Starting phenix.real_space_refine
on Fri Jul 25 05:36:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9izm_61037/07_2025/9izm_61037.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9izm_61037/07_2025/9izm_61037.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9izm_61037/07_2025/9izm_61037.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9izm_61037/07_2025/9izm_61037.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9izm_61037/07_2025/9izm_61037.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9izm_61037/07_2025/9izm_61037.cif"
  }
  resolution = 3.02
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.016 sd=   0.217
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
     P      48      5.49       5
     Mg      2      5.21       5
     S      30      5.16       5
     C    4388      2.51       5
     N    1192      2.21       5
     O    1500      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7160
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 739, 6137
          Classifications: {'peptide': 739}
          Link IDs: {'PTRANS': 12, 'TRANS': 726}
    Chain: "B"
      Number of atoms: 1021
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 1021
          Classifications: {'RNA': 48}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 21, 'rna3p_pyr': 16}
          Link IDs: {'rna2p': 11, 'rna3p': 36}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.25, per 1000 atoms: 0.59
  Number of scatterers: 7160
  At special positions: 0
  Unit cell: (94.62, 98.355, 100.845, 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)
     S      30     16.00
     P      48     15.00
     Mg      2     11.99
     O    1500      8.00
     N    1192      7.00
     C    4388      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.88
  Conformation dependent library (CDL) restraints added in 637.4 milliseconds
  

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1428

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 7 sheets defined
      53.5% alpha, 8.8% beta
      9 base pairs and 18 stacking pairs defined.
    Time for finding SS restraints: 2.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 37
      removed outlier: 3.655A  pdb=" N   ILE A  20 " --> pdb=" O   THR A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 54
      removed outlier: 3.514A  pdb=" N   MET A  46 " --> pdb=" O   THR A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 65
      removed outlier: 3.664A  pdb=" N   LEU A  65 " --> pdb=" O   ILE A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 79
    Processing helix  chain 'A' and resid 83 through 99
    Processing helix  chain 'A' and resid 111 through 116
    Processing helix  chain 'A' and resid 119 through 133
    Processing helix  chain 'A' and resid 149 through 165
      removed outlier: 3.544A  pdb=" N   GLN A 156 " --> pdb=" O   ASP A 152 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ILE A 161 " --> pdb=" O   THR A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 181
      removed outlier: 3.509A  pdb=" N   PHE A 175 " --> pdb=" O   ASP A 171 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   TYR A 178 " --> pdb=" O   GLU A 174 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ASN A 181 " --> pdb=" O   SER A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 201
      removed outlier: 4.091A  pdb=" N   ILE A 190 " --> pdb=" O   ASN A 186 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   CYS A 201 " --> pdb=" O   ARG A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 210
    Processing helix  chain 'A' and resid 212 through 218
    Processing helix  chain 'A' and resid 270 through 274
      removed outlier: 3.618A  pdb=" N   ASN A 274 " --> pdb=" O   ARG A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 286
      removed outlier: 3.566A  pdb=" N   ASP A 281 " --> pdb=" O   THR A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 355
      removed outlier: 3.973A  pdb=" N   HIS A 355 " --> pdb=" O   TYR A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 360
      removed outlier: 3.800A  pdb=" N   THR A 359 " --> pdb=" O   HIS A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 374
      removed outlier: 3.538A  pdb=" N   LYS A 368 " --> pdb=" O   ASN A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 388
    Processing helix  chain 'A' and resid 400 through 419
    Processing helix  chain 'A' and resid 420 through 458
    Processing helix  chain 'A' and resid 467 through 478
      removed outlier: 3.633A  pdb=" N   LYS A 473 " --> pdb=" O   GLU A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 519
    Processing helix  chain 'A' and resid 541 through 547
      removed outlier: 3.556A  pdb=" N   LEU A 546 " --> pdb=" O   ILE A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 554
      removed outlier: 4.234A  pdb=" N   ASN A 553 " --> pdb=" O   LYS A 550 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLN A 554 " --> pdb=" O   LEU A 551 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 550 through 554'
    Processing helix  chain 'A' and resid 562 through 571
      removed outlier: 3.558A  pdb=" N   LYS A 566 " --> pdb=" O   SER A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 590 through 605
    Processing helix  chain 'A' and resid 605 through 610
    Processing helix  chain 'A' and resid 616 through 624
    Processing helix  chain 'A' and resid 678 through 693
      removed outlier: 3.615A  pdb=" N   VAL A 691 " --> pdb=" O   ILE A 687 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 693 through 700
    Processing helix  chain 'A' and resid 720 through 731
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8
      removed outlier: 3.587A  pdb=" N   ILE A   5 " --> pdb=" O   PHE A 304 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   SER A 305 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   ASN A 290 " --> pdb=" O   SER A 305 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 242 through 245
      removed outlier: 3.828A  pdb=" N   LYS A 242 " --> pdb=" O   ASN A 255 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 258
    Processing sheet with id=AA4, first strand: chain 'A' and resid 376 through 379
      removed outlier: 5.614A  pdb=" N   VAL A 377 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   GLY A 322 " --> pdb=" O   SER A 335 " (cutoff:3.500A)
      removed outlier: 9.298A  pdb=" N   LYS A 337 " --> pdb=" O   THR A 320 " (cutoff:3.500A)
      removed outlier: 12.927A  pdb=" N   THR A 320 " --> pdb=" O   LYS A 337 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   VAL A 321 " --> pdb=" O   ALA A 524 " (cutoff:3.500A)
      removed outlier: 8.177A  pdb=" N   GLU A 526 " --> pdb=" O   VAL A 321 " (cutoff:3.500A)
      removed outlier: 8.749A  pdb=" N   LEU A 323 " --> pdb=" O   GLU A 526 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 577 through 578
    Processing sheet with id=AA6, first strand: chain 'A' and resid 658 through 660
    Processing sheet with id=AA7, first strand: chain 'A' and resid 701 through 702

    291 hydrogen bonds defined for protein.
    843 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      20 hydrogen bonds
      40 hydrogen bond angles
      0 basepair planarities
      9 basepair parallelities
      18 stacking parallelities
  Total time for adding SS restraints: 2.23

  Time building geometry restraints manager: 2.18 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1487
        1.33 -     1.45: 1863
        1.45 -     1.57: 3901
        1.57 -     1.69: 95
        1.69 -     1.81: 47
  Bond restraints: 7393
  Sorted by residual:
  bond pdb=" CG1 ILE A 216 "
       pdb=" CD1 ILE A 216 "
    ideal  model  delta    sigma   weight residual
    1.513  1.465  0.048 3.90e-02 6.57e+02 1.49e+00
  bond pdb=" CB  ILE A   5 "
       pdb=" CG2 ILE A   5 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.09e+00
  bond pdb=" CG  LEU A 490 "
       pdb=" CD1 LEU A 490 "
    ideal  model  delta    sigma   weight residual
    1.521  1.488  0.033 3.30e-02 9.18e+02 1.01e+00
  bond pdb=" CA  ASP A 338 "
       pdb=" C   ASP A 338 "
    ideal  model  delta    sigma   weight residual
    1.530  1.519  0.011 1.10e-02 8.26e+03 1.01e+00
  bond pdb=" CG1 ILE A 522 "
       pdb=" CD1 ILE A 522 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 1.00e+00
  ... (remaining 7388 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 9783
        1.37 -     2.73: 346
        2.73 -     4.10: 38
        4.10 -     5.46: 3
        5.46 -     6.83: 4
  Bond angle restraints: 10174
  Sorted by residual:
  angle pdb=" N   GLU A 212 "
        pdb=" CA  GLU A 212 "
        pdb=" C   GLU A 212 "
      ideal   model   delta    sigma   weight residual
     112.93  106.82    6.11 1.33e+00 5.65e-01 2.11e+01
  angle pdb=" C   CYS A 398 "
        pdb=" N   LYS A 399 "
        pdb=" CA  LYS A 399 "
      ideal   model   delta    sigma   weight residual
     121.54  125.96   -4.42 1.91e+00 2.74e-01 5.36e+00
  angle pdb=" CA  ASN A 419 "
        pdb=" C   ASN A 419 "
        pdb=" N   ARG A 420 "
      ideal   model   delta    sigma   weight residual
     115.67  118.49   -2.82 1.23e+00 6.61e-01 5.25e+00
  angle pdb=" CA  PHE A 637 "
        pdb=" CB  PHE A 637 "
        pdb=" CG  PHE A 637 "
      ideal   model   delta    sigma   weight residual
     113.80  116.06   -2.26 1.00e+00 1.00e+00 5.13e+00
  angle pdb=" C   ASN A 581 "
        pdb=" N   ASN A 582 "
        pdb=" CA  ASN A 582 "
      ideal   model   delta    sigma   weight residual
     121.54  125.84   -4.30 1.91e+00 2.74e-01 5.06e+00
  ... (remaining 10169 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.76: 4058
       18.76 -    37.52: 356
       37.52 -    56.27: 81
       56.27 -    75.03: 61
       75.03 -    93.79: 7
  Dihedral angle restraints: 4563
    sinusoidal: 2353
      harmonic: 2210
  Sorted by residual:
  dihedral pdb=" O4'   U B   5 "
           pdb=" C1'   U B   5 "
           pdb=" N1    U B   5 "
           pdb=" C2    U B   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -71.32  -56.68     1      1.70e+01 3.46e-03 1.50e+01
  dihedral pdb=" O4'   U B -22 "
           pdb=" C1'   U B -22 "
           pdb=" N1    U B -22 "
           pdb=" C2    U B -22 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -72.23  -55.77     1      1.70e+01 3.46e-03 1.45e+01
  dihedral pdb=" CA  GLU A 445 "
           pdb=" C   GLU A 445 "
           pdb=" N   LYS A 446 "
           pdb=" CA  LYS A 446 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.39   17.61     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 4560 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 669
       0.029 -    0.058: 333
       0.058 -    0.087: 103
       0.087 -    0.117: 37
       0.117 -    0.146: 8
  Chirality restraints: 1150
  Sorted by residual:
  chirality pdb=" CA  VAL A 633 "
            pdb=" N   VAL A 633 "
            pdb=" C   VAL A 633 "
            pdb=" CB  VAL A 633 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.31e-01
  chirality pdb=" CA  PHE A 637 "
            pdb=" N   PHE A 637 "
            pdb=" C   PHE A 637 "
            pdb=" CB  PHE A 637 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.96e-01
  chirality pdb=" CA  ILE A 237 "
            pdb=" N   ILE A 237 "
            pdb=" C   ILE A 237 "
            pdb=" CB  ILE A 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.69e-01
  ... (remaining 1147 not shown)

  Planarity restraints: 1116
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 637 "   -0.011 2.00e-02 2.50e+03   1.31e-02 2.99e+00
        pdb=" CG  PHE A 637 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 637 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 637 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 637 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 637 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 637 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A  72 "    0.028 5.00e-02 4.00e+02   4.27e-02 2.92e+00
        pdb=" N   PRO A  73 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A  73 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A  73 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B -24 "   -0.020 2.00e-02 2.50e+03   8.88e-03 2.17e+00
        pdb=" N9    A B -24 "    0.019 2.00e-02 2.50e+03
        pdb=" C8    A B -24 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    A B -24 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    A B -24 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    A B -24 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6    A B -24 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    A B -24 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    A B -24 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    A B -24 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    A B -24 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1113 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 48
        2.50 -     3.10: 5129
        3.10 -     3.70: 10950
        3.70 -     4.30: 17265
        4.30 -     4.90: 26356
  Nonbonded interactions: 59748
  Sorted by model distance:
  nonbonded pdb=" OP1   G B -30 "
            pdb="MG    MG B 102 "
     model   vdw
     1.902 2.170
  nonbonded pdb=" O2'   C B  -1 "
            pdb=" OP1   G B   1 "
     model   vdw
     2.124 3.040
  nonbonded pdb=" OE2 GLU A 401 "
            pdb=" OG  SER A 405 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" OH  TYR A 349 "
            pdb=" OE2 GLU A 383 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" NZ  LYS A  24 "
            pdb=" OD1 ASN A 232 "
     model   vdw
     2.209 3.120
  ... (remaining 59743 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.150
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
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      :  0.005   0.048   7393  Z= 0.208
  Angle     :  0.603   6.828  10174  Z= 0.350
  Chirality :  0.040   0.146   1150
  Planarity :  0.004   0.045   1116
  Dihedral  : 16.450  93.788   3135
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  7.56 %
    Favored  : 91.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.30), residues: 737
  helix:  0.31 (0.27), residues: 356
  sheet: -1.26 (0.58), residues: 73
  loop : -1.25 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A  69 
 HIS   0.005   0.001   HIS A 230 
 PHE   0.030   0.002   PHE A 637 
 TYR   0.019   0.002   TYR A  23 
 ARG   0.003   0.001   ARG A 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18302 (  311)
  hydrogen bonds       : angle       6.59418 (  883)
  covalent geometry    : bond        0.00454 ( 7393)
  covalent geometry    : angle       0.60349 (10174)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 183
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 MET cc_start: 0.6982 (mmm) cc_final: 0.6584 (mmm)
REVERT: A  206 MET cc_start: 0.7119 (tpp) cc_final: 0.6814 (tpp)
REVERT: A  227 MET cc_start: 0.8410 (ttm) cc_final: 0.8006 (ttm)
REVERT: A  391 TYR cc_start: 0.8139 (t80) cc_final: 0.7846 (t80)
REVERT: A  545 LEU cc_start: 0.7728 (tp) cc_final: 0.7488 (tp)
REVERT: A  589 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.7108 (m-80)
REVERT: A  614 SER cc_start: 0.8619 (m) cc_final: 0.8378 (t)
REVERT: A  640 GLN cc_start: 0.7380 (tt0) cc_final: 0.7047 (tm-30)
REVERT: A  708 GLU cc_start: 0.7015 (tt0) cc_final: 0.6723 (tt0)
  outliers start: 6
  outliers final: 0
  residues processed: 186
  average time/residue: 0.2270
  time to fit residues: 54.4824
Evaluate side-chains
  121 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  589 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:   30.0000
   chunk 58 optimal weight:    9.9990
   chunk 32 optimal weight:    7.9990
   chunk 19 optimal weight:   20.0000
   chunk 39 optimal weight:    0.0270
   chunk 31 optimal weight:    0.0670
   chunk 60 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   overall best weight:    1.2180

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

Flipped N/Q/H residues before XYZ refinement:
A 221 ASN
A 297 ASN
A 402 GLN
A 509 ASN
A 554 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.199372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.159422 restraints weight = 8946.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3964 rms_B_bonded: 1.94
r_work: 0.3714 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.2480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   7393  Z= 0.131
  Angle     :  0.530   6.760  10174  Z= 0.290
  Chirality :  0.038   0.184   1150
  Planarity :  0.003   0.030   1116
  Dihedral  : 17.405  94.924   1532
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 12.65 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.31), residues: 737
  helix:  0.62 (0.27), residues: 378
  sheet: -1.35 (0.56), residues: 73
  loop : -1.35 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 268 
 HIS   0.009   0.001   HIS A 726 
 PHE   0.036   0.002   PHE A 222 
 TYR   0.019   0.002   TYR A  75 
 ARG   0.002   0.000   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04616 (  311)
  hydrogen bonds       : angle       4.74216 (  883)
  covalent geometry    : bond        0.00281 ( 7393)
  covalent geometry    : angle       0.53007 (10174)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 LYS cc_start: 0.8370 (mtmm) cc_final: 0.7994 (mtmm)
REVERT: A  206 MET cc_start: 0.7464 (tpp) cc_final: 0.7027 (tpp)
REVERT: A  212 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6258 (mp0)
REVERT: A  371 GLU cc_start: 0.7673 (tt0) cc_final: 0.7452 (mt-10)
REVERT: A  391 TYR cc_start: 0.7953 (t80) cc_final: 0.7537 (t80)
REVERT: A  589 TYR cc_start: 0.7627 (OUTLIER) cc_final: 0.6835 (m-80)
REVERT: A  609 SER cc_start: 0.8223 (t) cc_final: 0.7894 (t)
REVERT: A  614 SER cc_start: 0.8668 (m) cc_final: 0.8395 (t)
REVERT: A  708 GLU cc_start: 0.7037 (tt0) cc_final: 0.6715 (tt0)
  outliers start: 13
  outliers final: 5
  residues processed: 142
  average time/residue: 0.2227
  time to fit residues: 41.2398
Evaluate side-chains
  115 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 109
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 PHE
Chi-restraints excluded: chain A residue  396 LYS
Chi-restraints excluded: chain A residue  589 TYR
Chi-restraints excluded: chain A residue  608 LYS
Chi-restraints excluded: chain A residue  621 LEU
Chi-restraints excluded: chain A residue  666 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 5 optimal weight:    8.9990
   chunk 3 optimal weight:   10.0000
   chunk 36 optimal weight:    9.9990
   chunk 15 optimal weight:    9.9990
   chunk 57 optimal weight:   20.0000
   chunk 23 optimal weight:    0.0980
   chunk 2 optimal weight:    0.9980
   chunk 73 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   overall best weight:    4.4186

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

Flipped N/Q/H residues before XYZ refinement:
A  76 HIS
A 191 ASN
A 297 ASN
A 487 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.193418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.150989 restraints weight = 9018.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3863 rms_B_bonded: 2.16
r_work: 0.3598 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.081   7393  Z= 0.253
  Angle     :  0.604   7.558  10174  Z= 0.324
  Chirality :  0.042   0.171   1150
  Planarity :  0.004   0.048   1116
  Dihedral  : 17.580  93.217   1532
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 13.66 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.30), residues: 737
  helix:  0.35 (0.26), residues: 377
  sheet: -1.58 (0.56), residues: 73
  loop : -1.40 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A  69 
 HIS   0.003   0.001   HIS A 646 
 PHE   0.028   0.002   PHE A 478 
 TYR   0.028   0.003   TYR A  75 
 ARG   0.003   0.000   ARG A 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05221 (  311)
  hydrogen bonds       : angle       4.88249 (  883)
  covalent geometry    : bond        0.00575 ( 7393)
  covalent geometry    : angle       0.60365 (10174)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 TYR cc_start: 0.5927 (m-80) cc_final: 0.5705 (m-80)
REVERT: A  206 MET cc_start: 0.7549 (tpp) cc_final: 0.7079 (tpp)
REVERT: A  217 GLU cc_start: 0.7433 (tp30) cc_final: 0.7057 (mm-30)
REVERT: A  588 LYS cc_start: 0.7633 (ttpp) cc_final: 0.7175 (tttp)
REVERT: A  609 SER cc_start: 0.8561 (t) cc_final: 0.8092 (t)
REVERT: A  614 SER cc_start: 0.8771 (m) cc_final: 0.8467 (t)
  outliers start: 18
  outliers final: 11
  residues processed: 120
  average time/residue: 0.2624
  time to fit residues: 41.3040
Evaluate side-chains
  111 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  331 PHE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  396 LYS
Chi-restraints excluded: chain A residue  589 TYR
Chi-restraints excluded: chain A residue  621 LEU
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  711 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 75 optimal weight:    8.9990
   chunk 24 optimal weight:    9.9990
   chunk 15 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 5 optimal weight:   20.0000
   chunk 6 optimal weight:    0.0030
   chunk 25 optimal weight:    6.9990
   chunk 73 optimal weight:    7.9990
   chunk 29 optimal weight:    1.9990
   chunk 18 optimal weight:   20.0000
   chunk 19 optimal weight:    9.9990
   overall best weight:    3.3996

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

Flipped N/Q/H residues before XYZ refinement:
A 230 HIS
A 498 GLN
** A 673 HIS ** 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 = 0.4360 r_free = 0.4360 target = 0.195527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.155097 restraints weight = 9100.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3909 rms_B_bonded: 2.11
r_work: 0.3641 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.3303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   7393  Z= 0.204
  Angle     :  0.563   6.910  10174  Z= 0.303
  Chirality :  0.039   0.170   1150
  Planarity :  0.004   0.039   1116
  Dihedral  : 17.441  93.405   1532
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 12.94 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.31), residues: 737
  helix:  0.56 (0.26), residues: 380
  sheet: -1.44 (0.57), residues: 73
  loop : -1.42 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  33 
 HIS   0.003   0.001   HIS A  76 
 PHE   0.022   0.002   PHE A 478 
 TYR   0.022   0.002   TYR A  75 
 ARG   0.001   0.000   ARG A 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04709 (  311)
  hydrogen bonds       : angle       4.62835 (  883)
  covalent geometry    : bond        0.00460 ( 7393)
  covalent geometry    : angle       0.56333 (10174)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.794 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 ASN cc_start: 0.6586 (t0) cc_final: 0.6143 (p0)
REVERT: A  206 MET cc_start: 0.7537 (tpp) cc_final: 0.7072 (tpp)
REVERT: A  391 TYR cc_start: 0.8124 (t80) cc_final: 0.7651 (t80)
REVERT: A  614 SER cc_start: 0.8720 (m) cc_final: 0.8417 (t)
REVERT: A  651 LYS cc_start: 0.8271 (pttt) cc_final: 0.7980 (pttm)
REVERT: A  708 GLU cc_start: 0.7859 (mp0) cc_final: 0.7626 (mp0)
  outliers start: 22
  outliers final: 13
  residues processed: 120
  average time/residue: 0.2198
  time to fit residues: 34.5340
Evaluate side-chains
  112 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  331 PHE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  396 LYS
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  589 TYR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  711 VAL
Chi-restraints excluded: chain A residue  727 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 20 optimal weight:   20.0000
   chunk 39 optimal weight:    0.2980
   chunk 66 optimal weight:    0.0470
   chunk 62 optimal weight:    7.9990
   chunk 15 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 13 optimal weight:    8.9990
   chunk 30 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.8684

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

Flipped N/Q/H residues before XYZ refinement:
A 316 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.197785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.157320 restraints weight = 8888.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3930 rms_B_bonded: 2.10
r_work: 0.3674 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.3639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7393  Z= 0.140
  Angle     :  0.509   6.771  10174  Z= 0.274
  Chirality :  0.038   0.167   1150
  Planarity :  0.003   0.028   1116
  Dihedral  : 17.238  95.082   1532
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 15.26 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.32), residues: 737
  helix:  0.86 (0.27), residues: 388
  sheet: -1.33 (0.53), residues: 85
  loop : -1.37 (0.39), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  33 
 HIS   0.004   0.001   HIS A 726 
 PHE   0.019   0.002   PHE A 478 
 TYR   0.020   0.002   TYR A 447 
 ARG   0.003   0.000   ARG A 667 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04218 (  311)
  hydrogen bonds       : angle       4.38277 (  883)
  covalent geometry    : bond        0.00311 ( 7393)
  covalent geometry    : angle       0.50862 (10174)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 ASP cc_start: 0.7937 (m-30) cc_final: 0.7592 (m-30)
REVERT: A  167 ASN cc_start: 0.6743 (t0) cc_final: 0.6353 (p0)
REVERT: A  206 MET cc_start: 0.7500 (tpp) cc_final: 0.7034 (tpp)
REVERT: A  391 TYR cc_start: 0.8002 (t80) cc_final: 0.7660 (t80)
REVERT: A  614 SER cc_start: 0.8760 (m) cc_final: 0.8445 (t)
REVERT: A  651 LYS cc_start: 0.8128 (pttt) cc_final: 0.7725 (pttm)
  outliers start: 17
  outliers final: 16
  residues processed: 120
  average time/residue: 0.3258
  time to fit residues: 51.3282
Evaluate side-chains
  114 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  159 TYR
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  331 PHE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  396 LYS
Chi-restraints excluded: chain A residue  589 TYR
Chi-restraints excluded: chain A residue  608 LYS
Chi-restraints excluded: chain A residue  621 LEU
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  675 ASN
Chi-restraints excluded: chain A residue  711 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 74 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 25 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 58 optimal weight:    9.9990
   chunk 36 optimal weight:    8.9990
   chunk 52 optimal weight:   10.0000
   chunk 73 optimal weight:    7.9990
   chunk 48 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 67 optimal weight:    0.6980
   overall best weight:    3.9386

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.195048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.154034 restraints weight = 8930.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 2.03
r_work: 0.3630 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.3714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074   7393  Z= 0.227
  Angle     :  0.576   6.153  10174  Z= 0.309
  Chirality :  0.040   0.162   1150
  Planarity :  0.004   0.043   1116
  Dihedral  : 17.391  93.968   1532
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 15.99 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.31), residues: 737
  helix:  0.69 (0.26), residues: 387
  sheet: -1.36 (0.54), residues: 83
  loop : -1.43 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  33 
 HIS   0.004   0.001   HIS A  76 
 PHE   0.018   0.002   PHE A 478 
 TYR   0.021   0.002   TYR A  23 
 ARG   0.002   0.000   ARG A 420 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04846 (  311)
  hydrogen bonds       : angle       4.64361 (  883)
  covalent geometry    : bond        0.00514 ( 7393)
  covalent geometry    : angle       0.57580 (10174)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 ASN cc_start: 0.6720 (t0) cc_final: 0.6272 (p0)
REVERT: A  206 MET cc_start: 0.7526 (tpp) cc_final: 0.7027 (tpp)
REVERT: A  609 SER cc_start: 0.8573 (t) cc_final: 0.8118 (t)
REVERT: A  614 SER cc_start: 0.8716 (m) cc_final: 0.8381 (t)
REVERT: A  651 LYS cc_start: 0.8141 (pttt) cc_final: 0.7879 (pttm)
  outliers start: 16
  outliers final: 14
  residues processed: 115
  average time/residue: 0.2858
  time to fit residues: 43.9527
Evaluate side-chains
  108 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  234 MET
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  331 PHE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  396 LYS
Chi-restraints excluded: chain A residue  589 TYR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  675 ASN
Chi-restraints excluded: chain A residue  711 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 75 optimal weight:   10.0000
   chunk 10 optimal weight:    5.9990
   chunk 46 optimal weight:   30.0000
   chunk 29 optimal weight:    0.3980
   chunk 58 optimal weight:    8.9990
   chunk 71 optimal weight:    8.9990
   chunk 39 optimal weight:    0.0040
   chunk 16 optimal weight:    9.9990
   chunk 34 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    2.4798

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.196647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.157876 restraints weight = 8885.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3941 rms_B_bonded: 1.95
r_work: 0.3686 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.3854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   7393  Z= 0.163
  Angle     :  0.530   6.900  10174  Z= 0.283
  Chirality :  0.038   0.167   1150
  Planarity :  0.003   0.030   1116
  Dihedral  : 17.228  95.550   1532
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 16.72 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.31), residues: 737
  helix:  0.92 (0.27), residues: 387
  sheet: -1.27 (0.54), residues: 85
  loop : -1.36 (0.39), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  33 
 HIS   0.003   0.001   HIS A  76 
 PHE   0.017   0.002   PHE A 478 
 TYR   0.021   0.002   TYR A 447 
 ARG   0.002   0.000   ARG A 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04357 (  311)
  hydrogen bonds       : angle       4.44849 (  883)
  covalent geometry    : bond        0.00366 ( 7393)
  covalent geometry    : angle       0.53007 (10174)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 ASP cc_start: 0.7941 (m-30) cc_final: 0.7596 (m-30)
REVERT: A  167 ASN cc_start: 0.6746 (t0) cc_final: 0.6376 (p0)
REVERT: A  206 MET cc_start: 0.7513 (tpp) cc_final: 0.7029 (tpp)
REVERT: A  391 TYR cc_start: 0.8035 (t80) cc_final: 0.7644 (t80)
REVERT: A  589 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.6323 (m-80)
REVERT: A  614 SER cc_start: 0.8608 (m) cc_final: 0.8276 (t)
REVERT: A  651 LYS cc_start: 0.8151 (pttt) cc_final: 0.7892 (pttm)
  outliers start: 15
  outliers final: 13
  residues processed: 116
  average time/residue: 0.2565
  time to fit residues: 39.1784
Evaluate side-chains
  109 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  331 PHE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  396 LYS
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain A residue  589 TYR
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  675 ASN
Chi-restraints excluded: chain A residue  711 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 63 optimal weight:    0.0010
   chunk 49 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 66 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 9 optimal weight:    7.9990
   chunk 76 optimal weight:   10.0000
   overall best weight:    2.3994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.197087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.157741 restraints weight = 9021.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3938 rms_B_bonded: 1.97
r_work: 0.3680 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.4021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   7393  Z= 0.162
  Angle     :  0.539   6.803  10174  Z= 0.289
  Chirality :  0.038   0.172   1150
  Planarity :  0.003   0.029   1116
  Dihedral  : 17.156  95.625   1532
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.01 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.32), residues: 737
  helix:  1.01 (0.27), residues: 387
  sheet: -1.30 (0.57), residues: 75
  loop : -1.36 (0.38), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  33 
 HIS   0.002   0.001   HIS A  76 
 PHE   0.017   0.002   PHE A 478 
 TYR   0.022   0.002   TYR A 447 
 ARG   0.002   0.000   ARG A 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04329 (  311)
  hydrogen bonds       : angle       4.39611 (  883)
  covalent geometry    : bond        0.00363 ( 7393)
  covalent geometry    : angle       0.53890 (10174)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 1.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 ASP cc_start: 0.7963 (m-30) cc_final: 0.7613 (m-30)
REVERT: A  167 ASN cc_start: 0.6699 (t0) cc_final: 0.6351 (p0)
REVERT: A  206 MET cc_start: 0.7530 (tpp) cc_final: 0.7038 (tpp)
REVERT: A  391 TYR cc_start: 0.8029 (t80) cc_final: 0.7654 (t80)
REVERT: A  589 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.6627 (m-80)
REVERT: A  614 SER cc_start: 0.8604 (m) cc_final: 0.8278 (t)
REVERT: A  651 LYS cc_start: 0.8151 (pttt) cc_final: 0.7872 (pttm)
REVERT: A  708 GLU cc_start: 0.7931 (mp0) cc_final: 0.7688 (mp0)
  outliers start: 16
  outliers final: 13
  residues processed: 108
  average time/residue: 0.2381
  time to fit residues: 34.3439
Evaluate side-chains
  103 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  331 PHE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  396 LYS
Chi-restraints excluded: chain A residue  589 TYR
Chi-restraints excluded: chain A residue  608 LYS
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  675 ASN
Chi-restraints excluded: chain A residue  711 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 47 optimal weight:   20.0000
   chunk 72 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 56 optimal weight:    6.9990
   chunk 31 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9990
   chunk 17 optimal weight:    8.9990
   chunk 61 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   overall best weight:    2.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.196240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.155697 restraints weight = 9078.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3915 rms_B_bonded: 1.96
r_work: 0.3679 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.4046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   7393  Z= 0.187
  Angle     :  0.560   6.787  10174  Z= 0.299
  Chirality :  0.039   0.171   1150
  Planarity :  0.003   0.035   1116
  Dihedral  : 17.144  95.447   1532
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 17.30 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.31), residues: 737
  helix:  0.93 (0.27), residues: 387
  sheet: -1.32 (0.57), residues: 75
  loop : -1.39 (0.38), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  33 
 HIS   0.003   0.001   HIS A  76 
 PHE   0.016   0.002   PHE A 478 
 TYR   0.023   0.002   TYR A 447 
 ARG   0.003   0.000   ARG A 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04527 (  311)
  hydrogen bonds       : angle       4.48039 (  883)
  covalent geometry    : bond        0.00421 ( 7393)
  covalent geometry    : angle       0.56021 (10174)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 ASP cc_start: 0.7970 (m-30) cc_final: 0.7623 (m-30)
REVERT: A  167 ASN cc_start: 0.6744 (t0) cc_final: 0.6404 (p0)
REVERT: A  206 MET cc_start: 0.7498 (tpp) cc_final: 0.7008 (tpp)
REVERT: A  391 TYR cc_start: 0.8056 (t80) cc_final: 0.7650 (t80)
REVERT: A  589 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6816 (m-80)
REVERT: A  609 SER cc_start: 0.8431 (t) cc_final: 0.7955 (t)
REVERT: A  651 LYS cc_start: 0.8151 (pttt) cc_final: 0.7849 (pttm)
  outliers start: 15
  outliers final: 14
  residues processed: 111
  average time/residue: 0.2156
  time to fit residues: 31.6343
Evaluate side-chains
  106 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  331 PHE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  396 LYS
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain A residue  589 TYR
Chi-restraints excluded: chain A residue  608 LYS
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  675 ASN
Chi-restraints excluded: chain A residue  711 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 14 optimal weight:   50.0000
   chunk 55 optimal weight:   20.0000
   chunk 2 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   chunk 43 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 56 optimal weight:    3.9990
   chunk 45 optimal weight:    7.9990
   chunk 76 optimal weight:   10.0000
   chunk 33 optimal weight:    8.9990
   overall best weight:    4.9990

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.194268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.153867 restraints weight = 9114.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3891 rms_B_bonded: 2.04
r_work: 0.3616 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.4082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.089   7393  Z= 0.281
  Angle     :  0.662   8.182  10174  Z= 0.352
  Chirality :  0.043   0.193   1150
  Planarity :  0.004   0.053   1116
  Dihedral  : 17.347  94.754   1532
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 17.88 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.30), residues: 737
  helix:  0.52 (0.26), residues: 389
  sheet: -1.39 (0.58), residues: 73
  loop : -1.53 (0.36), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  33 
 HIS   0.004   0.001   HIS A  76 
 PHE   0.018   0.002   PHE A 637 
 TYR   0.030   0.003   TYR A 447 
 ARG   0.002   0.000   ARG A 420 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05171 (  311)
  hydrogen bonds       : angle       4.74139 (  883)
  covalent geometry    : bond        0.00639 ( 7393)
  covalent geometry    : angle       0.66231 (10174)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 MET cc_start: 0.7827 (mmm) cc_final: 0.7551 (tpt)
REVERT: A  167 ASN cc_start: 0.6777 (t0) cc_final: 0.6395 (p0)
REVERT: A  206 MET cc_start: 0.7497 (tpp) cc_final: 0.6986 (tpp)
REVERT: A  308 TYR cc_start: 0.7922 (p90) cc_final: 0.7506 (p90)
REVERT: A  589 TYR cc_start: 0.7391 (OUTLIER) cc_final: 0.6918 (m-80)
REVERT: A  609 SER cc_start: 0.8505 (t) cc_final: 0.7958 (t)
REVERT: A  651 LYS cc_start: 0.8335 (pttt) cc_final: 0.8071 (pttm)
REVERT: A  708 GLU cc_start: 0.7922 (mp0) cc_final: 0.7084 (tt0)
  outliers start: 15
  outliers final: 13
  residues processed: 106
  average time/residue: 0.2218
  time to fit residues: 31.3440
Evaluate side-chains
  106 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 ILE
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  247 GLU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  331 PHE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain A residue  589 TYR
Chi-restraints excluded: chain A residue  608 LYS
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  675 ASN
Chi-restraints excluded: chain A residue  711 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    8.9990
   chunk 36 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   chunk 64 optimal weight:    0.0770
   chunk 39 optimal weight:    0.4980
   chunk 28 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 20 optimal weight:   20.0000
   overall best weight:    0.8342

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.199390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.161314 restraints weight = 8949.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3984 rms_B_bonded: 1.83
r_work: 0.3740 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.4386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7393  Z= 0.120
  Angle     :  0.566   9.207  10174  Z= 0.298
  Chirality :  0.037   0.180   1150
  Planarity :  0.003   0.029   1116
  Dihedral  : 16.888  97.071   1532
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 18.17 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.32), residues: 737
  helix:  1.07 (0.27), residues: 388
  sheet: -1.12 (0.54), residues: 85
  loop : -1.36 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  33 
 HIS   0.002   0.001   HIS A 230 
 PHE   0.016   0.001   PHE A 478 
 TYR   0.026   0.002   TYR A 454 
 ARG   0.002   0.000   ARG A 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03926 (  311)
  hydrogen bonds       : angle       4.29195 (  883)
  covalent geometry    : bond        0.00267 ( 7393)
  covalent geometry    : angle       0.56619 (10174)

===============================================================================
Job complete
usr+sys time: 4271.94 seconds
wall clock time: 77 minutes 40.36 seconds (4660.36 seconds total)