Starting phenix.real_space_refine
on Mon Apr 28 15:51:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qat_18302/04_2025/8qat_18302.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qat_18302/04_2025/8qat_18302.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qat_18302/04_2025/8qat_18302.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qat_18302/04_2025/8qat_18302.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qat_18302/04_2025/8qat_18302.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qat_18302/04_2025/8qat_18302.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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: 4
    Type Number    sf(0)   Gaussians
     S      39      5.16       5
     C    4978      2.51       5
     N    1348      2.21       5
     O    1393      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7758
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 646
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "B"
      Number of atoms: 522
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 522
          Classifications: {'peptide': 63}
          Link IDs: {'PTRANS': 1, 'TRANS': 61}
    Chain: "C"
      Number of atoms: 4767
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 606, 4767
          Classifications: {'peptide': 606}
          Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 565}
          Chain breaks: 4
    Chain: "D"
      Number of atoms: 1823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1823
          Classifications: {'peptide': 222}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 203}
  Time building chain proxies: 5.00, per 1000 atoms: 0.64
  Number of scatterers: 7758
  At special positions: 0
  Unit cell: (145.083, 120.726, 83.661, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      39     16.00
     O    1393      8.00
     N    1348      7.00
     C    4978      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: 1.57
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1856

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 2 sheets defined
      69.2% alpha, 2.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 627 through 687
      removed outlier: 3.702A  pdb=" N   ALA A 632 " --> pdb=" O   PRO A 628 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ALA A 681 " --> pdb=" O   HIS A 677 " (cutoff:3.500A)
      removed outlier: 4.889A  pdb=" N   GLU A 682 " --> pdb=" O   LYS A 678 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   LEU A 685 " --> pdb=" O   ALA A 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 693 through 702
    Processing helix  chain 'B' and resid 628 through 689
      removed outlier: 3.832A  pdb=" N   LYS B 663 " --> pdb=" O   GLU B 659 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   TYR B 664 " --> pdb=" O   MET B 660 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   MET B 672 " --> pdb=" O   ALA B 668 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLY B 689 " --> pdb=" O   LEU B 685 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 33 through 53
      removed outlier: 3.614A  pdb=" N   LEU C  37 " --> pdb=" O   PRO C  33 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 82
    Processing helix  chain 'C' and resid 94 through 101
    Processing helix  chain 'C' and resid 104 through 117
      removed outlier: 3.511A  pdb=" N   TRP C 116 " --> pdb=" O   TRP C 112 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 120
      No H-bonds generated for 'chain 'C' and resid 118 through 120'
    Processing helix  chain 'C' and resid 122 through 141
      removed outlier: 3.789A  pdb=" N   ALA C 128 " --> pdb=" O   GLU C 124 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA C 141 " --> pdb=" O   LEU C 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 147
      removed outlier: 3.641A  pdb=" N   ARG C 147 " --> pdb=" O   PRO C 144 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 144 through 147'
    Processing helix  chain 'C' and resid 148 through 162
      removed outlier: 3.616A  pdb=" N   ARG C 152 " --> pdb=" O   HIS C 148 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 169 through 190
    Processing helix  chain 'C' and resid 193 through 198
    Processing helix  chain 'C' and resid 210 through 215
      removed outlier: 3.804A  pdb=" N   ARG C 215 " --> pdb=" O   LEU C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 216 through 220
      removed outlier: 3.744A  pdb=" N   VAL C 220 " --> pdb=" O   VAL C 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 223 through 242
      removed outlier: 3.650A  pdb=" N   GLY C 227 " --> pdb=" O   GLU C 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 255
      removed outlier: 3.862A  pdb=" N   SER C 255 " --> pdb=" O   ILE C 251 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 256 through 269
    Processing helix  chain 'C' and resid 287 through 292
    Processing helix  chain 'C' and resid 294 through 314
      removed outlier: 3.570A  pdb=" N   LEU C 299 " --> pdb=" O   PRO C 295 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   PHE C 300 " --> pdb=" O   ALA C 296 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 315 through 331
    Processing helix  chain 'C' and resid 334 through 340
      removed outlier: 4.007A  pdb=" N   HIS C 340 " --> pdb=" O   GLY C 336 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 343 through 361
    Processing helix  chain 'C' and resid 363 through 377
      removed outlier: 3.545A  pdb=" N   HIS C 377 " --> pdb=" O   PHE C 373 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 384 through 391
    Processing helix  chain 'C' and resid 396 through 412
    Processing helix  chain 'C' and resid 414 through 422
      removed outlier: 4.033A  pdb=" N   LEU C 418 " --> pdb=" O   CYS C 414 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 422 through 427
    Processing helix  chain 'C' and resid 436 through 441
      removed outlier: 3.587A  pdb=" N   VAL C 440 " --> pdb=" O   LYS C 437 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 447 through 455
    Processing helix  chain 'C' and resid 550 through 568
      removed outlier: 3.593A  pdb=" N   TYR C 554 " --> pdb=" O   ASN C 550 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 739 through 751
    Processing helix  chain 'C' and resid 756 through 772
    Processing helix  chain 'C' and resid 775 through 783
      removed outlier: 3.542A  pdb=" N   PHE C 781 " --> pdb=" O   LEU C 777 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 795 through 814
    Processing helix  chain 'C' and resid 816 through 835
      removed outlier: 3.557A  pdb=" N   LEU C 828 " --> pdb=" O   ALA C 824 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   GLY C 832 " --> pdb=" O   LEU C 828 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 915 through 945
      removed outlier: 3.654A  pdb=" N   VAL C 929 " --> pdb=" O   VAL C 925 " (cutoff:3.500A)
      Proline residue:  C 932  - end of helix
    Processing helix  chain 'D' and resid 70 through 89
    Processing helix  chain 'D' and resid 159 through 163
      removed outlier: 4.097A  pdb=" N   ARG D 162 " --> pdb=" O   ASP D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 173 through 184
      removed outlier: 3.568A  pdb=" N   VAL D 177 " --> pdb=" O   HIS D 173 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 195 through 203
    Processing helix  chain 'D' and resid 205 through 223
      removed outlier: 3.532A  pdb=" N   ARG D 223 " --> pdb=" O   VAL D 219 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 242 through 255
      removed outlier: 4.841A  pdb=" N   GLU D 248 " --> pdb=" O   SER D 244 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 378 through 379
    Processing sheet with id=AA2, first strand: chain 'D' and resid 94 through 98
      removed outlier: 4.245A  pdb=" N   GLY D 120 " --> pdb=" O   ILE D 112 " (cutoff:3.500A)
      removed outlier: 4.853A  pdb=" N   LEU D 140 " --> pdb=" O   LEU D 158 " (cutoff:3.500A)

    486 hydrogen bonds defined for protein.
    1440 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.03

  Time building geometry restraints manager: 1.97 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2051
        1.34 -     1.46: 1475
        1.46 -     1.58: 4355
        1.58 -     1.70: 1
        1.70 -     1.82: 60
  Bond restraints: 7942
  Sorted by residual:
  bond pdb=" CB  PRO D 193 "
       pdb=" CG  PRO D 193 "
    ideal  model  delta    sigma   weight residual
    1.492  1.674 -0.182 5.00e-02 4.00e+02 1.32e+01
  bond pdb=" C   VAL C 332 "
       pdb=" N   PRO C 333 "
    ideal  model  delta    sigma   weight residual
    1.337  1.380 -0.043 1.24e-02 6.50e+03 1.20e+01
  bond pdb=" C   GLY C 149 "
       pdb=" N   PRO C 150 "
    ideal  model  delta    sigma   weight residual
    1.335  1.371 -0.036 1.36e-02 5.41e+03 6.89e+00
  bond pdb=" C   PHE C 817 "
       pdb=" N   PRO C 818 "
    ideal  model  delta    sigma   weight residual
    1.335  1.362 -0.027 1.28e-02 6.10e+03 4.48e+00
  bond pdb=" CB  GLU B 682 "
       pdb=" CG  GLU B 682 "
    ideal  model  delta    sigma   weight residual
    1.520  1.575 -0.055 3.00e-02 1.11e+03 3.35e+00
  ... (remaining 7937 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.66: 10623
        3.66 -     7.32: 121
        7.32 -    10.98: 21
       10.98 -    14.65: 2
       14.65 -    18.31: 1
  Bond angle restraints: 10768
  Sorted by residual:
  angle pdb=" CA  PRO D 193 "
        pdb=" N   PRO D 193 "
        pdb=" CD  PRO D 193 "
      ideal   model   delta    sigma   weight residual
     112.00   93.69   18.31 1.40e+00 5.10e-01 1.71e+02
  angle pdb=" N   PRO D 193 "
        pdb=" CA  PRO D 193 "
        pdb=" C   PRO D 193 "
      ideal   model   delta    sigma   weight residual
     110.40  120.13   -9.73 1.61e+00 3.86e-01 3.65e+01
  angle pdb=" N   SER C 270 "
        pdb=" CA  SER C 270 "
        pdb=" C   SER C 270 "
      ideal   model   delta    sigma   weight residual
     114.75  108.02    6.73 1.26e+00 6.30e-01 2.85e+01
  angle pdb=" CA  GLN D 227 "
        pdb=" CB  GLN D 227 "
        pdb=" CG  GLN D 227 "
      ideal   model   delta    sigma   weight residual
     114.10  124.73  -10.63 2.00e+00 2.50e-01 2.82e+01
  angle pdb=" N   HIS C  43 "
        pdb=" CA  HIS C  43 "
        pdb=" CB  HIS C  43 "
      ideal   model   delta    sigma   weight residual
     110.12  117.45   -7.33 1.47e+00 4.63e-01 2.49e+01
  ... (remaining 10763 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 4215
       17.81 -    35.61: 456
       35.61 -    53.42: 132
       53.42 -    71.22: 13
       71.22 -    89.03: 11
  Dihedral angle restraints: 4827
    sinusoidal: 1977
      harmonic: 2850
  Sorted by residual:
  dihedral pdb=" CA  VAL C 313 "
           pdb=" C   VAL C 313 "
           pdb=" N   ALA C 314 "
           pdb=" CA  ALA C 314 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.26  -23.74     0      5.00e+00 4.00e-02 2.25e+01
  dihedral pdb=" CA  GLU C 933 "
           pdb=" C   GLU C 933 "
           pdb=" N   PHE C 934 "
           pdb=" CA  PHE C 934 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.01   22.99     0      5.00e+00 4.00e-02 2.11e+01
  dihedral pdb=" CA  GLU C 415 "
           pdb=" C   GLU C 415 "
           pdb=" N   ASP C 416 "
           pdb=" CA  ASP C 416 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.33  -21.67     0      5.00e+00 4.00e-02 1.88e+01
  ... (remaining 4824 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 1081
       0.090 -    0.180: 117
       0.180 -    0.270: 2
       0.270 -    0.360: 1
       0.360 -    0.450: 1
  Chirality restraints: 1202
  Sorted by residual:
  chirality pdb=" CB  VAL C  39 "
            pdb=" CA  VAL C  39 "
            pdb=" CG1 VAL C  39 "
            pdb=" CG2 VAL C  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.18   -0.45 2.00e-01 2.50e+01 5.07e+00
  chirality pdb=" CA  PRO D 193 "
            pdb=" N   PRO D 193 "
            pdb=" C   PRO D 193 "
            pdb=" CB  PRO D 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.41    0.30 2.00e-01 2.50e+01 2.30e+00
  chirality pdb=" CB  VAL C  48 "
            pdb=" CA  VAL C  48 "
            pdb=" CG1 VAL C  48 "
            pdb=" CG2 VAL C  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.26 2.00e-01 2.50e+01 1.75e+00
  ... (remaining 1199 not shown)

  Planarity restraints: 1382
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D 192 "    0.088 5.00e-02 4.00e+02   1.18e-01 2.25e+01
        pdb=" N   PRO D 193 "   -0.204 5.00e-02 4.00e+02
        pdb=" CA  PRO D 193 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO D 193 "    0.065 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO D 193 "   -0.019 2.00e-02 2.50e+03   3.77e-02 1.42e+01
        pdb=" C   PRO D 193 "    0.065 2.00e-02 2.50e+03
        pdb=" O   PRO D 193 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   LEU D 194 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 817 "   -0.020 2.00e-02 2.50e+03   2.40e-02 1.01e+01
        pdb=" CG  PHE C 817 "    0.055 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 817 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 817 "   -0.018 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 817 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 817 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 817 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1379 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 385
        2.73 -     3.28: 7523
        3.28 -     3.82: 12656
        3.82 -     4.36: 15120
        4.36 -     4.90: 25404
  Nonbonded interactions: 61088
  Sorted by model distance:
  nonbonded pdb=" O   VAL C  69 "
            pdb=" OG1 THR C  73 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" O   ARG A 699 "
            pdb=" OG1 THR A 702 "
     model   vdw
     2.348 3.040
  nonbonded pdb=" OG  SER D  99 "
            pdb=" OD2 ASP D 232 "
     model   vdw
     2.366 3.040
  nonbonded pdb=" O   TYR D  74 "
            pdb=" OG  SER D  78 "
     model   vdw
     2.367 3.040
  nonbonded pdb=" O   LEU C 339 "
            pdb=" NH2 ARG C 391 "
     model   vdw
     2.368 3.120
  ... (remaining 61083 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:             1.250
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.650
  Find NCS groups from input model:        0.060
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
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   0.182   7942  Z= 0.247
  Angle     :  1.029  18.308  10768  Z= 0.569
  Chirality :  0.053   0.450   1202
  Planarity :  0.009   0.118   1382
  Dihedral  : 16.201  89.031   2971
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.89 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  : 15.45 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.24), residues: 954
  helix: -1.35 (0.17), residues: 626
  sheet: -2.60 (0.84), residues: 30
  loop : -0.51 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.004   TRP C  44 
 HIS   0.020   0.002   HIS A 677 
 PHE   0.055   0.003   PHE C 817 
 TYR   0.011   0.002   TYR A 651 
 ARG   0.007   0.001   ARG C 570 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17728 (  486)
  hydrogen bonds       : angle       6.59731 ( 1440)
  covalent geometry    : bond        0.00536 ( 7942)
  covalent geometry    : angle       1.02853 (10768)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 142
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  671 ASN cc_start: 0.7331 (m110) cc_final: 0.7085 (m110)
REVERT: B  652 GLU cc_start: 0.8596 (tp30) cc_final: 0.8386 (tp30)
REVERT: C   40 PHE cc_start: 0.8180 (t80) cc_final: 0.7974 (t80)
REVERT: C   43 HIS cc_start: 0.8050 (m90) cc_final: 0.7060 (m-70)
REVERT: C   76 MET cc_start: 0.8233 (mtp) cc_final: 0.7448 (mmp)
REVERT: C  112 TRP cc_start: 0.8685 (t60) cc_final: 0.8453 (t60)
REVERT: C  433 MET cc_start: 0.7556 (pmm) cc_final: 0.7111 (pmm)
REVERT: C  436 GLN cc_start: 0.7760 (tt0) cc_final: 0.7530 (tt0)
  outliers start: 3
  outliers final: 1
  residues processed: 144
  average time/residue: 0.2399
  time to fit residues: 46.1221
Evaluate side-chains
  121 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  318 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0070
   chunk 38 optimal weight:    5.9990
   chunk 74 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   chunk 86 optimal weight:    2.9990
   overall best weight:    0.9000

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

Flipped N/Q/H residues before XYZ refinement:
B 636 GLN
C 143 GLN
** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 308 ASN
** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 751 ASN
** C 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 798 GLN
** D  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 207 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.152571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.107332 restraints weight = 10210.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 3.11
r_work: 0.3391 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.1358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   7942  Z= 0.139
  Angle     :  0.604  11.495  10768  Z= 0.310
  Chirality :  0.041   0.155   1202
  Planarity :  0.006   0.056   1382
  Dihedral  :  4.652  24.694   1057
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.68 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 15.80 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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:  0.35 (0.27), residues: 954
  helix:  0.60 (0.20), residues: 636
  sheet: -2.37 (0.75), residues: 30
  loop : -0.03 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 669 
 HIS   0.007   0.001   HIS A 677 
 PHE   0.012   0.001   PHE C  99 
 TYR   0.015   0.001   TYR C 827 
 ARG   0.003   0.000   ARG A 640 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04411 (  486)
  hydrogen bonds       : angle       4.26429 ( 1440)
  covalent geometry    : bond        0.00306 ( 7942)
  covalent geometry    : angle       0.60370 (10768)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
REVERT: A  638 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8329 (pp30)
REVERT: A  639 GLU cc_start: 0.8598 (tp30) cc_final: 0.8278 (tp30)
REVERT: A  642 ARG cc_start: 0.7851 (tmm-80) cc_final: 0.7650 (ttt-90)
REVERT: A  671 ASN cc_start: 0.7448 (m110) cc_final: 0.7024 (m110)
REVERT: A  698 GLN cc_start: 0.6853 (mm-40) cc_final: 0.6633 (mm-40)
REVERT: B  656 SER cc_start: 0.7640 (m) cc_final: 0.7358 (p)
REVERT: C   37 LEU cc_start: 0.8492 (mm) cc_final: 0.8198 (tp)
REVERT: C   43 HIS cc_start: 0.8500 (m90) cc_final: 0.7864 (m-70)
  outliers start: 19
  outliers final: 8
  residues processed: 134
  average time/residue: 0.1996
  time to fit residues: 36.2431
Evaluate side-chains
  124 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 116
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain C residue  325 TYR
Chi-restraints excluded: chain C residue  326 ILE
Chi-restraints excluded: chain C residue  427 VAL
Chi-restraints excluded: chain C residue  792 SER
Chi-restraints excluded: chain C residue  813 SER
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  184 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 81 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 71 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   chunk 73 optimal weight:    0.3980
   chunk 62 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 636 GLN
** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 784 ASN ** 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 = 0.4132 r_free = 0.4132 target = 0.152534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.107890 restraints weight = 10323.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 2.96
r_work: 0.3397 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.1674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7942  Z= 0.116
  Angle     :  0.560   8.195  10768  Z= 0.282
  Chirality :  0.041   0.167   1202
  Planarity :  0.005   0.052   1382
  Dihedral  :  4.293  22.280   1056
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.57 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 18.28 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.28), residues: 954
  helix:  1.37 (0.21), residues: 635
  sheet: -1.98 (0.78), residues: 30
  loop :  0.15 (0.38), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 669 
 HIS   0.006   0.001   HIS A 677 
 PHE   0.015   0.001   PHE D 209 
 TYR   0.010   0.001   TYR A 651 
 ARG   0.004   0.000   ARG D 223 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03844 (  486)
  hydrogen bonds       : angle       3.97407 ( 1440)
  covalent geometry    : bond        0.00252 ( 7942)
  covalent geometry    : angle       0.55986 (10768)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.826 
Fit side-chains
   revert: symmetry clash
REVERT: A  639 GLU cc_start: 0.8651 (tp30) cc_final: 0.8401 (tp30)
REVERT: A  642 ARG cc_start: 0.7854 (tmm-80) cc_final: 0.7649 (ttt-90)
REVERT: A  671 ASN cc_start: 0.7446 (m110) cc_final: 0.6990 (m110)
REVERT: A  698 GLN cc_start: 0.6964 (mm-40) cc_final: 0.6741 (mm-40)
REVERT: B  656 SER cc_start: 0.7619 (m) cc_final: 0.7361 (p)
REVERT: C   37 LEU cc_start: 0.8607 (mm) cc_final: 0.8344 (tp)
REVERT: C   43 HIS cc_start: 0.8617 (m90) cc_final: 0.8140 (m-70)
REVERT: C   76 MET cc_start: 0.8289 (mtp) cc_final: 0.7445 (mmp)
REVERT: C  787 MET cc_start: 0.8523 (mtp) cc_final: 0.8315 (ttt)
  outliers start: 16
  outliers final: 10
  residues processed: 136
  average time/residue: 0.1956
  time to fit residues: 36.2287
Evaluate side-chains
  125 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  132 LYS
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  326 ILE
Chi-restraints excluded: chain C residue  427 VAL
Chi-restraints excluded: chain C residue  813 SER
Chi-restraints excluded: chain D residue  179 MET
Chi-restraints excluded: chain D residue  184 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 58 optimal weight:    0.0030
   chunk 93 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.9392

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

Flipped N/Q/H residues before XYZ refinement:
B 636 GLN
** C 784 ASN ** 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 = 0.4118 r_free = 0.4118 target = 0.151210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.106003 restraints weight = 10285.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 3.00
r_work: 0.3392 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7942  Z= 0.123
  Angle     :  0.556  12.670  10768  Z= 0.277
  Chirality :  0.041   0.182   1202
  Planarity :  0.005   0.050   1382
  Dihedral  :  4.097  19.990   1056
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.57 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 17.10 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.28), residues: 954
  helix:  1.71 (0.21), residues: 634
  sheet: -1.55 (0.80), residues: 30
  loop :  0.22 (0.39), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 669 
 HIS   0.005   0.001   HIS A 677 
 PHE   0.015   0.001   PHE D 209 
 TYR   0.016   0.001   TYR C 827 
 ARG   0.006   0.000   ARG A 697 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03631 (  486)
  hydrogen bonds       : angle       3.90260 ( 1440)
  covalent geometry    : bond        0.00276 ( 7942)
  covalent geometry    : angle       0.55604 (10768)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  671 ASN cc_start: 0.7470 (m110) cc_final: 0.6998 (m110)
REVERT: A  698 GLN cc_start: 0.7018 (mm-40) cc_final: 0.6791 (mm-40)
REVERT: B  642 ARG cc_start: 0.7947 (tmm160) cc_final: 0.7628 (tmm-80)
REVERT: B  653 LYS cc_start: 0.8850 (mptt) cc_final: 0.8584 (mptt)
REVERT: B  656 SER cc_start: 0.7584 (m) cc_final: 0.7316 (p)
REVERT: B  660 MET cc_start: 0.7315 (tmm) cc_final: 0.6653 (mmm)
REVERT: C   43 HIS cc_start: 0.8652 (m90) cc_final: 0.8099 (m-70)
REVERT: C   76 MET cc_start: 0.8343 (mtp) cc_final: 0.7412 (mmp)
  outliers start: 23
  outliers final: 17
  residues processed: 138
  average time/residue: 0.2270
  time to fit residues: 42.5614
Evaluate side-chains
  134 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  132 LYS
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  326 ILE
Chi-restraints excluded: chain C residue  427 VAL
Chi-restraints excluded: chain C residue  433 MET
Chi-restraints excluded: chain C residue  565 CYS
Chi-restraints excluded: chain C residue  766 LEU
Chi-restraints excluded: chain C residue  792 SER
Chi-restraints excluded: chain C residue  813 SER
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  130 ASP
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  230 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0270
   chunk 19 optimal weight:    6.9990
   chunk 70 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 7 optimal weight:   20.0000
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.7240

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

Flipped N/Q/H residues before XYZ refinement:
B 636 GLN
** C  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 377 HIS ** 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 = 0.4127 r_free = 0.4127 target = 0.151943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.106878 restraints weight = 10261.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 2.97
r_work: 0.3405 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.2083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7942  Z= 0.110
  Angle     :  0.533  11.391  10768  Z= 0.265
  Chirality :  0.040   0.180   1202
  Planarity :  0.005   0.046   1382
  Dihedral  :  3.938  19.302   1056
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.47 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 16.63 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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:  2.00 (0.28), residues: 954
  helix:  1.98 (0.21), residues: 634
  sheet: -1.26 (0.83), residues: 30
  loop :  0.28 (0.39), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 669 
 HIS   0.004   0.001   HIS A 677 
 PHE   0.013   0.001   PHE D 209 
 TYR   0.015   0.001   TYR C 827 
 ARG   0.008   0.000   ARG A 697 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03333 (  486)
  hydrogen bonds       : angle       3.74888 ( 1440)
  covalent geometry    : bond        0.00243 ( 7942)
  covalent geometry    : angle       0.53286 (10768)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
REVERT: A  639 GLU cc_start: 0.8601 (tp30) cc_final: 0.8146 (tp30)
REVERT: A  671 ASN cc_start: 0.7471 (m110) cc_final: 0.7014 (m110)
REVERT: A  698 GLN cc_start: 0.7048 (mm-40) cc_final: 0.6789 (mm-40)
REVERT: B  642 ARG cc_start: 0.7964 (tmm160) cc_final: 0.7652 (tmm-80)
REVERT: B  656 SER cc_start: 0.7602 (m) cc_final: 0.7342 (p)
REVERT: C   43 HIS cc_start: 0.8679 (m90) cc_final: 0.8111 (m-70)
  outliers start: 26
  outliers final: 15
  residues processed: 141
  average time/residue: 0.2304
  time to fit residues: 43.7922
Evaluate side-chains
  131 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  326 ILE
Chi-restraints excluded: chain C residue  427 VAL
Chi-restraints excluded: chain C residue  433 MET
Chi-restraints excluded: chain C residue  565 CYS
Chi-restraints excluded: chain C residue  745 LEU
Chi-restraints excluded: chain C residue  766 LEU
Chi-restraints excluded: chain C residue  813 SER
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  130 ASP
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  230 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   chunk 72 optimal weight:    0.9980
   chunk 89 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 57 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 92 optimal weight:   20.0000
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 636 GLN
** C  43 HIS ** 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 = 0.4085 r_free = 0.4085 target = 0.148123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.102965 restraints weight = 10287.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 2.89
r_work: 0.3351 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7942  Z= 0.174
  Angle     :  0.598  13.479  10768  Z= 0.295
  Chirality :  0.043   0.170   1202
  Planarity :  0.005   0.058   1382
  Dihedral  :  4.044  19.388   1056
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.20 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 16.04 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.28), residues: 954
  helix:  1.86 (0.21), residues: 634
  sheet: -1.46 (0.83), residues: 30
  loop :  0.26 (0.40), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 669 
 HIS   0.007   0.001   HIS D 148 
 PHE   0.015   0.002   PHE C 761 
 TYR   0.016   0.001   TYR D  77 
 ARG   0.006   0.000   ARG D 162 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03837 (  486)
  hydrogen bonds       : angle       3.88892 ( 1440)
  covalent geometry    : bond        0.00411 ( 7942)
  covalent geometry    : angle       0.59844 (10768)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 1.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  638 GLN cc_start: 0.8601 (tm-30) cc_final: 0.7815 (mt0)
REVERT: A  642 ARG cc_start: 0.8142 (ttt-90) cc_final: 0.7931 (tmm-80)
REVERT: A  671 ASN cc_start: 0.7548 (m110) cc_final: 0.7098 (m110)
REVERT: A  698 GLN cc_start: 0.7136 (mm-40) cc_final: 0.6872 (mm-40)
REVERT: B  642 ARG cc_start: 0.7965 (tmm160) cc_final: 0.7675 (tmm-80)
REVERT: B  656 SER cc_start: 0.7648 (m) cc_final: 0.7360 (p)
REVERT: B  660 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6678 (mmm)
REVERT: B  682 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7703 (mm-30)
REVERT: C   43 HIS cc_start: 0.8782 (m90) cc_final: 0.8168 (m-70)
  outliers start: 32
  outliers final: 26
  residues processed: 135
  average time/residue: 0.1985
  time to fit residues: 36.5291
Evaluate side-chains
  138 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain B residue  630 ILE
Chi-restraints excluded: chain B residue  660 MET
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  132 LYS
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  222 LEU
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  326 ILE
Chi-restraints excluded: chain C residue  415 GLU
Chi-restraints excluded: chain C residue  427 VAL
Chi-restraints excluded: chain C residue  433 MET
Chi-restraints excluded: chain C residue  546 GLU
Chi-restraints excluded: chain C residue  565 CYS
Chi-restraints excluded: chain C residue  745 LEU
Chi-restraints excluded: chain C residue  761 PHE
Chi-restraints excluded: chain C residue  766 LEU
Chi-restraints excluded: chain C residue  792 SER
Chi-restraints excluded: chain C residue  813 SER
Chi-restraints excluded: chain D residue   76 GLU
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  130 ASP
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  230 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 67 optimal weight:    4.9990
   chunk 86 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0670
   overall best weight:    0.7720

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

Flipped N/Q/H residues before XYZ refinement:
B 636 GLN
** C  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.150578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.105576 restraints weight = 10287.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 2.92
r_work: 0.3389 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7942  Z= 0.115
  Angle     :  0.554  13.388  10768  Z= 0.272
  Chirality :  0.041   0.169   1202
  Planarity :  0.005   0.053   1382
  Dihedral  :  3.915  19.156   1056
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.78 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 17.81 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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:  2.00 (0.28), residues: 954
  helix:  1.98 (0.21), residues: 640
  sheet: -1.26 (0.85), residues: 30
  loop :  0.21 (0.40), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 669 
 HIS   0.003   0.001   HIS D 148 
 PHE   0.022   0.001   PHE C  99 
 TYR   0.012   0.001   TYR C 827 
 ARG   0.006   0.000   ARG C 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03371 (  486)
  hydrogen bonds       : angle       3.74201 ( 1440)
  covalent geometry    : bond        0.00260 ( 7942)
  covalent geometry    : angle       0.55371 (10768)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  671 ASN cc_start: 0.7470 (m110) cc_final: 0.6998 (m110)
REVERT: A  698 GLN cc_start: 0.7077 (mm-40) cc_final: 0.6863 (mm-40)
REVERT: B  642 ARG cc_start: 0.7955 (tmm160) cc_final: 0.7668 (tmm-80)
REVERT: B  656 SER cc_start: 0.7612 (m) cc_final: 0.7343 (p)
REVERT: C   43 HIS cc_start: 0.8791 (m90) cc_final: 0.8134 (m-70)
  outliers start: 23
  outliers final: 21
  residues processed: 137
  average time/residue: 0.2151
  time to fit residues: 39.8439
Evaluate side-chains
  134 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  630 ILE
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  132 LYS
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  326 ILE
Chi-restraints excluded: chain C residue  427 VAL
Chi-restraints excluded: chain C residue  433 MET
Chi-restraints excluded: chain C residue  565 CYS
Chi-restraints excluded: chain C residue  745 LEU
Chi-restraints excluded: chain C residue  766 LEU
Chi-restraints excluded: chain C residue  792 SER
Chi-restraints excluded: chain C residue  813 SER
Chi-restraints excluded: chain D residue   76 GLU
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  130 ASP
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  230 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   chunk 45 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 86 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
B 636 GLN
** C  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  72 HIS ** 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 = 0.4107 r_free = 0.4107 target = 0.150093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.105484 restraints weight = 10313.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 3.11
r_work: 0.3357 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7942  Z= 0.129
  Angle     :  0.568  12.461  10768  Z= 0.279
  Chirality :  0.041   0.174   1202
  Planarity :  0.005   0.054   1382
  Dihedral  :  3.917  18.819   1056
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.89 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 17.45 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.28), residues: 954
  helix:  1.96 (0.21), residues: 641
  sheet: -1.24 (0.85), residues: 30
  loop :  0.20 (0.40), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 669 
 HIS   0.004   0.001   HIS D 148 
 PHE   0.020   0.001   PHE B 644 
 TYR   0.011   0.001   TYR C 554 
 ARG   0.003   0.000   ARG A 642 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03418 (  486)
  hydrogen bonds       : angle       3.75813 ( 1440)
  covalent geometry    : bond        0.00299 ( 7942)
  covalent geometry    : angle       0.56790 (10768)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
REVERT: A  671 ASN cc_start: 0.7495 (m110) cc_final: 0.7029 (m110)
REVERT: A  698 GLN cc_start: 0.7131 (mm-40) cc_final: 0.6912 (mm-40)
REVERT: B  642 ARG cc_start: 0.7968 (tmm160) cc_final: 0.7691 (tmm-80)
REVERT: C   43 HIS cc_start: 0.8817 (m90) cc_final: 0.8212 (m-70)
REVERT: C   76 MET cc_start: 0.8313 (mtp) cc_final: 0.7385 (mmp)
REVERT: C  415 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8162 (tp30)
REVERT: D  147 PHE cc_start: 0.8440 (t80) cc_final: 0.8236 (t80)
REVERT: D  157 GLU cc_start: 0.8244 (tt0) cc_final: 0.7902 (tt0)
  outliers start: 28
  outliers final: 24
  residues processed: 135
  average time/residue: 0.2039
  time to fit residues: 37.3731
Evaluate side-chains
  135 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  630 ILE
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  132 LYS
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  238 MET
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  326 ILE
Chi-restraints excluded: chain C residue  415 GLU
Chi-restraints excluded: chain C residue  427 VAL
Chi-restraints excluded: chain C residue  433 MET
Chi-restraints excluded: chain C residue  565 CYS
Chi-restraints excluded: chain C residue  745 LEU
Chi-restraints excluded: chain C residue  761 PHE
Chi-restraints excluded: chain C residue  766 LEU
Chi-restraints excluded: chain C residue  792 SER
Chi-restraints excluded: chain C residue  813 SER
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain D residue  130 ASP
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  230 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 69 optimal weight:    9.9990
   chunk 89 optimal weight:    0.9980
   chunk 94 optimal weight:    0.0970
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 636 GLN
C  43 HIS
C  72 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.151174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.107090 restraints weight = 10442.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 3.07
r_work: 0.3365 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.2460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7942  Z= 0.115
  Angle     :  0.570  15.391  10768  Z= 0.277
  Chirality :  0.041   0.240   1202
  Planarity :  0.005   0.052   1382
  Dihedral  :  3.836  17.894   1056
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.78 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 17.57 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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:  2.04 (0.28), residues: 954
  helix:  2.01 (0.21), residues: 641
  sheet: -1.15 (0.85), residues: 30
  loop :  0.21 (0.40), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 669 
 HIS   0.003   0.001   HIS D 148 
 PHE   0.024   0.001   PHE C  99 
 TYR   0.009   0.001   TYR C 554 
 ARG   0.005   0.000   ARG A 642 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03272 (  486)
  hydrogen bonds       : angle       3.72517 ( 1440)
  covalent geometry    : bond        0.00262 ( 7942)
  covalent geometry    : angle       0.56975 (10768)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 1.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  671 ASN cc_start: 0.7469 (m110) cc_final: 0.6992 (m110)
REVERT: A  698 GLN cc_start: 0.7147 (mm-40) cc_final: 0.6900 (mm-40)
REVERT: B  642 ARG cc_start: 0.7964 (tmm160) cc_final: 0.7687 (tmm-80)
REVERT: C   76 MET cc_start: 0.8324 (mtp) cc_final: 0.7406 (mmp)
  outliers start: 29
  outliers final: 23
  residues processed: 133
  average time/residue: 0.3368
  time to fit residues: 65.3727
Evaluate side-chains
  133 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 2.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  136 MET
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  326 ILE
Chi-restraints excluded: chain C residue  343 SER
Chi-restraints excluded: chain C residue  415 GLU
Chi-restraints excluded: chain C residue  427 VAL
Chi-restraints excluded: chain C residue  433 MET
Chi-restraints excluded: chain C residue  565 CYS
Chi-restraints excluded: chain C residue  745 LEU
Chi-restraints excluded: chain C residue  761 PHE
Chi-restraints excluded: chain C residue  766 LEU
Chi-restraints excluded: chain C residue  792 SER
Chi-restraints excluded: chain C residue  813 SER
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  130 ASP
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  230 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 29 optimal weight:   50.0000
   chunk 77 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0980
   chunk 2 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0010
   chunk 25 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 636 GLN
C  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.151880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.108450 restraints weight = 10316.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 2.95
r_work: 0.3400 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7942  Z= 0.112
  Angle     :  0.587  15.306  10768  Z= 0.284
  Chirality :  0.042   0.306   1202
  Planarity :  0.005   0.051   1382
  Dihedral  :  3.805  17.799   1056
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.68 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 18.75 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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:  2.10 (0.28), residues: 954
  helix:  2.06 (0.21), residues: 641
  sheet: -1.09 (0.84), residues: 30
  loop :  0.23 (0.40), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 669 
 HIS   0.003   0.001   HIS A 677 
 PHE   0.013   0.001   PHE B 644 
 TYR   0.010   0.001   TYR C 554 
 ARG   0.010   0.000   ARG A 642 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03203 (  486)
  hydrogen bonds       : angle       3.71736 ( 1440)
  covalent geometry    : bond        0.00251 ( 7942)
  covalent geometry    : angle       0.58749 (10768)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
REVERT: A  671 ASN cc_start: 0.7470 (m110) cc_final: 0.7011 (m110)
REVERT: A  698 GLN cc_start: 0.7052 (mm-40) cc_final: 0.6805 (mm-40)
REVERT: B  642 ARG cc_start: 0.7965 (tmm160) cc_final: 0.7686 (tmm-80)
REVERT: C   43 HIS cc_start: 0.8880 (m-70) cc_final: 0.8489 (m-70)
REVERT: D  157 GLU cc_start: 0.8152 (tt0) cc_final: 0.7881 (tt0)
  outliers start: 21
  outliers final: 18
  residues processed: 131
  average time/residue: 0.2064
  time to fit residues: 36.9474
Evaluate side-chains
  128 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  136 MET
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  343 SER
Chi-restraints excluded: chain C residue  427 VAL
Chi-restraints excluded: chain C residue  433 MET
Chi-restraints excluded: chain C residue  565 CYS
Chi-restraints excluded: chain C residue  745 LEU
Chi-restraints excluded: chain C residue  761 PHE
Chi-restraints excluded: chain C residue  766 LEU
Chi-restraints excluded: chain C residue  792 SER
Chi-restraints excluded: chain C residue  813 SER
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  130 ASP
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  188 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 636 GLN
C  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.150654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.107261 restraints weight = 10238.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 2.92
r_work: 0.3383 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7942  Z= 0.126
  Angle     :  0.605  14.983  10768  Z= 0.293
  Chirality :  0.042   0.291   1202
  Planarity :  0.005   0.062   1382
  Dihedral  :  3.841  17.650   1056
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.99 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 18.51 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    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:  2.00 (0.28), residues: 954
  helix:  1.97 (0.21), residues: 641
  sheet: -1.09 (0.85), residues: 30
  loop :  0.20 (0.40), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 669 
 HIS   0.004   0.001   HIS D 148 
 PHE   0.024   0.001   PHE C  99 
 TYR   0.011   0.001   TYR C 554 
 ARG   0.009   0.000   ARG A 642 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03309 (  486)
  hydrogen bonds       : angle       3.74679 ( 1440)
  covalent geometry    : bond        0.00289 ( 7942)
  covalent geometry    : angle       0.60488 (10768)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6115.19 seconds
wall clock time: 109 minutes 25.62 seconds (6565.62 seconds total)