Starting phenix.real_space_refine
on Wed Sep 17 04:48:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9r6o_53679/09_2025/9r6o_53679.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9r6o_53679/09_2025/9r6o_53679.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9r6o_53679/09_2025/9r6o_53679.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9r6o_53679/09_2025/9r6o_53679.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9r6o_53679/09_2025/9r6o_53679.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9r6o_53679/09_2025/9r6o_53679.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.007
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      35      5.16       5
     C    2707      2.51       5
     N     697      2.21       5
     O     810      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4249
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2125
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2125
          Classifications: {'peptide': 264}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 252}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2082
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2082
          Classifications: {'peptide': 273}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 257}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.32, per 1000 atoms: 0.31
  Number of scatterers: 4249
  At special positions: 0
  Unit cell: (84.68, 90.48, 83.52, 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      35     16.00
     O     810      8.00
     N     697      7.00
     C    2707      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  21 " - pdb=" SG  CYS A 165 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 160 " - pdb=" SG  CYS A 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 172 " - pdb=" SG  CYS A 252 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 331 " - pdb=" SG  CYS B 356 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 374 " - pdb=" SG  CYS B 427 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 386 " - pdb=" SG  CYS B 601 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 473 " - pdb=" SG  CYS B 548 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 481 " - pdb=" SG  CYS B 497 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 483 " - pdb=" SG  CYS B 563 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 488 " - pdb=" SG  CYS B 516 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 506 " - pdb=" SG  CYS B 518 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 520 " - pdb=" SG  CYS B 535 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 558 " - pdb=" SG  CYS B 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 578 " - pdb=" SG  CYS B 584 " distance=2.03

  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
  Links applied
    NAG-ASN
      " NAG A1401 " - " ASN A 133 "
      " NAG A1402 " - " ASN A 198 "
      " NAG B1401 " - " ASN B 437 "
  Time building additional restraints: 0.31
  Conformation dependent library (CDL) restraints added in 131.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  998

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 13 sheets defined
      12.1% alpha, 33.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 89 through 92
    Processing helix  chain 'B' and resid 332 through 338
      removed outlier: 3.532A  pdb=" N   TRP B 336 " --> pdb=" O   ASP B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 367
    Processing helix  chain 'B' and resid 378 through 383
    Processing helix  chain 'B' and resid 398 through 406
      removed outlier: 4.950A  pdb=" N   VAL B 403 " --> pdb=" O   SER B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 417
    Processing helix  chain 'B' and resid 436 through 438
      No H-bonds generated for 'chain 'B' and resid 436 through 438'
    Processing helix  chain 'B' and resid 446 through 452
      removed outlier: 3.748A  pdb=" N   ARG B 450 " --> pdb=" O   SER B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 459
      removed outlier: 4.352A  pdb=" N   PHE B 459 " --> pdb=" O   ASN B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 530 through 534
      removed outlier: 4.034A  pdb=" N   THR B 534 " --> pdb=" O   ASN B 531 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 568
      No H-bonds generated for 'chain 'B' and resid 566 through 568'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27
    Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36
      removed outlier: 4.093A  pdb=" N   SER A  35 " --> pdb=" O   ASN A  77 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 64
      removed outlier: 3.683A  pdb=" N   LEU A  62 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 68 through 69
      removed outlier: 4.610A  pdb=" N   GLU A 259 " --> pdb=" O   LYS A 108 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LYS A 108 " --> pdb=" O   GLU A 259 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   GLY A 102 " --> pdb=" O   LEU A 265 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA A 105 " --> pdb=" O   PHE A 210 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   HIS A 211 " --> pdb=" O   TYR A 222 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   TYR A 213 " --> pdb=" O   TYR A 220 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   PHE A 219 " --> pdb=" O   LYS A 235 " (cutoff:3.500A)
      removed outlier: 5.321A  pdb=" N   LYS A 235 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   ALA A 221 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82
      removed outlier: 6.711A  pdb=" N   THR A 170 " --> pdb=" O   THR A 251 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 97 through 98
      removed outlier: 3.723A  pdb=" N   SER A  97 " --> pdb=" O   TYR A 245 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL A 139 " --> pdb=" O   SER A 158 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 97 through 98
      removed outlier: 3.723A  pdb=" N   SER A  97 " --> pdb=" O   TYR A 245 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL A 139 " --> pdb=" O   SER A 158 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   GLY A 153 " --> pdb=" O   TYR A 201 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ILE A 157 " --> pdb=" O   ARG A 197 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 113 through 114
    Processing sheet with id=AA9, first strand: chain 'B' and resid 349 through 353
      removed outlier: 7.190A  pdb=" N   PHE B 387 " --> pdb=" O   VAL B 595 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   VAL B 595 " --> pdb=" O   PHE B 387 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 349 through 353
      removed outlier: 7.190A  pdb=" N   PHE B 387 " --> pdb=" O   VAL B 595 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   VAL B 595 " --> pdb=" O   PHE B 387 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 466 through 470
    Processing sheet with id=AB3, first strand: chain 'B' and resid 473 through 475
      removed outlier: 4.318A  pdb=" N   CYS B 473 " --> pdb=" O   VAL B 540 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 552 through 553

    142 hydrogen bonds defined for protein.
    342 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.60

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1336
        1.34 -     1.46: 1164
        1.46 -     1.58: 1822
        1.58 -     1.70: 0
        1.70 -     1.82: 41
  Bond restraints: 4363
  Sorted by residual:
  bond pdb=" N   VAL A 159 "
       pdb=" CA  VAL A 159 "
    ideal  model  delta    sigma   weight residual
    1.474  1.457  0.018 1.57e-02 4.06e+03 1.26e+00
  bond pdb=" N   GLU A 141 "
       pdb=" CA  GLU A 141 "
    ideal  model  delta    sigma   weight residual
    1.454  1.443  0.011 1.30e-02 5.92e+03 7.26e-01
  bond pdb=" CB  PHE A 270 "
       pdb=" CG  PHE A 270 "
    ideal  model  delta    sigma   weight residual
    1.502  1.485  0.017 2.30e-02 1.89e+03 5.74e-01
  bond pdb=" C   ASP A  42 "
       pdb=" N   VAL A  43 "
    ideal  model  delta    sigma   weight residual
    1.335  1.328  0.006 9.00e-03 1.23e+04 5.20e-01
  bond pdb=" CA  CYS B 386 "
       pdb=" CB  CYS B 386 "
    ideal  model  delta    sigma   weight residual
    1.535  1.526  0.009 1.32e-02 5.74e+03 4.89e-01
  ... (remaining 4358 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 5802
        1.47 -     2.94: 127
        2.94 -     4.41: 15
        4.41 -     5.88: 2
        5.88 -     7.35: 1
  Bond angle restraints: 5947
  Sorted by residual:
  angle pdb=" N   VAL A  43 "
        pdb=" CA  VAL A  43 "
        pdb=" C   VAL A  43 "
      ideal   model   delta    sigma   weight residual
     113.20  109.20    4.00 9.60e-01 1.09e+00 1.73e+01
  angle pdb=" CA  VAL A 159 "
        pdb=" C   VAL A 159 "
        pdb=" O   VAL A 159 "
      ideal   model   delta    sigma   weight residual
     122.63  120.72    1.91 8.70e-01 1.32e+00 4.83e+00
  angle pdb=" N   CYS B 386 "
        pdb=" CA  CYS B 386 "
        pdb=" C   CYS B 386 "
      ideal   model   delta    sigma   weight residual
     108.34  111.11   -2.77 1.31e+00 5.83e-01 4.46e+00
  angle pdb=" CA  LEU B 592 "
        pdb=" CB  LEU B 592 "
        pdb=" CG  LEU B 592 "
      ideal   model   delta    sigma   weight residual
     116.30  108.95    7.35 3.50e+00 8.16e-02 4.41e+00
  angle pdb=" C   VAL A 159 "
        pdb=" CA  VAL A 159 "
        pdb=" CB  VAL A 159 "
      ideal   model   delta    sigma   weight residual
     113.22  110.90    2.32 1.12e+00 7.97e-01 4.28e+00
  ... (remaining 5942 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.04: 2338
       16.04 -    32.08: 197
       32.08 -    48.11: 55
       48.11 -    64.15: 10
       64.15 -    80.19: 7
  Dihedral angle restraints: 2607
    sinusoidal: 1046
      harmonic: 1561
  Sorted by residual:
  dihedral pdb=" CB  CYS A  21 "
           pdb=" SG  CYS A  21 "
           pdb=" SG  CYS A 165 "
           pdb=" CB  CYS A 165 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  152.17  -59.17     1      1.00e+01 1.00e-02 4.68e+01
  dihedral pdb=" CB  CYS B 473 "
           pdb=" SG  CYS B 473 "
           pdb=" SG  CYS B 548 "
           pdb=" CB  CYS B 548 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -135.10   49.10     1      1.00e+01 1.00e-02 3.32e+01
  dihedral pdb=" CB  CYS A 172 "
           pdb=" SG  CYS A 172 "
           pdb=" SG  CYS A 252 "
           pdb=" CB  CYS A 252 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   46.37   46.63     1      1.00e+01 1.00e-02 3.01e+01
  ... (remaining 2604 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 614
       0.085 -    0.169: 50
       0.169 -    0.254: 1
       0.254 -    0.339: 0
       0.339 -    0.423: 1
  Chirality restraints: 666
  Sorted by residual:
  chirality pdb=" C1  NAG A1401 "
            pdb=" ND2 ASN A 133 "
            pdb=" C2  NAG A1401 "
            pdb=" O5  NAG A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.98   -0.42 2.00e-01 2.50e+01 4.48e+00
  chirality pdb=" C1  NAG A1402 "
            pdb=" ND2 ASN A 198 "
            pdb=" C2  NAG A1402 "
            pdb=" O5  NAG A1402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CB  VAL A  43 "
            pdb=" CA  VAL A  43 "
            pdb=" CG1 VAL A  43 "
            pdb=" CG2 VAL A  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 663 not shown)

  Planarity restraints: 762
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 133 "   -0.019 2.00e-02 2.50e+03   1.77e-02 3.90e+00
        pdb=" CG  ASN A 133 "    0.018 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 133 "   -0.001 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 133 "    0.022 2.00e-02 2.50e+03
        pdb=" C1  NAG A1401 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  33 "    0.026 5.00e-02 4.00e+02   3.98e-02 2.53e+00
        pdb=" N   PRO A  34 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A  34 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A  34 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 548 "    0.023 5.00e-02 4.00e+02   3.48e-02 1.94e+00
        pdb=" N   PRO B 549 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO B 549 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 549 "    0.019 5.00e-02 4.00e+02
  ... (remaining 759 not shown)

  Histogram of nonbonded interaction distances:
        2.48 -     2.96: 2194
        2.96 -     3.45: 4495
        3.45 -     3.93: 7081
        3.93 -     4.42: 7866
        4.42 -     4.90: 12437
  Nonbonded interactions: 34073
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 133 "
            pdb=" O5  NAG A1401 "
     model   vdw
     2.478 3.040
  nonbonded pdb=" OD1 ASN A 133 "
            pdb=" OG1 THR A 163 "
     model   vdw
     2.578 3.040
  nonbonded pdb=" OG  SER B 344 "
            pdb=" O   THR B 441 "
     model   vdw
     2.585 3.040
  nonbonded pdb=" N   GLY A 239 "
            pdb=" N   THR A 240 "
     model   vdw
     2.600 2.560
  nonbonded pdb=" N   VAL A  43 "
            pdb=" N   THR A  44 "
     model   vdw
     2.613 2.560
  ... (remaining 34068 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.970
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.220
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
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      :  0.003   0.025   4380  Z= 0.153
  Angle     :  0.576  10.227   5984  Z= 0.303
  Chirality :  0.044   0.423    666
  Planarity :  0.004   0.040    759
  Dihedral  : 13.193  80.191   1567
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.97 (0.35), residues: 529
  helix: -1.77 (0.83), residues: 35
  sheet: -0.86 (0.46), residues: 132
  loop : -1.50 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 350 
 TYR   0.013   0.001   TYR A  67 
 PHE   0.018   0.001   PHE A 270 
 TRP   0.008   0.001   TRP B 573 
 HIS   0.003   0.001   HIS B 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 4363)
  covalent geometry    : angle       0.54194 ( 5947)
  SS BOND              : bond        0.00192 (   14)
  SS BOND              : angle       0.83272 (   28)
  hydrogen bonds       : bond        0.18005 (  116)
  hydrogen bonds       : angle       9.56612 (  342)
  link_NAG-ASN         : bond        0.01579 (    3)
  link_NAG-ASN         : angle       4.96843 (    9)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.9658 (tp) cc_final: 0.9379 (tt)
REVERT: A  164 MET cc_start: 0.9446 (mpp) cc_final: 0.9132 (mpp)
REVERT: A  235 LYS cc_start: 0.9454 (ptmm) cc_final: 0.8752 (ttpp)
REVERT: A  248 MET cc_start: 0.9386 (tpt) cc_final: 0.8980 (tpt)
REVERT: A  269 GLN cc_start: 0.9185 (tt0) cc_final: 0.8890 (tm-30)
REVERT: A  274 PHE cc_start: 0.9292 (m-80) cc_final: 0.8907 (m-80)
REVERT: B  349 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7712 (tm-30)
REVERT: B  360 MET cc_start: 0.9621 (mmp) cc_final: 0.9418 (mmm)
REVERT: B  383 TYR cc_start: 0.9523 (m-80) cc_final: 0.9018 (m-80)
REVERT: B  393 ASP cc_start: 0.9119 (m-30) cc_final: 0.8610 (m-30)
REVERT: B  419 LYS cc_start: 0.9556 (tptp) cc_final: 0.9330 (tppt)
REVERT: B  420 ILE cc_start: 0.9667 (tp) cc_final: 0.9403 (tp)
REVERT: B  443 TYR cc_start: 0.9133 (t80) cc_final: 0.8836 (t80)
REVERT: B  451 ARG cc_start: 0.9637 (ttt180) cc_final: 0.9378 (ttp-110)
REVERT: B  593 ASN cc_start: 0.8789 (t0) cc_final: 0.8554 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0834
  time to fit residues: 4.1585
Evaluate side-chains
  40 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    8.9990
   chunk 26 optimal weight:    0.0570
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    0.0070
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.5320

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 GLN
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 589 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.063327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.046080 restraints weight = 26243.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.047598 restraints weight = 16619.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.048614 restraints weight = 12571.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.049271 restraints weight = 10508.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.049673 restraints weight = 9361.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.0861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4380  Z= 0.098
  Angle     :  0.507  10.397   5984  Z= 0.261
  Chirality :  0.042   0.218    666
  Planarity :  0.004   0.039    759
  Dihedral  :  4.262  28.528    643
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.74 (0.36), residues: 529
  helix: -1.99 (0.80), residues: 36
  sheet: -0.45 (0.46), residues: 138
  loop : -1.41 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 197 
 TYR   0.014   0.001   TYR B 383 
 PHE   0.013   0.001   PHE A 270 
 TRP   0.006   0.001   TRP B 573 
 HIS   0.002   0.001   HIS A 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 4363)
  covalent geometry    : angle       0.47268 ( 5947)
  SS BOND              : bond        0.00150 (   14)
  SS BOND              : angle       0.70664 (   28)
  hydrogen bonds       : bond        0.04384 (  116)
  hydrogen bonds       : angle       7.10274 (  342)
  link_NAG-ASN         : bond        0.01217 (    3)
  link_NAG-ASN         : angle       4.69262 (    9)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.9503 (tp) cc_final: 0.9270 (tt)
REVERT: A  164 MET cc_start: 0.9367 (mpp) cc_final: 0.9056 (mpp)
REVERT: A  235 LYS cc_start: 0.9452 (ptmm) cc_final: 0.8906 (ttpp)
REVERT: A  248 MET cc_start: 0.9297 (tpt) cc_final: 0.8745 (tpp)
REVERT: A  269 GLN cc_start: 0.9119 (tt0) cc_final: 0.8777 (tm-30)
REVERT: A  274 PHE cc_start: 0.9219 (m-80) cc_final: 0.8708 (m-80)
REVERT: B  349 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7244 (tm-30)
REVERT: B  360 MET cc_start: 0.9629 (mmp) cc_final: 0.9381 (mmm)
REVERT: B  383 TYR cc_start: 0.9534 (m-80) cc_final: 0.9029 (m-80)
REVERT: B  393 ASP cc_start: 0.9211 (m-30) cc_final: 0.8640 (m-30)
REVERT: B  419 LYS cc_start: 0.9552 (tptp) cc_final: 0.9316 (tppt)
REVERT: B  420 ILE cc_start: 0.9635 (tp) cc_final: 0.8970 (pt)
REVERT: B  443 TYR cc_start: 0.9132 (t80) cc_final: 0.8813 (t80)
REVERT: B  451 ARG cc_start: 0.9622 (ttt180) cc_final: 0.9381 (ttp-110)
REVERT: B  593 ASN cc_start: 0.8838 (t0) cc_final: 0.8574 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.0876
  time to fit residues: 4.9982
Evaluate side-chains
  39 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 GLN
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 589 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 = 0.3314 r_free = 0.3314 target = 0.061662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.044577 restraints weight = 27223.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.045941 restraints weight = 17970.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.046860 restraints weight = 13896.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.047463 restraints weight = 11780.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.047857 restraints weight = 10586.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.0978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4380  Z= 0.202
  Angle     :  0.589  10.165   5984  Z= 0.300
  Chirality :  0.041   0.209    666
  Planarity :  0.004   0.041    759
  Dihedral  :  4.716  28.874    643
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.82 (0.35), residues: 529
  helix: -2.20 (0.77), residues: 35
  sheet: -0.31 (0.46), residues: 136
  loop : -1.54 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 350 
 TYR   0.014   0.002   TYR A  67 
 PHE   0.017   0.002   PHE A 270 
 TRP   0.007   0.001   TRP B 336 
 HIS   0.004   0.001   HIS B 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 4363)
  covalent geometry    : angle       0.56269 ( 5947)
  SS BOND              : bond        0.00204 (   14)
  SS BOND              : angle       0.74571 (   28)
  hydrogen bonds       : bond        0.04391 (  116)
  hydrogen bonds       : angle       6.98131 (  342)
  link_NAG-ASN         : bond        0.01123 (    3)
  link_NAG-ASN         : angle       4.44332 (    9)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.9516 (tp) cc_final: 0.9196 (tt)
REVERT: A  235 LYS cc_start: 0.9502 (ptmm) cc_final: 0.8959 (ttpp)
REVERT: A  248 MET cc_start: 0.9292 (tpt) cc_final: 0.8779 (tpp)
REVERT: A  269 GLN cc_start: 0.9155 (tt0) cc_final: 0.8862 (tm-30)
REVERT: A  274 PHE cc_start: 0.9251 (m-80) cc_final: 0.8810 (m-80)
REVERT: B  349 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7570 (tm-30)
REVERT: B  360 MET cc_start: 0.9647 (mmp) cc_final: 0.9390 (mmm)
REVERT: B  383 TYR cc_start: 0.9547 (m-80) cc_final: 0.9051 (m-80)
REVERT: B  393 ASP cc_start: 0.9191 (m-30) cc_final: 0.8713 (m-30)
REVERT: B  420 ILE cc_start: 0.9642 (tp) cc_final: 0.9139 (pt)
REVERT: B  443 TYR cc_start: 0.9196 (t80) cc_final: 0.8869 (t80)
REVERT: B  451 ARG cc_start: 0.9627 (ttt180) cc_final: 0.9379 (ttp-110)
REVERT: B  593 ASN cc_start: 0.8888 (t0) cc_final: 0.8604 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0924
  time to fit residues: 4.4632
Evaluate side-chains
  39 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 9 optimal weight:    7.9990
   chunk 14 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 211 HIS
A 214 GLN
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 589 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.062258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.044989 restraints weight = 25996.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.046373 restraints weight = 17144.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.047307 restraints weight = 13219.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.047932 restraints weight = 11199.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.048347 restraints weight = 10049.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.1174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4380  Z= 0.147
  Angle     :  0.542  10.010   5984  Z= 0.277
  Chirality :  0.041   0.207    666
  Planarity :  0.004   0.039    759
  Dihedral  :  4.631  28.672    643
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.80 (0.35), residues: 529
  helix: -2.22 (0.76), residues: 36
  sheet: -0.41 (0.45), residues: 138
  loop : -1.47 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 350 
 TYR   0.012   0.001   TYR A 162 
 PHE   0.016   0.001   PHE A 270 
 TRP   0.007   0.001   TRP B 573 
 HIS   0.003   0.001   HIS B 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 4363)
  covalent geometry    : angle       0.51239 ( 5947)
  SS BOND              : bond        0.00309 (   14)
  SS BOND              : angle       0.78505 (   28)
  hydrogen bonds       : bond        0.03967 (  116)
  hydrogen bonds       : angle       6.51488 (  342)
  link_NAG-ASN         : bond        0.01272 (    3)
  link_NAG-ASN         : angle       4.49047 (    9)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.9466 (tp) cc_final: 0.8961 (tt)
REVERT: A  164 MET cc_start: 0.9353 (mpp) cc_final: 0.9007 (pmm)
REVERT: A  235 LYS cc_start: 0.9446 (ptmm) cc_final: 0.8922 (ttpp)
REVERT: A  248 MET cc_start: 0.9257 (tpt) cc_final: 0.8691 (tpp)
REVERT: A  269 GLN cc_start: 0.9118 (tt0) cc_final: 0.8752 (tm-30)
REVERT: A  274 PHE cc_start: 0.9225 (m-80) cc_final: 0.8754 (m-80)
REVERT: B  349 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7472 (tm-30)
REVERT: B  360 MET cc_start: 0.9653 (mmp) cc_final: 0.9407 (mmm)
REVERT: B  383 TYR cc_start: 0.9561 (m-80) cc_final: 0.9058 (m-80)
REVERT: B  393 ASP cc_start: 0.9212 (m-30) cc_final: 0.8708 (m-30)
REVERT: B  419 LYS cc_start: 0.9538 (tptp) cc_final: 0.9321 (tppt)
REVERT: B  420 ILE cc_start: 0.9603 (tp) cc_final: 0.9053 (pt)
REVERT: B  430 TYR cc_start: 0.8664 (m-10) cc_final: 0.8416 (m-10)
REVERT: B  443 TYR cc_start: 0.9210 (t80) cc_final: 0.8876 (t80)
REVERT: B  451 ARG cc_start: 0.9633 (ttt180) cc_final: 0.9418 (ttp-110)
REVERT: B  593 ASN cc_start: 0.8847 (t0) cc_final: 0.8561 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.0801
  time to fit residues: 4.2579
Evaluate side-chains
  40 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 47 optimal weight:    0.5980
   chunk 9 optimal weight:    8.9990
   chunk 50 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 1 optimal weight:    6.9990
   chunk 14 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
** B 359 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 = 0.3283 r_free = 0.3283 target = 0.060372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.043533 restraints weight = 26968.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.044778 restraints weight = 18108.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.045664 restraints weight = 14114.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.046251 restraints weight = 11965.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.046636 restraints weight = 10740.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.1502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   4380  Z= 0.254
  Angle     :  0.647  10.045   5984  Z= 0.330
  Chirality :  0.042   0.196    666
  Planarity :  0.004   0.039    759
  Dihedral  :  5.298  26.899    643
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 16.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.93 (0.35), residues: 529
  helix: -2.36 (0.72), residues: 35
  sheet: -0.36 (0.46), residues: 137
  loop : -1.63 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 462 
 TYR   0.014   0.002   TYR A  67 
 PHE   0.014   0.002   PHE A 270 
 TRP   0.007   0.002   TRP B 336 
 HIS   0.005   0.002   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 ( 4363)
  covalent geometry    : angle       0.62255 ( 5947)
  SS BOND              : bond        0.00249 (   14)
  SS BOND              : angle       0.90239 (   28)
  hydrogen bonds       : bond        0.04403 (  116)
  hydrogen bonds       : angle       6.93085 (  342)
  link_NAG-ASN         : bond        0.01101 (    3)
  link_NAG-ASN         : angle       4.46348 (    9)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.9512 (tp) cc_final: 0.9087 (tt)
REVERT: A  164 MET cc_start: 0.9332 (mpp) cc_final: 0.8962 (pmm)
REVERT: A  235 LYS cc_start: 0.9454 (ptmm) cc_final: 0.8949 (ttpp)
REVERT: A  248 MET cc_start: 0.9271 (tpt) cc_final: 0.8820 (tpp)
REVERT: A  269 GLN cc_start: 0.9157 (tt0) cc_final: 0.8798 (tm-30)
REVERT: A  274 PHE cc_start: 0.9281 (m-80) cc_final: 0.8814 (m-80)
REVERT: B  349 GLU cc_start: 0.8489 (tm-30) cc_final: 0.7650 (tm-30)
REVERT: B  360 MET cc_start: 0.9650 (mmp) cc_final: 0.9386 (mmm)
REVERT: B  383 TYR cc_start: 0.9553 (m-80) cc_final: 0.9047 (m-80)
REVERT: B  393 ASP cc_start: 0.9182 (m-30) cc_final: 0.8744 (m-30)
REVERT: B  451 ARG cc_start: 0.9639 (ttt180) cc_final: 0.9398 (ttp-110)
REVERT: B  593 ASN cc_start: 0.8876 (t0) cc_final: 0.8658 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0975
  time to fit residues: 4.9651
Evaluate side-chains
  37 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0670
   chunk 9 optimal weight:    2.9990
   chunk 41 optimal weight:    0.1980
   chunk 13 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.7320

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 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 = 0.3336 r_free = 0.3336 target = 0.062521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.045294 restraints weight = 26511.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.046740 restraints weight = 16976.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.047691 restraints weight = 12979.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.048345 restraints weight = 10955.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.048787 restraints weight = 9762.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.1474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4380  Z= 0.108
  Angle     :  0.532  10.452   5984  Z= 0.271
  Chirality :  0.042   0.212    666
  Planarity :  0.004   0.039    759
  Dihedral  :  4.656  27.110    643
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.71 (0.36), residues: 529
  helix: -2.18 (0.77), residues: 36
  sheet: -0.06 (0.47), residues: 131
  loop : -1.53 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 197 
 TYR   0.008   0.001   TYR A 162 
 PHE   0.019   0.001   PHE A 270 
 TRP   0.010   0.001   TRP B 573 
 HIS   0.004   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 4363)
  covalent geometry    : angle       0.49839 ( 5947)
  SS BOND              : bond        0.00265 (   14)
  SS BOND              : angle       0.93201 (   28)
  hydrogen bonds       : bond        0.03781 (  116)
  hydrogen bonds       : angle       6.33885 (  342)
  link_NAG-ASN         : bond        0.01216 (    3)
  link_NAG-ASN         : angle       4.63899 (    9)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.9422 (tp) cc_final: 0.9088 (tt)
REVERT: A  164 MET cc_start: 0.9368 (mpp) cc_final: 0.9061 (pmm)
REVERT: A  235 LYS cc_start: 0.9327 (ptmm) cc_final: 0.8833 (ttpp)
REVERT: A  248 MET cc_start: 0.9185 (tpt) cc_final: 0.8676 (tpp)
REVERT: A  269 GLN cc_start: 0.9110 (tt0) cc_final: 0.8740 (tm-30)
REVERT: A  274 PHE cc_start: 0.9279 (m-80) cc_final: 0.8758 (m-80)
REVERT: B  349 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7190 (tm-30)
REVERT: B  360 MET cc_start: 0.9656 (mmp) cc_final: 0.9407 (mmm)
REVERT: B  383 TYR cc_start: 0.9580 (m-80) cc_final: 0.9067 (m-80)
REVERT: B  393 ASP cc_start: 0.9230 (m-30) cc_final: 0.8696 (m-30)
REVERT: B  420 ILE cc_start: 0.9595 (tp) cc_final: 0.9050 (pt)
REVERT: B  443 TYR cc_start: 0.9197 (t80) cc_final: 0.8865 (t80)
REVERT: B  451 ARG cc_start: 0.9622 (ttt180) cc_final: 0.9399 (ttp-110)
REVERT: B  593 ASN cc_start: 0.8883 (t0) cc_final: 0.8678 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0975
  time to fit residues: 5.4303
Evaluate side-chains
  41 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 1 optimal weight:    9.9990
   chunk 32 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0770
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 589 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.062675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.045325 restraints weight = 26617.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.046772 restraints weight = 17105.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.047755 restraints weight = 13086.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.048395 restraints weight = 11019.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.048817 restraints weight = 9843.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4380  Z= 0.105
  Angle     :  0.533  10.728   5984  Z= 0.272
  Chirality :  0.043   0.206    666
  Planarity :  0.004   0.038    759
  Dihedral  :  4.544  28.330    643
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.59 (0.36), residues: 529
  helix: -2.02 (0.78), residues: 36
  sheet: -0.19 (0.46), residues: 136
  loop : -1.36 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 268 
 TYR   0.009   0.001   TYR A  67 
 PHE   0.021   0.001   PHE A 270 
 TRP   0.007   0.001   TRP B 573 
 HIS   0.003   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 4363)
  covalent geometry    : angle       0.49569 ( 5947)
  SS BOND              : bond        0.00186 (   14)
  SS BOND              : angle       0.88525 (   28)
  hydrogen bonds       : bond        0.03626 (  116)
  hydrogen bonds       : angle       6.14312 (  342)
  link_NAG-ASN         : bond        0.01111 (    3)
  link_NAG-ASN         : angle       4.94376 (    9)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.9367 (tp) cc_final: 0.9004 (tt)
REVERT: A  164 MET cc_start: 0.9415 (mpp) cc_final: 0.9056 (pmm)
REVERT: A  235 LYS cc_start: 0.9340 (ptmm) cc_final: 0.8837 (ttpp)
REVERT: A  248 MET cc_start: 0.9208 (tpt) cc_final: 0.8667 (tpp)
REVERT: A  269 GLN cc_start: 0.9117 (tt0) cc_final: 0.8779 (tm-30)
REVERT: A  274 PHE cc_start: 0.9207 (m-80) cc_final: 0.8707 (m-80)
REVERT: B  349 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7127 (tm-30)
REVERT: B  360 MET cc_start: 0.9672 (mmp) cc_final: 0.9404 (mmm)
REVERT: B  383 TYR cc_start: 0.9567 (m-80) cc_final: 0.9087 (m-80)
REVERT: B  393 ASP cc_start: 0.9194 (m-30) cc_final: 0.8645 (m-30)
REVERT: B  420 ILE cc_start: 0.9573 (tp) cc_final: 0.9008 (pt)
REVERT: B  443 TYR cc_start: 0.9198 (t80) cc_final: 0.8833 (t80)
REVERT: B  451 ARG cc_start: 0.9629 (ttt180) cc_final: 0.9387 (ttp-110)
REVERT: B  593 ASN cc_start: 0.8868 (t0) cc_final: 0.8650 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0766
  time to fit residues: 4.3147
Evaluate side-chains
  42 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 27 optimal weight:    0.3980
   chunk 44 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 2 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0170
   chunk 1 optimal weight:    8.9990
   chunk 42 optimal weight:   20.0000
   chunk 5 optimal weight:    0.6980
   chunk 12 optimal weight:    6.9990
   chunk 26 optimal weight:    0.0170
   overall best weight:    0.4056

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 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 = 0.3372 r_free = 0.3372 target = 0.063650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.046235 restraints weight = 25774.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.047738 restraints weight = 16680.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.048751 restraints weight = 12799.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.049405 restraints weight = 10800.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.049802 restraints weight = 9652.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4380  Z= 0.090
  Angle     :  0.515  10.867   5984  Z= 0.263
  Chirality :  0.042   0.206    666
  Planarity :  0.004   0.039    759
  Dihedral  :  4.260  29.127    643
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.42 (0.37), residues: 529
  helix: -1.84 (0.81), residues: 36
  sheet:  0.07 (0.47), residues: 131
  loop : -1.30 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 401 
 TYR   0.012   0.001   TYR A 281 
 PHE   0.019   0.001   PHE A 270 
 TRP   0.008   0.001   TRP B 573 
 HIS   0.003   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00191 ( 4363)
  covalent geometry    : angle       0.47849 ( 5947)
  SS BOND              : bond        0.00159 (   14)
  SS BOND              : angle       0.81783 (   28)
  hydrogen bonds       : bond        0.03499 (  116)
  hydrogen bonds       : angle       5.83872 (  342)
  link_NAG-ASN         : bond        0.01135 (    3)
  link_NAG-ASN         : angle       4.79085 (    9)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.9302 (tp) cc_final: 0.8900 (tt)
REVERT: A  164 MET cc_start: 0.9376 (mpp) cc_final: 0.9067 (pmm)
REVERT: A  235 LYS cc_start: 0.9379 (ptmm) cc_final: 0.8891 (ttpp)
REVERT: A  248 MET cc_start: 0.9193 (tpt) cc_final: 0.8619 (tpp)
REVERT: A  269 GLN cc_start: 0.9040 (tt0) cc_final: 0.8495 (tm-30)
REVERT: A  274 PHE cc_start: 0.9306 (m-80) cc_final: 0.8761 (m-80)
REVERT: B  349 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7174 (tm-30)
REVERT: B  360 MET cc_start: 0.9667 (mmp) cc_final: 0.9392 (mmm)
REVERT: B  383 TYR cc_start: 0.9557 (m-80) cc_final: 0.9089 (m-80)
REVERT: B  393 ASP cc_start: 0.9135 (m-30) cc_final: 0.8546 (m-30)
REVERT: B  420 ILE cc_start: 0.9516 (tp) cc_final: 0.8838 (pt)
REVERT: B  443 TYR cc_start: 0.9186 (t80) cc_final: 0.8819 (t80)
REVERT: B  451 ARG cc_start: 0.9620 (ttt180) cc_final: 0.9402 (ttp-110)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0890
  time to fit residues: 5.0065
Evaluate side-chains
  42 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 27 optimal weight:    0.3980
   chunk 46 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 26 optimal weight:    0.3980
   chunk 11 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0370
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.4658

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 589 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.063791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.046365 restraints weight = 25950.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.047806 restraints weight = 16769.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.048771 restraints weight = 12891.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.049452 restraints weight = 10958.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.049897 restraints weight = 9752.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4380  Z= 0.091
  Angle     :  0.520  10.857   5984  Z= 0.267
  Chirality :  0.042   0.209    666
  Planarity :  0.003   0.039    759
  Dihedral  :  4.340  29.059    643
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.32 (0.37), residues: 529
  helix: -1.73 (0.84), residues: 36
  sheet:  0.12 (0.48), residues: 131
  loop : -1.23 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 401 
 TYR   0.016   0.001   TYR A 281 
 PHE   0.018   0.001   PHE A 270 
 TRP   0.006   0.001   TRP B 573 
 HIS   0.003   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00198 ( 4363)
  covalent geometry    : angle       0.48082 ( 5947)
  SS BOND              : bond        0.00156 (   14)
  SS BOND              : angle       1.12634 (   28)
  hydrogen bonds       : bond        0.03510 (  116)
  hydrogen bonds       : angle       5.74212 (  342)
  link_NAG-ASN         : bond        0.01082 (    3)
  link_NAG-ASN         : angle       4.82008 (    9)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.9280 (tp) cc_final: 0.8861 (tt)
REVERT: A  164 MET cc_start: 0.9338 (mpp) cc_final: 0.9049 (pmm)
REVERT: A  235 LYS cc_start: 0.9451 (ptmm) cc_final: 0.8901 (ttpp)
REVERT: A  248 MET cc_start: 0.9184 (tpt) cc_final: 0.8638 (tpp)
REVERT: A  269 GLN cc_start: 0.9005 (tt0) cc_final: 0.8460 (tm-30)
REVERT: A  274 PHE cc_start: 0.9274 (m-80) cc_final: 0.8923 (m-80)
REVERT: A  281 TYR cc_start: 0.8896 (p90) cc_final: 0.8436 (p90)
REVERT: B  349 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7205 (tm-30)
REVERT: B  360 MET cc_start: 0.9657 (mmp) cc_final: 0.9384 (mmm)
REVERT: B  383 TYR cc_start: 0.9549 (m-80) cc_final: 0.9072 (m-80)
REVERT: B  393 ASP cc_start: 0.9128 (m-30) cc_final: 0.8540 (m-30)
REVERT: B  420 ILE cc_start: 0.9499 (tp) cc_final: 0.8830 (pt)
REVERT: B  443 TYR cc_start: 0.9162 (t80) cc_final: 0.8782 (t80)
REVERT: B  451 ARG cc_start: 0.9581 (ttt180) cc_final: 0.9374 (ttp-110)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.0883
  time to fit residues: 5.0287
Evaluate side-chains
  43 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 26 optimal weight:    0.0980
   chunk 32 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 17 optimal weight:    6.9990
   chunk 49 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
** B 359 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 = 0.3342 r_free = 0.3342 target = 0.062413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.045076 restraints weight = 25894.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.046505 restraints weight = 16956.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.047480 restraints weight = 13091.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.048120 restraints weight = 11071.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.048536 restraints weight = 9911.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4380  Z= 0.150
  Angle     :  0.552  10.559   5984  Z= 0.283
  Chirality :  0.042   0.211    666
  Planarity :  0.004   0.038    759
  Dihedral  :  4.550  27.380    643
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.36 (0.37), residues: 529
  helix: -1.44 (0.84), residues: 36
  sheet: -0.09 (0.47), residues: 136
  loop : -1.23 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 350 
 TYR   0.013   0.001   TYR A 281 
 PHE   0.017   0.001   PHE B 387 
 TRP   0.008   0.001   TRP A 261 
 HIS   0.004   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4363)
  covalent geometry    : angle       0.51532 ( 5947)
  SS BOND              : bond        0.00178 (   14)
  SS BOND              : angle       1.04229 (   28)
  hydrogen bonds       : bond        0.03908 (  116)
  hydrogen bonds       : angle       5.87251 (  342)
  link_NAG-ASN         : bond        0.01064 (    3)
  link_NAG-ASN         : angle       4.84766 (    9)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 LEU cc_start: 0.9267 (tp) cc_final: 0.9021 (tp)
REVERT: A  164 MET cc_start: 0.9347 (mpp) cc_final: 0.9007 (pmm)
REVERT: A  235 LYS cc_start: 0.9427 (ptmm) cc_final: 0.8945 (ttpp)
REVERT: A  248 MET cc_start: 0.9213 (tpt) cc_final: 0.8702 (tpp)
REVERT: A  269 GLN cc_start: 0.9046 (tt0) cc_final: 0.8502 (tm-30)
REVERT: A  274 PHE cc_start: 0.9308 (m-80) cc_final: 0.8893 (m-80)
REVERT: A  281 TYR cc_start: 0.8903 (p90) cc_final: 0.8539 (p90)
REVERT: B  349 GLU cc_start: 0.7666 (tm-30) cc_final: 0.6931 (tm-30)
REVERT: B  360 MET cc_start: 0.9661 (mmp) cc_final: 0.9383 (mmm)
REVERT: B  383 TYR cc_start: 0.9554 (m-80) cc_final: 0.9069 (m-80)
REVERT: B  393 ASP cc_start: 0.9151 (m-30) cc_final: 0.8654 (m-30)
REVERT: B  420 ILE cc_start: 0.9564 (tp) cc_final: 0.8949 (pt)
REVERT: B  443 TYR cc_start: 0.9180 (t80) cc_final: 0.8809 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.0888
  time to fit residues: 4.8294
Evaluate side-chains
  42 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 5 optimal weight:    0.3980
   chunk 15 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 4 optimal weight:    5.9990
   chunk 7 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 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 = 0.3366 r_free = 0.3366 target = 0.063210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.045673 restraints weight = 26034.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.047139 restraints weight = 16971.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.048143 restraints weight = 13051.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.048784 restraints weight = 11040.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.049206 restraints weight = 9888.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4380  Z= 0.106
  Angle     :  0.528  10.672   5984  Z= 0.270
  Chirality :  0.043   0.216    666
  Planarity :  0.004   0.038    759
  Dihedral  :  4.446  27.289    643
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.31 (0.37), residues: 529
  helix: -1.30 (0.86), residues: 36
  sheet: -0.04 (0.47), residues: 136
  loop : -1.21 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 450 
 TYR   0.013   0.001   TYR A 281 
 PHE   0.018   0.001   PHE A 270 
 TRP   0.007   0.001   TRP B 573 
 HIS   0.003   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 4363)
  covalent geometry    : angle       0.49152 ( 5947)
  SS BOND              : bond        0.00149 (   14)
  SS BOND              : angle       0.92260 (   28)
  hydrogen bonds       : bond        0.03648 (  116)
  hydrogen bonds       : angle       5.75783 (  342)
  link_NAG-ASN         : bond        0.01115 (    3)
  link_NAG-ASN         : angle       4.80214 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 932.25 seconds
wall clock time: 16 minutes 45.24 seconds (1005.24 seconds total)