model   vdw
     1.944 3.440
  nonbonded pdb=" OE1 GLU A 407 "
            pdb="CA    CA A 803 "
     model   vdw
     2.047 2.510
  nonbonded pdb=" O   GLU A  28 "
            pdb=" CB  GLN A  32 "
     model   vdw
     2.090 3.440
  nonbonded pdb=" NE2 HIS A 331 "
            pdb="FE   HEM A 801 "
     model   vdw
     2.125 3.080
  nonbonded pdb=" OH  TYR A 408 "
            pdb=" O2A HEM A 802 "
     model   vdw
     2.161 3.040
  ... (remaining 48193 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             0.220
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.840
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
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   0.861   6074  Z= 1.177
  Angle     :  1.341  10.484   8326  Z= 0.759
  Chirality :  0.076   0.386    883
  Planarity :  0.009   0.051   1040
  Dihedral  : 15.460  87.178   2018
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 15.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Cbeta Deviations :  0.15 %
  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 are not related in a simple way.
  whole: -4.09 (0.25), residues: 741
  helix: -2.59 (0.17), residues: 488
  sheet:  None (None), residues: 0
  loop : -2.60 (0.37), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A  90 
 TYR   0.026   0.003   TYR A 156 
 PHE   0.029   0.003   PHE A 493 
 TRP   0.030   0.003   TRP A 338 
 HIS   0.020   0.003   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00917 ( 6071)
  covalent geometry    : angle       1.34133 ( 8326)
  hydrogen bonds       : bond        0.16218 (  334)
  hydrogen bonds       : angle       6.96996 (  972)
  Misc. bond           : bond        0.51405 (    3)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 THR cc_start: 0.9256 (m) cc_final: 0.8640 (m)
REVERT: A   62 GLN cc_start: 0.9068 (mt0) cc_final: 0.8609 (mt0)
REVERT: A   87 TRP cc_start: 0.8792 (t-100) cc_final: 0.7958 (t60)
REVERT: A   88 LEU cc_start: 0.9579 (tp) cc_final: 0.9338 (tp)
REVERT: A   93 MET cc_start: 0.8691 (mmt) cc_final: 0.8421 (mmp)
REVERT: A  101 ARG cc_start: 0.9240 (tpp-160) cc_final: 0.8919 (mmm-85)
REVERT: A  119 LEU cc_start: 0.9324 (mm) cc_final: 0.8996 (mp)
REVERT: A  138 LYS cc_start: 0.9439 (mmtt) cc_final: 0.9079 (mmtm)
REVERT: A  153 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6604 (tm-30)
REVERT: A  157 ASP cc_start: 0.8097 (m-30) cc_final: 0.7398 (m-30)
REVERT: A  296 GLN cc_start: 0.9451 (tm-30) cc_final: 0.9164 (tm-30)
REVERT: A  330 TRP cc_start: 0.9039 (m-10) cc_final: 0.8459 (m-10)
REVERT: A  382 PHE cc_start: 0.9401 (m-10) cc_final: 0.9062 (m-80)
REVERT: A  404 GLN cc_start: 0.9337 (tt0) cc_final: 0.8928 (tt0)
REVERT: A  420 PHE cc_start: 0.8903 (t80) cc_final: 0.8581 (t80)
REVERT: A  424 CYS cc_start: 0.9549 (m) cc_final: 0.9315 (m)
REVERT: A  468 TYR cc_start: 0.8718 (p90) cc_final: 0.8436 (p90)
REVERT: A  481 ARG cc_start: 0.9161 (ttt-90) cc_final: 0.8880 (ptm-80)
REVERT: A  493 PHE cc_start: 0.9361 (m-10) cc_final: 0.9143 (m-80)
REVERT: A  515 MET cc_start: 0.7994 (mmm) cc_final: 0.7596 (mmp)
REVERT: A  601 MET cc_start: 0.7937 (ttt) cc_final: 0.7270 (mmm)
REVERT: A  621 GLN cc_start: 0.7655 (tm-30) cc_final: 0.7036 (tm-30)
REVERT: A  638 TYR cc_start: 0.9152 (m-80) cc_final: 0.8886 (m-10)
REVERT: A  665 LYS cc_start: 0.8613 (pttp) cc_final: 0.8016 (pttm)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.0720
  time to fit residues: 19.6064
Evaluate side-chains
  161 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:   30.0000
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
A  89 HIS
A 217 HIS
A 333 GLN
** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.096027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.067364 restraints weight = 49099.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.071902 restraints weight = 20792.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.075077 restraints weight = 12424.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.077340 restraints weight = 8720.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.078643 restraints weight = 6757.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3168
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3168
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.212   6074  Z= 0.189
  Angle     :  0.850  18.818   8326  Z= 0.400
  Chirality :  0.046   0.186    883
  Planarity :  0.005   0.033   1040
  Dihedral  :  7.082  71.434    821
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.20 (0.29), residues: 741
  helix: -0.94 (0.21), residues: 497
  sheet:  None (None), residues: 0
  loop : -2.35 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 703 
 TYR   0.017   0.002   TYR A 408 
 PHE   0.023   0.002   PHE A 727 
 TRP   0.035   0.002   TRP A 480 
 HIS   0.009   0.002   HIS A 631 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 6071)
  covalent geometry    : angle       0.85024 ( 8326)
  hydrogen bonds       : bond        0.04198 (  334)
  hydrogen bonds       : angle       4.67461 (  972)
  Misc. bond           : bond        0.15819 (    3)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 THR cc_start: 0.9340 (m) cc_final: 0.8952 (m)
REVERT: A   62 GLN cc_start: 0.9215 (mt0) cc_final: 0.8676 (mt0)
REVERT: A   87 TRP cc_start: 0.9218 (t-100) cc_final: 0.8323 (t60)
REVERT: A   93 MET cc_start: 0.8820 (mmt) cc_final: 0.8584 (mmp)
REVERT: A   97 ASP cc_start: 0.9399 (t70) cc_final: 0.9191 (t0)
REVERT: A  101 ARG cc_start: 0.9266 (tpp-160) cc_final: 0.8939 (mmm-85)
REVERT: A  153 GLU cc_start: 0.7510 (tm-30) cc_final: 0.6595 (tm-30)
REVERT: A  157 ASP cc_start: 0.7868 (m-30) cc_final: 0.6833 (m-30)
REVERT: A  330 TRP cc_start: 0.9120 (m-10) cc_final: 0.8883 (m-10)
REVERT: A  371 PHE cc_start: 0.9255 (t80) cc_final: 0.8978 (t80)
REVERT: A  408 TYR cc_start: 0.9254 (m-80) cc_final: 0.8413 (m-80)
REVERT: A  424 CYS cc_start: 0.9527 (m) cc_final: 0.9246 (m)
REVERT: A  481 ARG cc_start: 0.9193 (ttt-90) cc_final: 0.8760 (ttt-90)
REVERT: A  515 MET cc_start: 0.8311 (mmm) cc_final: 0.7812 (mmp)
REVERT: A  592 CYS cc_start: 0.9217 (m) cc_final: 0.9005 (m)
REVERT: A  601 MET cc_start: 0.7828 (ttt) cc_final: 0.6994 (mmm)
REVERT: A  708 MET cc_start: 0.8713 (mtm) cc_final: 0.8415 (mtm)
REVERT: A  720 ARG cc_start: 0.8617 (ttt-90) cc_final: 0.8380 (ttt90)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.0570
  time to fit residues: 14.8445
Evaluate side-chains
  168 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 23 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 71 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    2.9186

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

Flipped N/Q/H residues before XYZ refinement:
** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 404 GLN
A 672 ASN
** A 690 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 = 0.3455 r_free = 0.3455 target = 0.095121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.072548 restraints weight = 22192.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.075751 restraints weight = 12870.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.077853 restraints weight = 8801.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.079758 restraints weight = 6798.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.080686 restraints weight = 5486.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3191
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3191
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.448   6074  Z= 0.192
  Angle     :  0.782   9.237   8326  Z= 0.377
  Chirality :  0.045   0.186    883
  Planarity :  0.005   0.037   1040
  Dihedral  :  7.037  70.616    821
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 14.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  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 are not related in a simple way.
  whole: -1.29 (0.30), residues: 741
  helix: -0.27 (0.23), residues: 501
  sheet:  None (None), residues: 0
  loop : -1.96 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 703 
 TYR   0.022   0.002   TYR A 173 
 PHE   0.025   0.002   PHE A 295 
 TRP   0.031   0.002   TRP A 480 
 HIS   0.009   0.002   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 6071)
  covalent geometry    : angle       0.78183 ( 8326)
  hydrogen bonds       : bond        0.03830 (  334)
  hydrogen bonds       : angle       4.52505 (  972)
  Misc. bond           : bond        0.28761 (    3)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.9385 (mt0) cc_final: 0.8710 (mt0)
REVERT: A   87 TRP cc_start: 0.9196 (t-100) cc_final: 0.8277 (t60)
REVERT: A   93 MET cc_start: 0.8778 (mmt) cc_final: 0.8526 (mmp)
REVERT: A   97 ASP cc_start: 0.9339 (t70) cc_final: 0.9139 (t0)
REVERT: A  101 ARG cc_start: 0.9214 (tpp-160) cc_final: 0.8914 (mmm-85)
REVERT: A  157 ASP cc_start: 0.7833 (m-30) cc_final: 0.7126 (m-30)
REVERT: A  371 PHE cc_start: 0.9208 (t80) cc_final: 0.8801 (t80)
REVERT: A  408 TYR cc_start: 0.9115 (m-80) cc_final: 0.8496 (m-80)
REVERT: A  420 PHE cc_start: 0.8925 (t80) cc_final: 0.8697 (t80)
REVERT: A  424 CYS cc_start: 0.9516 (m) cc_final: 0.9218 (m)
REVERT: A  477 MET cc_start: 0.8973 (tpp) cc_final: 0.8559 (tpp)
REVERT: A  478 GLU cc_start: 0.9438 (tp30) cc_final: 0.9216 (tp30)
REVERT: A  481 ARG cc_start: 0.9155 (ttt-90) cc_final: 0.8685 (ptm160)
REVERT: A  515 MET cc_start: 0.8243 (mmm) cc_final: 0.7664 (mmp)
REVERT: A  528 MET cc_start: 0.7913 (ptt) cc_final: 0.7705 (ptt)
REVERT: A  601 MET cc_start: 0.7941 (ttt) cc_final: 0.7110 (tpt)
REVERT: A  621 GLN cc_start: 0.7032 (tm-30) cc_final: 0.6751 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.0571
  time to fit residues: 14.3576
Evaluate side-chains
  160 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 18 optimal weight:    7.9990
   chunk 50 optimal weight:    8.9990
   chunk 58 optimal weight:    0.0670
   chunk 12 optimal weight:    4.9990
   chunk 49 optimal weight:    0.3980
   chunk 38 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 29 optimal weight:   10.0000
   chunk 48 optimal weight:    9.9990
   chunk 73 optimal weight:    5.9990
   overall best weight:    2.0922

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN
** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 404 GLN
** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 690 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 = 0.3461 r_free = 0.3461 target = 0.095574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.071115 restraints weight = 22374.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.074433 restraints weight = 13393.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.076825 restraints weight = 9306.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.078572 restraints weight = 7184.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.079855 restraints weight = 5901.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.3012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.442   6074  Z= 0.159
  Angle     :  0.739   7.758   8326  Z= 0.355
  Chirality :  0.044   0.185    883
  Planarity :  0.004   0.040   1040
  Dihedral  :  6.748  65.204    821
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 13.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  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 are not related in a simple way.
  whole: -0.86 (0.31), residues: 741
  helix:  0.11 (0.23), residues: 506
  sheet:  None (None), residues: 0
  loop : -1.95 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 187 
 TYR   0.016   0.002   TYR A 638 
 PHE   0.012   0.002   PHE A 640 
 TRP   0.031   0.002   TRP A 480 
 HIS   0.011   0.002   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 6071)
  covalent geometry    : angle       0.73906 ( 8326)
  hydrogen bonds       : bond        0.03564 (  334)
  hydrogen bonds       : angle       4.34860 (  972)
  Misc. bond           : bond        0.27819 (    3)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.9331 (mt0) cc_final: 0.8611 (mt0)
REVERT: A   87 TRP cc_start: 0.9172 (t-100) cc_final: 0.8155 (t60)
REVERT: A   93 MET cc_start: 0.8788 (mmt) cc_final: 0.8541 (mmp)
REVERT: A   97 ASP cc_start: 0.9378 (t70) cc_final: 0.9148 (t0)
REVERT: A  101 ARG cc_start: 0.9283 (tpp-160) cc_final: 0.8988 (mmm-85)
REVERT: A  157 ASP cc_start: 0.8037 (m-30) cc_final: 0.7676 (m-30)
REVERT: A  190 THR cc_start: 0.9353 (t) cc_final: 0.8972 (t)
REVERT: A  285 TYR cc_start: 0.8333 (m-80) cc_final: 0.8035 (m-80)
REVERT: A  371 PHE cc_start: 0.9320 (t80) cc_final: 0.9075 (t80)
REVERT: A  408 TYR cc_start: 0.8978 (m-80) cc_final: 0.8578 (m-80)
REVERT: A  420 PHE cc_start: 0.8938 (t80) cc_final: 0.8719 (t80)
REVERT: A  424 CYS cc_start: 0.9493 (m) cc_final: 0.9218 (m)
REVERT: A  477 MET cc_start: 0.8868 (tpp) cc_final: 0.8467 (tpp)
REVERT: A  478 GLU cc_start: 0.9393 (tp30) cc_final: 0.9096 (tp30)
REVERT: A  481 ARG cc_start: 0.9029 (ttt-90) cc_final: 0.8590 (ptm160)
REVERT: A  592 CYS cc_start: 0.9121 (m) cc_final: 0.8918 (m)
REVERT: A  601 MET cc_start: 0.7907 (ttt) cc_final: 0.7099 (tpt)
REVERT: A  659 LEU cc_start: 0.8443 (pp) cc_final: 0.8099 (pp)
REVERT: A  737 GLN cc_start: 0.9247 (tm-30) cc_final: 0.8796 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.0672
  time to fit residues: 17.0209
Evaluate side-chains
  163 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 10 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 42 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 690 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 = 0.3474 r_free = 0.3474 target = 0.096215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.068350 restraints weight = 46245.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.073029 restraints weight = 20146.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.076350 restraints weight = 12076.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.078567 restraints weight = 8464.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.080255 restraints weight = 6603.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.3307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.348   6074  Z= 0.140
  Angle     :  0.716   7.005   8326  Z= 0.345
  Chirality :  0.043   0.185    883
  Planarity :  0.004   0.048   1040
  Dihedral  :  6.762  72.671    821
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  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 are not related in a simple way.
  whole: -0.68 (0.31), residues: 741
  helix:  0.34 (0.23), residues: 497
  sheet:  None (None), residues: 0
  loop : -2.05 (0.40), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 413 
 TYR   0.017   0.002   TYR A 173 
 PHE   0.016   0.001   PHE A 466 
 TRP   0.036   0.002   TRP A 480 
 HIS   0.006   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 6071)
  covalent geometry    : angle       0.71585 ( 8326)
  hydrogen bonds       : bond        0.03543 (  334)
  hydrogen bonds       : angle       4.33888 (  972)
  Misc. bond           : bond        0.21662 (    3)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.9338 (mt0) cc_final: 0.8855 (mt0)
REVERT: A   87 TRP cc_start: 0.9191 (t-100) cc_final: 0.8352 (t60)
REVERT: A   93 MET cc_start: 0.8789 (mmt) cc_final: 0.8550 (mmp)
REVERT: A   97 ASP cc_start: 0.9355 (t70) cc_final: 0.9118 (t0)
REVERT: A  101 ARG cc_start: 0.9259 (tpp-160) cc_final: 0.8969 (mmm-85)
REVERT: A  157 ASP cc_start: 0.8063 (m-30) cc_final: 0.7708 (m-30)
REVERT: A  190 THR cc_start: 0.9326 (t) cc_final: 0.8984 (t)
REVERT: A  371 PHE cc_start: 0.9316 (t80) cc_final: 0.9080 (t80)
REVERT: A  404 GLN cc_start: 0.8956 (tt0) cc_final: 0.8657 (tt0)
REVERT: A  408 TYR cc_start: 0.8970 (m-80) cc_final: 0.8562 (m-80)
REVERT: A  416 GLN cc_start: 0.9379 (mt0) cc_final: 0.8706 (mt0)
REVERT: A  424 CYS cc_start: 0.9478 (m) cc_final: 0.9275 (m)
REVERT: A  478 GLU cc_start: 0.9388 (tp30) cc_final: 0.9148 (tp30)
REVERT: A  481 ARG cc_start: 0.9013 (ttt-90) cc_final: 0.8536 (ptm160)
REVERT: A  515 MET cc_start: 0.8535 (mmt) cc_final: 0.7867 (mmp)
REVERT: A  592 CYS cc_start: 0.9172 (m) cc_final: 0.8900 (m)
REVERT: A  601 MET cc_start: 0.8111 (ttt) cc_final: 0.7215 (tpt)
REVERT: A  612 ASN cc_start: 0.9393 (t0) cc_final: 0.9117 (m-40)
REVERT: A  683 LEU cc_start: 0.9461 (mm) cc_final: 0.9252 (mm)
REVERT: A  737 GLN cc_start: 0.9292 (tm-30) cc_final: 0.8892 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.0592
  time to fit residues: 15.0666
Evaluate side-chains
  156 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 43 optimal weight:    9.9990
   chunk 61 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 16 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0770
   chunk 48 optimal weight:    9.9990
   overall best weight:    1.1544

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

Flipped N/Q/H residues before XYZ refinement:
** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 612 ASN
** A 690 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 = 0.3504 r_free = 0.3504 target = 0.097721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.070597 restraints weight = 36570.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.075062 restraints weight = 17736.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.078198 restraints weight = 11136.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.080292 restraints weight = 8008.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.081864 restraints weight = 6330.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3231
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3231
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.3596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.291   6074  Z= 0.136
  Angle     :  0.729   9.207   8326  Z= 0.347
  Chirality :  0.044   0.262    883
  Planarity :  0.004   0.035   1040
  Dihedral  :  6.713  73.422    821
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.25 %
    Favored  : 98.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.31), residues: 741
  helix:  0.36 (0.23), residues: 498
  sheet:  None (None), residues: 0
  loop : -1.99 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 720 
 TYR   0.021   0.002   TYR A 306 
 PHE   0.024   0.001   PHE A 496 
 TRP   0.033   0.002   TRP A 480 
 HIS   0.005   0.001   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6071)
  covalent geometry    : angle       0.72939 ( 8326)
  hydrogen bonds       : bond        0.03546 (  334)
  hydrogen bonds       : angle       4.36181 (  972)
  Misc. bond           : bond        0.18162 (    3)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 177
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.9042 (mt0) cc_final: 0.8526 (mt0)
REVERT: A   87 TRP cc_start: 0.9174 (t-100) cc_final: 0.8414 (t-100)
REVERT: A   93 MET cc_start: 0.8773 (mmt) cc_final: 0.8547 (mmp)
REVERT: A   97 ASP cc_start: 0.9335 (t70) cc_final: 0.9100 (t0)
REVERT: A  101 ARG cc_start: 0.9271 (tpp-160) cc_final: 0.8985 (mmm-85)
REVERT: A  190 THR cc_start: 0.9309 (t) cc_final: 0.9045 (t)
REVERT: A  408 TYR cc_start: 0.8948 (m-80) cc_final: 0.8476 (m-80)
REVERT: A  416 GLN cc_start: 0.9443 (mt0) cc_final: 0.8737 (mt0)
REVERT: A  481 ARG cc_start: 0.9026 (ttt-90) cc_final: 0.8746 (ttt-90)
REVERT: A  592 CYS cc_start: 0.8985 (m) cc_final: 0.8735 (m)
REVERT: A  601 MET cc_start: 0.7995 (ttt) cc_final: 0.7147 (tpt)
  outliers start: 1
  outliers final: 1
  residues processed: 177
  average time/residue: 0.0524
  time to fit residues: 13.4430
Evaluate side-chains
  162 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 6 optimal weight:    0.4980
   chunk 70 optimal weight:    0.6980
   chunk 35 optimal weight:    0.1980
   chunk 19 optimal weight:   10.0000
   chunk 27 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    9.9990
   chunk 52 optimal weight:    6.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 690 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 = 0.3531 r_free = 0.3531 target = 0.099827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.075548 restraints weight = 21007.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.079041 restraints weight = 12447.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.081496 restraints weight = 8661.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.083249 restraints weight = 6663.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.084385 restraints weight = 5477.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3264
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.3831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.217   6074  Z= 0.128
  Angle     :  0.712   7.737   8326  Z= 0.339
  Chirality :  0.043   0.188    883
  Planarity :  0.004   0.035   1040
  Dihedral  :  6.632  74.581    821
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  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 are not related in a simple way.
  whole: -0.67 (0.31), residues: 741
  helix:  0.31 (0.23), residues: 497
  sheet:  None (None), residues: 0
  loop : -1.94 (0.41), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 720 
 TYR   0.025   0.002   TYR A 479 
 PHE   0.019   0.001   PHE A 496 
 TRP   0.025   0.002   TRP A 480 
 HIS   0.005   0.001   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6071)
  covalent geometry    : angle       0.71190 ( 8326)
  hydrogen bonds       : bond        0.03384 (  334)
  hydrogen bonds       : angle       4.29814 (  972)
  Misc. bond           : bond        0.12984 (    3)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.9258 (mt0) cc_final: 0.8562 (mt0)
REVERT: A   87 TRP cc_start: 0.9122 (t-100) cc_final: 0.8322 (t-100)
REVERT: A   93 MET cc_start: 0.8723 (mmt) cc_final: 0.8521 (mmp)
REVERT: A   97 ASP cc_start: 0.9320 (t70) cc_final: 0.9092 (t0)
REVERT: A  101 ARG cc_start: 0.9263 (tpp-160) cc_final: 0.8947 (mmm-85)
REVERT: A  155 TYR cc_start: 0.9295 (t80) cc_final: 0.9052 (t80)
REVERT: A  190 THR cc_start: 0.9306 (t) cc_final: 0.9055 (t)
REVERT: A  362 TYR cc_start: 0.6999 (m-10) cc_final: 0.6790 (m-10)
REVERT: A  371 PHE cc_start: 0.9204 (t80) cc_final: 0.8724 (t80)
REVERT: A  404 GLN cc_start: 0.8961 (tt0) cc_final: 0.8656 (tt0)
REVERT: A  408 TYR cc_start: 0.8931 (m-80) cc_final: 0.8479 (m-80)
REVERT: A  416 GLN cc_start: 0.9456 (mt0) cc_final: 0.8739 (mt0)
REVERT: A  426 TRP cc_start: 0.9318 (t60) cc_final: 0.8879 (t60)
REVERT: A  478 GLU cc_start: 0.9380 (tp30) cc_final: 0.8909 (tp30)
REVERT: A  481 ARG cc_start: 0.8991 (ttt-90) cc_final: 0.8550 (ptm160)
REVERT: A  515 MET cc_start: 0.8209 (mmt) cc_final: 0.7670 (mmp)
REVERT: A  563 LEU cc_start: 0.7148 (mt) cc_final: 0.6748 (mt)
REVERT: A  592 CYS cc_start: 0.8996 (m) cc_final: 0.8751 (m)
REVERT: A  601 MET cc_start: 0.7968 (ttt) cc_final: 0.7088 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.0553
  time to fit residues: 14.2739
Evaluate side-chains
  164 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 72 optimal weight:    8.9990
   chunk 46 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 45 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 52 optimal weight:    8.9990
   chunk 44 optimal weight:   10.0000
   chunk 40 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    2.6986

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

Flipped N/Q/H residues before XYZ refinement:
** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 690 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 = 0.3484 r_free = 0.3484 target = 0.097145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.069938 restraints weight = 37422.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.074229 restraints weight = 18276.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.077248 restraints weight = 11486.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.079326 restraints weight = 8293.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.080782 restraints weight = 6569.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3204
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3204
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.3912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.446   6074  Z= 0.173
  Angle     :  0.750   7.848   8326  Z= 0.356
  Chirality :  0.044   0.179    883
  Planarity :  0.005   0.040   1040
  Dihedral  :  6.781  76.937    821
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  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 are not related in a simple way.
  whole: -0.49 (0.32), residues: 741
  helix:  0.49 (0.24), residues: 496
  sheet:  None (None), residues: 0
  loop : -1.99 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 720 
 TYR   0.028   0.002   TYR A 479 
 PHE   0.023   0.002   PHE A 496 
 TRP   0.017   0.002   TRP A 195 
 HIS   0.004   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 6071)
  covalent geometry    : angle       0.75034 ( 8326)
  hydrogen bonds       : bond        0.03420 (  334)
  hydrogen bonds       : angle       4.32723 (  972)
  Misc. bond           : bond        0.28512 (    3)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.9328 (mt0) cc_final: 0.8771 (mt0)
REVERT: A   87 TRP cc_start: 0.9213 (t-100) cc_final: 0.8452 (t-100)
REVERT: A   93 MET cc_start: 0.8838 (mmt) cc_final: 0.8633 (mmp)
REVERT: A   97 ASP cc_start: 0.9325 (t70) cc_final: 0.9102 (t0)
REVERT: A  101 ARG cc_start: 0.9304 (tpp-160) cc_final: 0.9002 (mmm-85)
REVERT: A  173 TYR cc_start: 0.8706 (m-10) cc_final: 0.8288 (m-10)
REVERT: A  190 THR cc_start: 0.9387 (t) cc_final: 0.9136 (t)
REVERT: A  404 GLN cc_start: 0.9091 (tt0) cc_final: 0.8767 (tt0)
REVERT: A  408 TYR cc_start: 0.8809 (m-80) cc_final: 0.8415 (m-80)
REVERT: A  416 GLN cc_start: 0.9488 (mt0) cc_final: 0.8850 (mt0)
REVERT: A  481 ARG cc_start: 0.9026 (ttt-90) cc_final: 0.8758 (ptm-80)
REVERT: A  515 MET cc_start: 0.8221 (mmt) cc_final: 0.7631 (mmp)
REVERT: A  592 CYS cc_start: 0.9082 (m) cc_final: 0.8826 (m)
REVERT: A  601 MET cc_start: 0.8040 (ttt) cc_final: 0.7203 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.0597
  time to fit residues: 14.7634
Evaluate side-chains
  152 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 70 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 1 optimal weight:    0.9980
   chunk 72 optimal weight:   20.0000
   chunk 34 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 311 GLN
** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 690 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 = 0.3529 r_free = 0.3529 target = 0.099294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.072190 restraints weight = 38553.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.076831 restraints weight = 18081.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.080069 restraints weight = 11053.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.082238 restraints weight = 7843.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.083957 restraints weight = 6103.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3269
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3269
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.4140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.267   6074  Z= 0.131
  Angle     :  0.734   8.978   8326  Z= 0.346
  Chirality :  0.043   0.189    883
  Planarity :  0.004   0.035   1040
  Dihedral  :  6.540  75.440    821
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  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 are not related in a simple way.
  whole: -0.48 (0.31), residues: 741
  helix:  0.46 (0.24), residues: 494
  sheet:  None (None), residues: 0
  loop : -1.85 (0.40), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 720 
 TYR   0.029   0.002   TYR A 479 
 PHE   0.020   0.001   PHE A 496 
 TRP   0.017   0.002   TRP A 599 
 HIS   0.010   0.001   HIS A 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6071)
  covalent geometry    : angle       0.73383 ( 8326)
  hydrogen bonds       : bond        0.03394 (  334)
  hydrogen bonds       : angle       4.28692 (  972)
  Misc. bond           : bond        0.16445 (    3)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.9012 (mt0) cc_final: 0.8631 (mt0)
REVERT: A   87 TRP cc_start: 0.9149 (t-100) cc_final: 0.8389 (t-100)
REVERT: A   97 ASP cc_start: 0.9318 (t70) cc_final: 0.9082 (t0)
REVERT: A  101 ARG cc_start: 0.9266 (tpp-160) cc_final: 0.8967 (mmm-85)
REVERT: A  190 THR cc_start: 0.9355 (t) cc_final: 0.9148 (t)
REVERT: A  408 TYR cc_start: 0.8835 (m-80) cc_final: 0.8435 (m-80)
REVERT: A  416 GLN cc_start: 0.9461 (mt0) cc_final: 0.8913 (mt0)
REVERT: A  478 GLU cc_start: 0.9422 (tp30) cc_final: 0.9201 (tp30)
REVERT: A  481 ARG cc_start: 0.9056 (ttt-90) cc_final: 0.8596 (ptm160)
REVERT: A  515 MET cc_start: 0.8170 (mmt) cc_final: 0.7618 (mmp)
REVERT: A  563 LEU cc_start: 0.7089 (mt) cc_final: 0.6807 (mt)
REVERT: A  585 ASN cc_start: 0.9373 (m-40) cc_final: 0.9151 (m-40)
REVERT: A  592 CYS cc_start: 0.9020 (m) cc_final: 0.8782 (m)
REVERT: A  601 MET cc_start: 0.8107 (ttt) cc_final: 0.7257 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.0499
  time to fit residues: 12.6882
Evaluate side-chains
  157 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 71 optimal weight:    0.0060
   chunk 6 optimal weight:    0.5980
   chunk 44 optimal weight:    9.9990
   chunk 3 optimal weight:    0.0050
   chunk 22 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 36 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.4810

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 404 GLN
** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 690 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 = 0.3543 r_free = 0.3543 target = 0.100330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.072531 restraints weight = 43540.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.077358 restraints weight = 19433.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.080774 restraints weight = 11737.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.082979 restraints weight = 8212.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.084815 restraints weight = 6357.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3275
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3275 r_free = 0.3275    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3275 r_free = 0.3275    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3275
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.4317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.164   6074  Z= 0.128
  Angle     :  0.746   8.480   8326  Z= 0.351
  Chirality :  0.044   0.177    883
  Planarity :  0.004   0.034   1040
  Dihedral  :  6.485  76.185    821
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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 are not related in a simple way.
  whole: -0.33 (0.32), residues: 741
  helix:  0.50 (0.24), residues: 495
  sheet:  None (None), residues: 0
  loop : -1.64 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 720 
 TYR   0.026   0.002   TYR A 479 
 PHE   0.021   0.001   PHE A 496 
 TRP   0.016   0.001   TRP A 195 
 HIS   0.005   0.001   HIS A 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6071)
  covalent geometry    : angle       0.74620 ( 8326)
  hydrogen bonds       : bond        0.03343 (  334)
  hydrogen bonds       : angle       4.29833 (  972)
  Misc. bond           : bond        0.09942 (    3)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.9267 (mt0) cc_final: 0.8735 (mt0)
REVERT: A   87 TRP cc_start: 0.9092 (t-100) cc_final: 0.8340 (t-100)
REVERT: A   97 ASP cc_start: 0.9295 (t70) cc_final: 0.9040 (t0)
REVERT: A  101 ARG cc_start: 0.9253 (tpp-160) cc_final: 0.8952 (mmm-85)
REVERT: A  155 TYR cc_start: 0.9304 (t80) cc_final: 0.9092 (t80)
REVERT: A  408 TYR cc_start: 0.8904 (m-80) cc_final: 0.8463 (m-80)
REVERT: A  426 TRP cc_start: 0.9238 (t60) cc_final: 0.8762 (t60)
REVERT: A  458 ILE cc_start: 0.8852 (mm) cc_final: 0.8616 (tp)
REVERT: A  481 ARG cc_start: 0.9018 (ttt-90) cc_final: 0.8525 (ptm160)
REVERT: A  515 MET cc_start: 0.8123 (mmt) cc_final: 0.7574 (mmp)
REVERT: A  563 LEU cc_start: 0.7099 (mt) cc_final: 0.6794 (mt)
REVERT: A  592 CYS cc_start: 0.9027 (m) cc_final: 0.8770 (m)
REVERT: A  601 MET cc_start: 0.8066 (ttt) cc_final: 0.7131 (tpt)
REVERT: A  666 LEU cc_start: 0.8856 (mm) cc_final: 0.8581 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.0602
  time to fit residues: 15.4998
Evaluate side-chains
  160 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 404 GLN
A 600 ASN
** A 690 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 = 0.3518 r_free = 0.3518 target = 0.098604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.075005 restraints weight = 25309.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.078803 restraints weight = 13918.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.081511 restraints weight = 9245.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.083131 restraints weight = 6821.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.084768 restraints weight = 5532.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3280
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3280 r_free = 0.3280    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3280 r_free = 0.3280    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3280
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.4459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.259   6074  Z= 0.140
  Angle     :  0.741   7.298   8326  Z= 0.354
  Chirality :  0.043   0.173    883
  Planarity :  0.005   0.036   1040
  Dihedral  :  6.503  77.147    821
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  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 are not related in a simple way.
  whole: -0.29 (0.32), residues: 741
  helix:  0.57 (0.24), residues: 489
  sheet:  None (None), residues: 0
  loop : -1.65 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 413 
 TYR   0.028   0.002   TYR A 479 
 PHE   0.034   0.002   PHE A 593 
 TRP   0.017   0.002   TRP A 195 
 HIS   0.006   0.001   HIS A 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6071)
  covalent geometry    : angle       0.74114 ( 8326)
  hydrogen bonds       : bond        0.03262 (  334)
  hydrogen bonds       : angle       4.27767 (  972)
  Misc. bond           : bond        0.16325 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1114.83 seconds
wall clock time: 19 minutes 53.43 seconds (1193.43 seconds total)