Starting phenix.real_space_refine
on Mon Nov 17 15:42:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6t6v_10387/11_2025/6t6v_10387.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6t6v_10387/11_2025/6t6v_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6t6v_10387/11_2025/6t6v_10387.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6t6v_10387/11_2025/6t6v_10387.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6t6v_10387/11_2025/6t6v_10387.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6t6v_10387/11_2025/6t6v_10387.cif"
  }
  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-2.0-5881/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: 2.65, per 1000 atoms: 0.45
  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: 0.58
  Conformation dependent library (CDL) restraints added in 560.4 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: 0.23
  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: 0.95

  Time building geometry restraints manager: 0.76 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:             0.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.080
  Find NCS groups from input model:        0.040
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.670
-------------------------------------------------------------------------------
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  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 THR cc_start: 0.9255 (m) cc_final: 0.8639 (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: 0.8690 (mmt) cc_final: 0.8420 (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: 0.9440 (mmtt) cc_final: 0.9079 (mmtm)
REVERT: A  153 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6603 (tm-30)
REVERT: A  157 ASP cc_start: 0.8098 (m-30) cc_final: 0.7398 (m-30)
REVERT: A  296 GLN cc_start: 0.9452 (tm-30) cc_final: 0.9164 (tm-30)
REVERT: A  330 TRP cc_start: 0.9039 (m-10) cc_final: 0.8458 (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: 0.8719 (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: 0.7654 (tm-30) cc_final: 0.7035 (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: 0.0718
  time to fit residues: 19.5535
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  : 0.222 
-------------------------------------------------------------------------------
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  : 0.258 
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: 0.9214 (mt0) cc_final: 0.8676 (mt0)
REVERT: A   87 TRP cc_start: 0.9217 (t-100) cc_final: 0.8323 (t60)
REVERT: A   93 MET cc_start: 0.8821 (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: 0.7869 (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: 0.8977 (t80)
REVERT: A  408 TYR cc_start: 0.9254 (m-80) cc_final: 0.8412 (m-80)
REVERT: A  424 CYS cc_start: 0.9527 (m) cc_final: 0.9246 (m)
REVERT: A  481 ARG cc_start: 0.9194 (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: 0.0611
  time to fit residues: 15.9436
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  : 0.217 
-------------------------------------------------------------------------------
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  : 0.217 
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: 0.9195 (t-100) cc_final: 0.8276 (t60)
REVERT: A   93 MET cc_start: 0.8777 (mmt) cc_final: 0.8527 (mmp)
REVERT: A  101 ARG cc_start: 0.9214 (tpp-160) cc_final: 0.8915 (mmm-85)
REVERT: A  157 ASP cc_start: 0.7833 (m-30) cc_final: 0.7127 (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: 0.8696 (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: 0.7706 (ptt)
REVERT: A  601 MET cc_start: 0.7940 (ttt) cc_final: 0.7110 (tpt)
REVERT: A  621 GLN cc_start: 0.7030 (tm-30) cc_final: 0.6749 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.0628
  time to fit residues: 15.7333
Evaluate side-chains
  159 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
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 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 = 0.3462 r_free = 0.3462 target = 0.095503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.071271 restraints weight = 22363.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.074437 restraints weight = 13199.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.076815 restraints weight = 9244.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.078326 restraints weight = 7140.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.079567 restraints weight = 5970.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3188
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3188 r_free = 0.3188    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 = 0.3188 r_free = 0.3188    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3188
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.443   6074  Z= 0.160
  Angle     :  0.744   7.759   8326  Z= 0.358
  Chirality :  0.044   0.185    883
  Planarity :  0.004   0.040   1040
  Dihedral  :  6.740  65.146    821
  Min Nonbonded Distance : 2.373

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: -0.88 (0.31), residues: 741
  helix:  0.09 (0.23), residues: 506
  sheet:  None (None), residues: 0
  loop : -1.96 (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   0.013   0.001   PHE A 640 
 TRP   0.029   0.002   TRP A 480 
 HIS   0.012   0.002   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 6071)
  covalent geometry    : angle       0.74384 ( 8326)
  hydrogen bonds       : bond        0.03581 (  334)
  hydrogen bonds       : angle       4.35500 (  972)
  Misc. bond           : bond        0.27883 (    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
  182 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.9339 (mt0) cc_final: 0.8615 (mt0)
REVERT: A   87 TRP cc_start: 0.9178 (t-100) cc_final: 0.8159 (t60)
REVERT: A   93 MET cc_start: 0.8800 (mmt) cc_final: 0.8555 (mmp)
REVERT: A   97 ASP cc_start: 0.9342 (t0) cc_final: 0.9039 (t0)
REVERT: A  101 ARG cc_start: 0.9286 (tpp-160) cc_final: 0.8995 (mmm-85)
REVERT: A  157 ASP cc_start: 0.8055 (m-30) cc_final: 0.7692 (m-30)
REVERT: A  190 THR cc_start: 0.9375 (t) cc_final: 0.9013 (t)
REVERT: A  285 TYR cc_start: 0.8343 (m-80) cc_final: 0.8043 (m-80)
REVERT: A  371 PHE cc_start: 0.9312 (t80) cc_final: 0.9064 (t80)
REVERT: A  408 TYR cc_start: 0.8986 (m-80) cc_final: 0.8582 (m-80)
REVERT: A  420 PHE cc_start: 0.8957 (t80) cc_final: 0.8738 (t80)
REVERT: A  424 CYS cc_start: 0.9500 (m) cc_final: 0.9226 (m)
REVERT: A  477 MET cc_start: 0.8863 (tpp) cc_final: 0.8459 (tpp)
REVERT: A  478 GLU cc_start: 0.9403 (tp30) cc_final: 0.9104 (tp30)
REVERT: A  481 ARG cc_start: 0.9031 (ttt-90) cc_final: 0.8589 (ptm160)
REVERT: A  592 CYS cc_start: 0.9128 (m) cc_final: 0.8922 (m)
REVERT: A  601 MET cc_start: 0.7912 (ttt) cc_final: 0.7096 (tpt)
REVERT: A  659 LEU cc_start: 0.8451 (pp) cc_final: 0.8100 (pp)
REVERT: A  737 GLN cc_start: 0.9257 (tm-30) cc_final: 0.8813 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.0651
  time to fit residues: 16.6273
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  : 0.225 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 55 optimal weight:    0.7980
   chunk 17 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 10 optimal weight:    8.9990
   chunk 61 optimal weight:    5.9990
   chunk 6 optimal weight:    0.5980
   chunk 42 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    2.8786

-------------------------------------------------------------------------------
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 = 0.3437 r_free = 0.3437 target = 0.094252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.066090 restraints weight = 47559.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.070538 restraints weight = 21017.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.073679 restraints weight = 12804.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.075965 restraints weight = 9108.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.077545 restraints weight = 7092.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3143
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3143 r_free = 0.3143    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3143 r_free = 0.3143    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3143
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.3257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.530   6074  Z= 0.190
  Angle     :  0.758   8.455   8326  Z= 0.364
  Chirality :  0.045   0.189    883
  Planarity :  0.005   0.056   1040
  Dihedral  :  6.894  73.177    821
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 15.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  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: -0.70 (0.31), residues: 741
  helix:  0.28 (0.23), residues: 503
  sheet:  None (None), residues: 0
  loop : -2.02 (0.41), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  51 
 TYR   0.018   0.002   TYR A 173 
 PHE   0.017   0.002   PHE A 466 
 TRP   0.035   0.002   TRP A 480 
 HIS   0.006   0.002   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 6071)
  covalent geometry    : angle       0.75771 ( 8326)
  hydrogen bonds       : bond        0.03613 (  334)
  hydrogen bonds       : angle       4.39717 (  972)
  Misc. bond           : bond        0.33484 (    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
  171 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.9360 (mt0) cc_final: 0.8676 (mt0)
REVERT: A   87 TRP cc_start: 0.9215 (t-100) cc_final: 0.8232 (t60)
REVERT: A   93 MET cc_start: 0.8834 (mmt) cc_final: 0.8579 (mmp)
REVERT: A   97 ASP cc_start: 0.9324 (t0) cc_final: 0.9013 (t0)
REVERT: A  101 ARG cc_start: 0.9288 (tpp-160) cc_final: 0.9003 (mmm-85)
REVERT: A  157 ASP cc_start: 0.8099 (m-30) cc_final: 0.7740 (m-30)
REVERT: A  190 THR cc_start: 0.9343 (t) cc_final: 0.8955 (t)
REVERT: A  285 TYR cc_start: 0.8253 (m-80) cc_final: 0.8038 (m-80)
REVERT: A  370 LEU cc_start: 0.9415 (tt) cc_final: 0.9212 (tt)
REVERT: A  404 GLN cc_start: 0.9033 (tt0) cc_final: 0.8786 (tt0)
REVERT: A  408 TYR cc_start: 0.8940 (m-80) cc_final: 0.8517 (m-80)
REVERT: A  416 GLN cc_start: 0.9396 (mt0) cc_final: 0.8734 (mt0)
REVERT: A  424 CYS cc_start: 0.9484 (m) cc_final: 0.9275 (m)
REVERT: A  477 MET cc_start: 0.8890 (tpp) cc_final: 0.8431 (tpp)
REVERT: A  478 GLU cc_start: 0.9412 (tp30) cc_final: 0.9198 (tp30)
REVERT: A  481 ARG cc_start: 0.9034 (ttt-90) cc_final: 0.8593 (ptm160)
REVERT: A  515 MET cc_start: 0.8572 (mmt) cc_final: 0.7888 (mmp)
REVERT: A  592 CYS cc_start: 0.9193 (m) cc_final: 0.8941 (m)
REVERT: A  601 MET cc_start: 0.7939 (ttt) cc_final: 0.7157 (tpt)
REVERT: A  612 ASN cc_start: 0.9479 (t0) cc_final: 0.9184 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.0612
  time to fit residues: 14.8039
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  : 0.170 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 66 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0050
   chunk 48 optimal weight:    6.9990
   overall best weight:    1.3998

-------------------------------------------------------------------------------
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 = 0.3476 r_free = 0.3476 target = 0.096790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.069275 restraints weight = 36835.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.073644 restraints weight = 18173.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.076674 restraints weight = 11432.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.078773 restraints weight = 8311.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.080327 restraints weight = 6592.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3189
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    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 = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3189
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.3486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.375   6074  Z= 0.142
  Angle     :  0.720   6.989   8326  Z= 0.344
  Chirality :  0.043   0.184    883
  Planarity :  0.004   0.040   1040
  Dihedral  :  6.763  71.740    821
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  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: -0.54 (0.31), residues: 741
  helix:  0.44 (0.23), residues: 498
  sheet:  None (None), residues: 0
  loop : -1.98 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 187 
 TYR   0.018   0.002   TYR A 173 
 PHE   0.024   0.002   PHE A 371 
 TRP   0.030   0.002   TRP A 480 
 HIS   0.006   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 6071)
  covalent geometry    : angle       0.71961 ( 8326)
  hydrogen bonds       : bond        0.03471 (  334)
  hydrogen bonds       : angle       4.31658 (  972)
  Misc. bond           : bond        0.23382 (    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
  173 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.9318 (mt0) cc_final: 0.8714 (mt0)
REVERT: A   87 TRP cc_start: 0.9137 (t-100) cc_final: 0.8389 (t-100)
REVERT: A   93 MET cc_start: 0.8774 (mmt) cc_final: 0.8556 (mmp)
REVERT: A   97 ASP cc_start: 0.9299 (t0) cc_final: 0.8975 (t0)
REVERT: A  101 ARG cc_start: 0.9281 (tpp-160) cc_final: 0.9000 (mmm-85)
REVERT: A  157 ASP cc_start: 0.8094 (m-30) cc_final: 0.7727 (m-30)
REVERT: A  190 THR cc_start: 0.9329 (t) cc_final: 0.9045 (t)
REVERT: A  404 GLN cc_start: 0.8986 (tt0) cc_final: 0.8701 (tt0)
REVERT: A  408 TYR cc_start: 0.8873 (m-80) cc_final: 0.8485 (m-80)
REVERT: A  416 GLN cc_start: 0.9427 (mt0) cc_final: 0.8747 (mt0)
REVERT: A  478 GLU cc_start: 0.9382 (tp30) cc_final: 0.9163 (tp30)
REVERT: A  481 ARG cc_start: 0.8967 (ttt-90) cc_final: 0.8565 (ptm160)
REVERT: A  515 MET cc_start: 0.8463 (mmt) cc_final: 0.7807 (mmp)
REVERT: A  592 CYS cc_start: 0.9032 (m) cc_final: 0.8806 (m)
REVERT: A  601 MET cc_start: 0.7932 (ttt) cc_final: 0.7156 (tpt)
REVERT: A  612 ASN cc_start: 0.9396 (t0) cc_final: 0.9124 (m-40)
REVERT: A  659 LEU cc_start: 0.8476 (pp) cc_final: 0.8161 (pp)
REVERT: A  737 GLN cc_start: 0.9281 (tm-30) cc_final: 0.8790 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.0599
  time to fit residues: 14.6932
Evaluate side-chains
  158 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 70 optimal weight:    8.9990
   chunk 35 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 27 optimal weight:    6.9990
   chunk 28 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    9.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    1.1586

-------------------------------------------------------------------------------
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 ** 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 = 0.3500 r_free = 0.3500 target = 0.097981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.073874 restraints weight = 21238.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.077271 restraints weight = 12670.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.079679 restraints weight = 8853.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.081336 restraints weight = 6840.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.082595 restraints weight = 5647.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3245
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    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 = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3245
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.3799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.305   6074  Z= 0.138
  Angle     :  0.719   6.751   8326  Z= 0.344
  Chirality :  0.043   0.185    883
  Planarity :  0.004   0.037   1040
  Dihedral  :  6.690  74.230    821
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  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 (0.31), residues: 741
  helix:  0.48 (0.23), residues: 497
  sheet:  None (None), residues: 0
  loop : -1.97 (0.41), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 187 
 TYR   0.019   0.002   TYR A 406 
 PHE   0.023   0.002   PHE A 295 
 TRP   0.023   0.002   TRP A 480 
 HIS   0.004   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 6071)
  covalent geometry    : angle       0.71941 ( 8326)
  hydrogen bonds       : bond        0.03470 (  334)
  hydrogen bonds       : angle       4.35791 (  972)
  Misc. bond           : bond        0.19183 (    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
  171 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 TRP cc_start: 0.9147 (t-100) cc_final: 0.8363 (t-100)
REVERT: A  101 ARG cc_start: 0.9273 (tpp-160) cc_final: 0.9005 (mmm-85)
REVERT: A  190 THR cc_start: 0.9309 (t) cc_final: 0.9061 (t)
REVERT: A  408 TYR cc_start: 0.8917 (m-80) cc_final: 0.8535 (m-80)
REVERT: A  416 GLN cc_start: 0.9423 (mt0) cc_final: 0.8723 (mt0)
REVERT: A  515 MET cc_start: 0.8374 (mmt) cc_final: 0.7720 (mmp)
REVERT: A  536 PHE cc_start: 0.9479 (m-80) cc_final: 0.9204 (m-80)
REVERT: A  563 LEU cc_start: 0.7238 (mt) cc_final: 0.7011 (mt)
REVERT: A  592 CYS cc_start: 0.9063 (m) cc_final: 0.8839 (m)
REVERT: A  601 MET cc_start: 0.8042 (ttt) cc_final: 0.7172 (tpt)
REVERT: A  612 ASN cc_start: 0.9290 (t0) cc_final: 0.9067 (m-40)
REVERT: A  664 MET cc_start: 0.8332 (mtm) cc_final: 0.8033 (mtp)
REVERT: A  737 GLN cc_start: 0.9287 (tm-30) cc_final: 0.8861 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.0694
  time to fit residues: 16.3651
Evaluate side-chains
  154 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 71 optimal weight:    8.9990
   chunk 72 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 3 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 40 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 404 GLN
** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 612 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 = 0.3442 r_free = 0.3442 target = 0.094307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.068236 restraints weight = 37708.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.072368 restraints weight = 18124.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.075277 restraints weight = 11374.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.077314 restraints weight = 8213.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.078608 restraints weight = 6472.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3159
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3159 r_free = 0.3159    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 = 0.3159 r_free = 0.3159    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3159
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.3840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.504   6074  Z= 0.199
  Angle     :  0.771  10.196   8326  Z= 0.367
  Chirality :  0.045   0.186    883
  Planarity :  0.005   0.040   1040
  Dihedral  :  6.806  77.393    821
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 15.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    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: -0.32 (0.32), residues: 741
  helix:  0.56 (0.24), residues: 500
  sheet:  None (None), residues: 0
  loop : -1.82 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 481 
 TYR   0.027   0.002   TYR A 479 
 PHE   0.020   0.002   PHE A 496 
 TRP   0.015   0.002   TRP A 195 
 HIS   0.004   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 ( 6071)
  covalent geometry    : angle       0.77142 ( 8326)
  hydrogen bonds       : bond        0.03454 (  334)
  hydrogen bonds       : angle       4.42359 (  972)
  Misc. bond           : bond        0.33008 (    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
  169 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 TRP cc_start: 0.9218 (t-100) cc_final: 0.8463 (t-100)
REVERT: A  101 ARG cc_start: 0.9311 (tpp-160) cc_final: 0.9039 (mmm-85)
REVERT: A  362 TYR cc_start: 0.6867 (m-10) cc_final: 0.6635 (m-10)
REVERT: A  404 GLN cc_start: 0.9077 (tt0) cc_final: 0.8835 (tt0)
REVERT: A  408 TYR cc_start: 0.8804 (m-80) cc_final: 0.8503 (m-80)
REVERT: A  416 GLN cc_start: 0.9488 (mt0) cc_final: 0.8917 (mt0)
REVERT: A  515 MET cc_start: 0.8485 (mmt) cc_final: 0.7818 (mmp)
REVERT: A  536 PHE cc_start: 0.9563 (m-80) cc_final: 0.9313 (m-80)
REVERT: A  592 CYS cc_start: 0.9126 (m) cc_final: 0.8873 (m)
REVERT: A  601 MET cc_start: 0.8147 (ttt) cc_final: 0.7297 (tpt)
REVERT: A  659 LEU cc_start: 0.8556 (pp) cc_final: 0.8302 (pp)
REVERT: A  664 MET cc_start: 0.8428 (mtm) cc_final: 0.8191 (mtp)
REVERT: A  737 GLN cc_start: 0.9323 (tm-30) cc_final: 0.8777 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.0647
  time to fit residues: 15.3604
Evaluate side-chains
  150 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 70 optimal weight:    8.9990
   chunk 32 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 1 optimal weight:    1.9990
   chunk 72 optimal weight:    7.9990
   chunk 34 optimal weight:    4.9990
   chunk 63 optimal weight:    0.5980
   chunk 50 optimal weight:    6.9990
   chunk 36 optimal weight:    0.4980
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
A  62 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.097371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.069260 restraints weight = 39662.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.073578 restraints weight = 18932.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.076700 restraints weight = 11915.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.078878 restraints weight = 8608.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.080244 restraints weight = 6794.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3196
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    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 = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3196
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.3995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.393   6074  Z= 0.152
  Angle     :  0.739   7.700   8326  Z= 0.354
  Chirality :  0.045   0.186    883
  Planarity :  0.005   0.044   1040
  Dihedral  :  6.768  75.299    821
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  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: -0.39 (0.31), residues: 741
  helix:  0.50 (0.23), residues: 499
  sheet:  None (None), residues: 0
  loop : -1.82 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 187 
 TYR   0.023   0.002   TYR A 479 
 PHE   0.019   0.001   PHE A 496 
 TRP   0.022   0.002   TRP A 338 
 HIS   0.005   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 6071)
  covalent geometry    : angle       0.73896 ( 8326)
  hydrogen bonds       : bond        0.03515 (  334)
  hydrogen bonds       : angle       4.34779 (  972)
  Misc. bond           : bond        0.25205 (    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
  173 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 TRP cc_start: 0.9187 (t-100) cc_final: 0.8434 (t-100)
REVERT: A   93 MET cc_start: 0.8961 (mmt) cc_final: 0.8737 (mmp)
REVERT: A  101 ARG cc_start: 0.9320 (tpp-160) cc_final: 0.9048 (mmm-85)
REVERT: A  190 THR cc_start: 0.9335 (t) cc_final: 0.9055 (t)
REVERT: A  362 TYR cc_start: 0.6900 (m-10) cc_final: 0.6686 (m-10)
REVERT: A  404 GLN cc_start: 0.9020 (tt0) cc_final: 0.8673 (tt0)
REVERT: A  408 TYR cc_start: 0.8900 (m-80) cc_final: 0.8526 (m-80)
REVERT: A  416 GLN cc_start: 0.9327 (mt0) cc_final: 0.8776 (mt0)
REVERT: A  515 MET cc_start: 0.8414 (mmt) cc_final: 0.7753 (mmp)
REVERT: A  563 LEU cc_start: 0.7321 (mt) cc_final: 0.7051 (mt)
REVERT: A  592 CYS cc_start: 0.9081 (m) cc_final: 0.8853 (m)
REVERT: A  601 MET cc_start: 0.8106 (ttt) cc_final: 0.7303 (tpt)
REVERT: A  659 LEU cc_start: 0.8545 (pp) cc_final: 0.8270 (pp)
REVERT: A  664 MET cc_start: 0.8348 (mtm) cc_final: 0.8133 (mtp)
REVERT: A  737 GLN cc_start: 0.9272 (tm-30) cc_final: 0.8738 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.0562
  time to fit residues: 13.7499
Evaluate side-chains
  153 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 6 optimal weight:    0.0470
   chunk 44 optimal weight:   20.0000
   chunk 3 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 36 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   overall best weight:    1.9684

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

Flipped N/Q/H residues before XYZ refinement:
A  62 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.097581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.068770 restraints weight = 44724.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.073409 restraints weight = 20375.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.076632 restraints weight = 12435.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.078899 restraints weight = 8879.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.080317 restraints weight = 6964.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3189
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    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 = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3189
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.4154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.387   6074  Z= 0.157
  Angle     :  0.751   7.979   8326  Z= 0.359
  Chirality :  0.044   0.167    883
  Planarity :  0.005   0.040   1040
  Dihedral  :  6.789  76.642    821
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  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: -0.43 (0.31), residues: 741
  helix:  0.50 (0.24), residues: 497
  sheet:  None (None), residues: 0
  loop : -1.89 (0.40), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 413 
 TYR   0.027   0.002   TYR A 479 
 PHE   0.026   0.002   PHE A 467 
 TRP   0.021   0.002   TRP A 338 
 HIS   0.005   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 6071)
  covalent geometry    : angle       0.75094 ( 8326)
  hydrogen bonds       : bond        0.03532 (  334)
  hydrogen bonds       : angle       4.37519 (  972)
  Misc. bond           : bond        0.25324 (    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
  169 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 GLN cc_start: 0.8911 (pt0) cc_final: 0.8688 (pt0)
REVERT: A   87 TRP cc_start: 0.9191 (t-100) cc_final: 0.8455 (t-100)
REVERT: A   97 ASP cc_start: 0.9333 (t0) cc_final: 0.8996 (t0)
REVERT: A  101 ARG cc_start: 0.9309 (tpp-160) cc_final: 0.9003 (mmm-85)
REVERT: A  190 THR cc_start: 0.9338 (t) cc_final: 0.9097 (t)
REVERT: A  362 TYR cc_start: 0.6882 (m-10) cc_final: 0.6666 (m-10)
REVERT: A  404 GLN cc_start: 0.9007 (tt0) cc_final: 0.8424 (tt0)
REVERT: A  408 TYR cc_start: 0.8822 (m-80) cc_final: 0.8478 (m-80)
REVERT: A  416 GLN cc_start: 0.9319 (mt0) cc_final: 0.8935 (mt0)
REVERT: A  461 PHE cc_start: 0.9258 (m-80) cc_final: 0.8912 (m-80)
REVERT: A  515 MET cc_start: 0.8414 (mmt) cc_final: 0.7765 (mmp)
REVERT: A  592 CYS cc_start: 0.9092 (m) cc_final: 0.8842 (m)
REVERT: A  601 MET cc_start: 0.8201 (ttt) cc_final: 0.7376 (tpt)
REVERT: A  659 LEU cc_start: 0.8455 (pp) cc_final: 0.8183 (pp)
REVERT: A  664 MET cc_start: 0.8403 (mtm) cc_final: 0.8172 (mtp)
REVERT: A  737 GLN cc_start: 0.9267 (tm-30) cc_final: 0.8750 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.0588
  time to fit residues: 14.1317
Evaluate side-chains
  149 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
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:    0.0670
   chunk 2 optimal weight:    8.9990
   chunk 11 optimal weight:    6.9990
   chunk 23 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   chunk 71 optimal weight:    9.9990
   chunk 15 optimal weight:    0.0970
   chunk 66 optimal weight:    0.6980
   overall best weight:    1.5720

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3505 r_free = 0.3505 target = 0.098346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.072643 restraints weight = 25651.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.076345 restraints weight = 14489.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.078979 restraints weight = 9812.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.080697 restraints weight = 7427.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.082165 restraints weight = 6117.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3229
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3229
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.4264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.342   6074  Z= 0.144
  Angle     :  0.735   7.398   8326  Z= 0.349
  Chirality :  0.044   0.179    883
  Planarity :  0.005   0.040   1040
  Dihedral  :  6.582  76.964    821
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  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: -0.38 (0.31), residues: 741
  helix:  0.50 (0.24), residues: 497
  sheet:  None (None), residues: 0
  loop : -1.77 (0.40), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 187 
 TYR   0.024   0.002   TYR A 479 
 PHE   0.019   0.001   PHE A 496 
 TRP   0.021   0.002   TRP A 338 
 HIS   0.010   0.002   HIS A 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 6071)
  covalent geometry    : angle       0.73500 ( 8326)
  hydrogen bonds       : bond        0.03356 (  334)
  hydrogen bonds       : angle       4.32073 (  972)
  Misc. bond           : bond        0.22091 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1132.26 seconds
wall clock time: 20 minutes 13.27 seconds (1213.27 seconds total)