Starting phenix.real_space_refine
on Tue Jun 10 14:11:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7b5e_12027/06_2025/7b5e_12027.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7b5e_12027/06_2025/7b5e_12027.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/7b5e_12027/06_2025/7b5e_12027.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7b5e_12027/06_2025/7b5e_12027.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7b5e_12027/06_2025/7b5e_12027.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7b5e_12027/06_2025/7b5e_12027.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      4      9.91       5
     S      74      5.16       5
     C    7678      2.51       5
     N    1936      2.21       5
     O    2072      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 11764
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 718, 5880
          Classifications: {'peptide': 718}
          Link IDs: {'PTRANS': 31, 'TRANS': 686}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 12.08, per 1000 atoms: 1.03
  Number of scatterers: 11764
  At special positions: 0
  Unit cell: (122.452, 98.164, 121.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      4     19.99
     S      74     16.00
     O    2072      8.00
     N    1936      7.00
     C    7678      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 370 " - pdb=" SG  CYS A 395 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 836 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 382 " - pdb=" SG  CYS A 386 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 625 " - pdb=" SG  CYS A 630 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 370 " - pdb=" SG  CYS B 395 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 836 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 382 " - pdb=" SG  CYS B 386 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 625 " - pdb=" SG  CYS B 630 " 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
  Time building additional restraints: 2.92
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2752

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 6 sheets defined
      63.0% alpha, 1.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 181
      Proline residue:  A 177  - end of helix
    Processing helix  chain 'A' and resid 204 through 211
      removed outlier: 3.664A  pdb=" N   GLU A 211 " --> pdb=" O   PRO A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 257
      removed outlier: 3.651A  pdb=" N   THR A 257 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 275
    Processing helix  chain 'A' and resid 296 through 305
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 316 through 325
    Processing helix  chain 'A' and resid 325 through 359
      removed outlier: 3.752A  pdb=" N   GLY A 329 " --> pdb=" O   GLY A 325 " (cutoff:3.500A)
      Proline residue:  A 344  - end of helix
    Processing helix  chain 'A' and resid 363 through 371
      removed outlier: 3.899A  pdb=" N   MET A 367 " --> pdb=" O   ASN A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 393
    Processing helix  chain 'A' and resid 394 through 403
      removed outlier: 3.760A  pdb=" N   LEU A 403 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 438
    Processing helix  chain 'A' and resid 452 through 466
    Processing helix  chain 'A' and resid 489 through 518
      removed outlier: 4.285A  pdb=" N   ASN A 493 " --> pdb=" O   ALA A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 568
    Processing helix  chain 'A' and resid 572 through 592
    Processing helix  chain 'A' and resid 593 through 602
    Processing helix  chain 'A' and resid 630 through 648
      removed outlier: 4.194A  pdb=" N   LEU A 634 " --> pdb=" O   CYS A 630 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLN A 646 " --> pdb=" O   MET A 642 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 668
      Proline residue:  A 658  - end of helix
    Processing helix  chain 'A' and resid 685 through 693
      removed outlier: 4.320A  pdb=" N   ASN A 692 " --> pdb=" O   GLU A 688 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   LEU A 693 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 699 through 716
    Processing helix  chain 'A' and resid 722 through 745
      removed outlier: 4.211A  pdb=" N   PHE A 726 " --> pdb=" O   LEU A 722 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   ARG A 736 " --> pdb=" O   ILE A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 759 through 782
      removed outlier: 4.110A  pdb=" N   VAL A 772 " --> pdb=" O   GLY A 768 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   ILE A 773 " --> pdb=" O   LYS A 769 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   PHE A 777 " --> pdb=" O   ILE A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 794
    Processing helix  chain 'A' and resid 803 through 809
    Processing helix  chain 'A' and resid 815 through 817
      No H-bonds generated for 'chain 'A' and resid 815 through 817'
    Processing helix  chain 'A' and resid 854 through 885
      removed outlier: 3.899A  pdb=" N   TRP A 858 " --> pdb=" O   SER A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 895 through 908
    Processing helix  chain 'B' and resid 166 through 181
      Proline residue:  B 177  - end of helix
    Processing helix  chain 'B' and resid 204 through 211
      removed outlier: 3.664A  pdb=" N   GLU B 211 " --> pdb=" O   PRO B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 257
      removed outlier: 3.651A  pdb=" N   THR B 257 " --> pdb=" O   ILE B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 275
    Processing helix  chain 'B' and resid 296 through 305
    Processing helix  chain 'B' and resid 307 through 311
    Processing helix  chain 'B' and resid 316 through 325
    Processing helix  chain 'B' and resid 325 through 359
      removed outlier: 3.752A  pdb=" N   GLY B 329 " --> pdb=" O   GLY B 325 " (cutoff:3.500A)
      Proline residue:  B 344  - end of helix
    Processing helix  chain 'B' and resid 363 through 371
      removed outlier: 3.899A  pdb=" N   MET B 367 " --> pdb=" O   ASN B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 393
    Processing helix  chain 'B' and resid 394 through 403
      removed outlier: 3.760A  pdb=" N   LEU B 403 " --> pdb=" O   ARG B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 438
    Processing helix  chain 'B' and resid 452 through 466
    Processing helix  chain 'B' and resid 489 through 518
      removed outlier: 4.285A  pdb=" N   ASN B 493 " --> pdb=" O   ALA B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 536 through 568
    Processing helix  chain 'B' and resid 572 through 592
    Processing helix  chain 'B' and resid 593 through 602
    Processing helix  chain 'B' and resid 630 through 648
      removed outlier: 4.194A  pdb=" N   LEU B 634 " --> pdb=" O   CYS B 630 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   GLN B 646 " --> pdb=" O   MET B 642 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 668
      Proline residue:  B 658  - end of helix
    Processing helix  chain 'B' and resid 685 through 693
      removed outlier: 4.320A  pdb=" N   ASN B 692 " --> pdb=" O   GLU B 688 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   LEU B 693 " --> pdb=" O   VAL B 689 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 699 through 716
    Processing helix  chain 'B' and resid 722 through 745
      removed outlier: 4.211A  pdb=" N   PHE B 726 " --> pdb=" O   LEU B 722 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   ARG B 736 " --> pdb=" O   ILE B 732 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 759 through 782
      removed outlier: 4.111A  pdb=" N   VAL B 772 " --> pdb=" O   GLY B 768 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   ILE B 773 " --> pdb=" O   LYS B 769 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   PHE B 777 " --> pdb=" O   ILE B 773 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 785 through 794
    Processing helix  chain 'B' and resid 803 through 809
    Processing helix  chain 'B' and resid 815 through 817
      No H-bonds generated for 'chain 'B' and resid 815 through 817'
    Processing helix  chain 'B' and resid 854 through 885
      removed outlier: 3.898A  pdb=" N   TRP B 858 " --> pdb=" O   SER B 854 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 895 through 908
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 188
    Processing sheet with id=AA2, first strand: chain 'A' and resid 217 through 218
    Processing sheet with id=AA3, first strand: chain 'A' and resid 810 through 813
    Processing sheet with id=AA4, first strand: chain 'B' and resid 186 through 188
    Processing sheet with id=AA5, first strand: chain 'B' and resid 217 through 218
    Processing sheet with id=AA6, first strand: chain 'B' and resid 810 through 813

    652 hydrogen bonds defined for protein.
    1926 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: 3.39

  Time building geometry restraints manager: 3.48 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: 3639
        1.34 -     1.46: 2725
        1.46 -     1.58: 5572
        1.58 -     1.70: 0
        1.70 -     1.81: 122
  Bond restraints: 12058
  Sorted by residual:
  bond pdb=" C   ALA B 723 "
       pdb=" N   PRO B 724 "
    ideal  model  delta    sigma   weight residual
    1.335  1.370 -0.036 1.19e-02 7.06e+03 8.91e+00
  bond pdb=" C   ALA A 723 "
       pdb=" N   PRO A 724 "
    ideal  model  delta    sigma   weight residual
    1.335  1.370 -0.035 1.19e-02 7.06e+03 8.82e+00
  bond pdb=" C   ASP A 203 "
       pdb=" N   PRO A 204 "
    ideal  model  delta    sigma   weight residual
    1.337  1.362 -0.025 1.11e-02 8.12e+03 5.27e+00
  bond pdb=" C   ASP B 203 "
       pdb=" N   PRO B 204 "
    ideal  model  delta    sigma   weight residual
    1.337  1.362 -0.025 1.11e-02 8.12e+03 5.08e+00
  bond pdb=" C   SER A 527 "
       pdb=" N   PRO A 528 "
    ideal  model  delta    sigma   weight residual
    1.334  1.375 -0.041 2.34e-02 1.83e+03 3.05e+00
  ... (remaining 12053 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 15895
        2.50 -     5.00: 365
        5.00 -     7.50: 36
        7.50 -     9.99: 14
        9.99 -    12.49: 2
  Bond angle restraints: 16312
  Sorted by residual:
  angle pdb=" N   VAL A 181 "
        pdb=" CA  VAL A 181 "
        pdb=" C   VAL A 181 "
      ideal   model   delta    sigma   weight residual
     111.91  108.42    3.49 8.90e-01 1.26e+00 1.54e+01
  angle pdb=" N   VAL B 181 "
        pdb=" CA  VAL B 181 "
        pdb=" C   VAL B 181 "
      ideal   model   delta    sigma   weight residual
     111.91  108.42    3.49 8.90e-01 1.26e+00 1.53e+01
  angle pdb=" N   ASP A 123 "
        pdb=" CA  ASP A 123 "
        pdb=" C   ASP A 123 "
      ideal   model   delta    sigma   weight residual
     111.02  115.59   -4.57 1.25e+00 6.40e-01 1.34e+01
  angle pdb=" N   ASP B 123 "
        pdb=" CA  ASP B 123 "
        pdb=" C   ASP B 123 "
      ideal   model   delta    sigma   weight residual
     111.02  115.58   -4.56 1.25e+00 6.40e-01 1.33e+01
  angle pdb=" CA  LEU A 381 "
        pdb=" CB  LEU A 381 "
        pdb=" CG  LEU A 381 "
      ideal   model   delta    sigma   weight residual
     116.30  128.79  -12.49 3.50e+00 8.16e-02 1.27e+01
  ... (remaining 16307 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.00: 5973
       14.00 -    28.00: 884
       28.00 -    42.00: 273
       42.00 -    56.01: 64
       56.01 -    70.01: 20
  Dihedral angle restraints: 7214
    sinusoidal: 2962
      harmonic: 4252
  Sorted by residual:
  dihedral pdb=" CB  CYS B 625 "
           pdb=" SG  CYS B 625 "
           pdb=" SG  CYS B 630 "
           pdb=" CB  CYS B 630 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -151.87   65.87     1      1.00e+01 1.00e-02 5.68e+01
  dihedral pdb=" CB  CYS A 625 "
           pdb=" SG  CYS A 625 "
           pdb=" SG  CYS A 630 "
           pdb=" CB  CYS A 630 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -151.86   65.86     1      1.00e+01 1.00e-02 5.67e+01
  dihedral pdb=" CA  THR A 235 "
           pdb=" C   THR A 235 "
           pdb=" N   ASP A 236 "
           pdb=" CA  ASP A 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.71   24.29     0      5.00e+00 4.00e-02 2.36e+01
  ... (remaining 7211 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 1462
       0.072 -    0.144: 305
       0.144 -    0.216: 19
       0.216 -    0.289: 6
       0.289 -    0.361: 2
  Chirality restraints: 1794
  Sorted by residual:
  chirality pdb=" CB  ILE B 786 "
            pdb=" CA  ILE B 786 "
            pdb=" CG1 ILE B 786 "
            pdb=" CG2 ILE B 786 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.36 2.00e-01 2.50e+01 3.25e+00
  chirality pdb=" CB  ILE A 786 "
            pdb=" CA  ILE A 786 "
            pdb=" CG1 ILE A 786 "
            pdb=" CG2 ILE A 786 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.36 2.00e-01 2.50e+01 3.24e+00
  chirality pdb=" CB  VAL A 310 "
            pdb=" CA  VAL A 310 "
            pdb=" CG1 VAL A 310 "
            pdb=" CG2 VAL A 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.78e+00
  ... (remaining 1791 not shown)

  Planarity restraints: 2044
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 206 "    0.059 5.00e-02 4.00e+02   8.94e-02 1.28e+01
        pdb=" N   PRO A 207 "   -0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO A 207 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A 207 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 206 "   -0.059 5.00e-02 4.00e+02   8.93e-02 1.28e+01
        pdb=" N   PRO B 207 "    0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO B 207 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO B 207 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 406 "   -0.047 5.00e-02 4.00e+02   7.07e-02 8.00e+00
        pdb=" N   PRO A 407 "    0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO A 407 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 407 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 2041 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 3347
        2.80 -     3.33: 11951
        3.33 -     3.85: 19704
        3.85 -     4.37: 21530
        4.37 -     4.90: 35729
  Nonbonded interactions: 92261
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 778 "
            pdb=" OG1 THR A 782 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   VAL B 778 "
            pdb=" OG1 THR B 782 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   LYS B 740 "
            pdb=" OG1 THR B 744 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   LYS A 740 "
            pdb=" OG1 THR A 744 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OG  SER B 387 "
            pdb=" O   ASP B 825 "
     model   vdw
     2.293 3.040
  ... (remaining 92256 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     32.690
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
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      :  0.006   0.056  12066  Z= 0.285
  Angle     :  0.936  12.492  16328  Z= 0.514
  Chirality :  0.057   0.361   1794
  Planarity :  0.008   0.089   2044
  Dihedral  : 15.024  70.006   4438
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 10.56 %
    Favored  : 89.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.56 (0.18), residues: 1416
  helix: -1.68 (0.15), residues: 834
  sheet:  None (None), residues: 0
  loop : -3.37 (0.21), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 760 
 HIS   0.010   0.002   HIS B 402 
 PHE   0.017   0.002   PHE A 585 
 TYR   0.022   0.002   TYR A 666 
 ARG   0.005   0.001   ARG B 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09855 (  652)
  hydrogen bonds       : angle       5.99207 ( 1926)
  SS BOND              : bond        0.00559 (    8)
  SS BOND              : angle       1.79796 (   16)
  covalent geometry    : bond        0.00629 (12058)
  covalent geometry    : angle       0.93452 (16312)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 181
  time to evaluate  : 1.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 TYR cc_start: 0.8626 (t80) cc_final: 0.8365 (t80)
REVERT: A  416 MET cc_start: 0.7452 (tpp) cc_final: 0.7159 (tpp)
REVERT: A  424 MET cc_start: 0.8724 (tpp) cc_final: 0.8423 (tpp)
REVERT: A  436 TYR cc_start: 0.6872 (t80) cc_final: 0.5979 (t80)
REVERT: A  508 VAL cc_start: 0.8668 (t) cc_final: 0.8414 (p)
REVERT: A  580 LEU cc_start: 0.8626 (tp) cc_final: 0.8323 (tt)
REVERT: B  197 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8857 (t)
REVERT: B  436 TYR cc_start: 0.6566 (t80) cc_final: 0.6345 (t80)
REVERT: B  524 MET cc_start: -0.1256 (ttm) cc_final: -0.2110 (tmm)
REVERT: B  760 TRP cc_start: 0.8467 (m100) cc_final: 0.8225 (m-90)
  outliers start: 4
  outliers final: 0
  residues processed: 183
  average time/residue: 0.2662
  time to fit residues: 68.6896
Evaluate side-chains
  127 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 1.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 119 optimal weight:   10.0000
   chunk 107 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 72 optimal weight:   10.0000
   chunk 57 optimal weight:    0.7980
   chunk 111 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 82 optimal weight:    6.9990
   chunk 128 optimal weight:    4.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 896 GLN
B 183 HIS
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 898 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.102987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.085656 restraints weight = 33393.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.087229 restraints weight = 21418.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.088218 restraints weight = 16042.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.1835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12066  Z= 0.149
  Angle     :  0.659   9.786  16328  Z= 0.344
  Chirality :  0.043   0.249   1794
  Planarity :  0.006   0.070   2044
  Dihedral  :  5.348  20.904   1584
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.20), residues: 1416
  helix: -0.22 (0.17), residues: 826
  sheet: -3.76 (0.87), residues: 24
  loop : -2.86 (0.23), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 760 
 HIS   0.006   0.001   HIS A 402 
 PHE   0.013   0.001   PHE B 585 
 TYR   0.027   0.001   TYR A 436 
 ARG   0.005   0.000   ARG A 683 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04553 (  652)
  hydrogen bonds       : angle       4.83394 ( 1926)
  SS BOND              : bond        0.00355 (    8)
  SS BOND              : angle       0.79694 (   16)
  covalent geometry    : bond        0.00322 (12058)
  covalent geometry    : angle       0.65888 (16312)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 1.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  500 MET cc_start: 0.8100 (mtp) cc_final: 0.7415 (mtm)
REVERT: A  508 VAL cc_start: 0.8768 (t) cc_final: 0.8554 (p)
REVERT: A  704 MET cc_start: 0.8258 (mmm) cc_final: 0.7971 (mmt)
REVERT: B  704 MET cc_start: 0.8283 (tpp) cc_final: 0.7931 (mmt)
REVERT: B  760 TRP cc_start: 0.8472 (m100) cc_final: 0.8087 (m-90)
REVERT: B  900 GLU cc_start: 0.8396 (pt0) cc_final: 0.7946 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.2487
  time to fit residues: 59.6984
Evaluate side-chains
  111 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 1.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 5 optimal weight:    0.0020
   chunk 44 optimal weight:    0.9980
   chunk 134 optimal weight:    0.1980
   chunk 103 optimal weight:    6.9990
   chunk 101 optimal weight:   20.0000
   chunk 77 optimal weight:    0.9990
   chunk 1 optimal weight:   10.0000
   chunk 91 optimal weight:    0.9980
   chunk 17 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.6390

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 435 ASN
A 692 ASN
** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 762 ASN
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 435 ASN
B 709 GLN
B 730 ASN
B 762 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.105738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.088745 restraints weight = 33298.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.090348 restraints weight = 21182.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.091302 restraints weight = 15733.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  12066  Z= 0.120
  Angle     :  0.604  10.000  16328  Z= 0.312
  Chirality :  0.041   0.233   1794
  Planarity :  0.005   0.061   2044
  Dihedral  :  4.808  17.369   1584
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.91 %
    Favored  : 95.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.21), residues: 1416
  helix:  0.55 (0.17), residues: 832
  sheet: -3.65 (0.79), residues: 24
  loop : -2.54 (0.24), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 760 
 HIS   0.003   0.001   HIS B 402 
 PHE   0.018   0.001   PHE A 499 
 TYR   0.026   0.001   TYR A 436 
 ARG   0.004   0.000   ARG A 188 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04064 (  652)
  hydrogen bonds       : angle       4.52505 ( 1926)
  SS BOND              : bond        0.00256 (    8)
  SS BOND              : angle       1.12612 (   16)
  covalent geometry    : bond        0.00247 (12058)
  covalent geometry    : angle       0.60282 (16312)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 186
  time to evaluate  : 1.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  500 MET cc_start: 0.7971 (mtp) cc_final: 0.7237 (mtm)
REVERT: A  660 MET cc_start: 0.5096 (mmt) cc_final: 0.4843 (mmp)
REVERT: B  760 TRP cc_start: 0.8327 (m100) cc_final: 0.7999 (m-90)
REVERT: B  900 GLU cc_start: 0.8587 (pt0) cc_final: 0.8226 (tm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 188
  average time/residue: 0.2395
  time to fit residues: 64.9958
Evaluate side-chains
  127 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 141 optimal weight:    4.9990
   chunk 50 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   chunk 100 optimal weight:   20.0000
   chunk 43 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9980
   chunk 29 optimal weight:    8.9990
   chunk 105 optimal weight:    0.2980
   chunk 114 optimal weight:    7.9990
   chunk 76 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 709 GLN
A 730 ASN
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 435 ASN
** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.103067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.086023 restraints weight = 33625.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.087504 restraints weight = 21906.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.088554 restraints weight = 16455.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12066  Z= 0.161
  Angle     :  0.656  13.561  16328  Z= 0.335
  Chirality :  0.043   0.256   1794
  Planarity :  0.005   0.057   2044
  Dihedral  :  4.819  17.845   1584
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.22), residues: 1416
  helix:  0.71 (0.17), residues: 842
  sheet: -3.60 (0.81), residues: 24
  loop : -2.41 (0.25), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 760 
 HIS   0.008   0.001   HIS B 402 
 PHE   0.022   0.002   PHE A 712 
 TYR   0.014   0.002   TYR B 666 
 ARG   0.003   0.000   ARG B 621 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04287 (  652)
  hydrogen bonds       : angle       4.47769 ( 1926)
  SS BOND              : bond        0.00324 (    8)
  SS BOND              : angle       0.97679 (   16)
  covalent geometry    : bond        0.00358 (12058)
  covalent geometry    : angle       0.65572 (16312)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 1.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  405 ASP cc_start: 0.8532 (t0) cc_final: 0.8297 (t70)
REVERT: A  640 ILE cc_start: 0.8018 (pt) cc_final: 0.7767 (mm)
REVERT: B  405 ASP cc_start: 0.8599 (t0) cc_final: 0.8333 (t70)
REVERT: B  760 TRP cc_start: 0.8274 (m100) cc_final: 0.7968 (m-90)
REVERT: B  900 GLU cc_start: 0.8674 (pt0) cc_final: 0.8337 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.2313
  time to fit residues: 59.6378
Evaluate side-chains
  127 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 112 optimal weight:    1.9990
   chunk 132 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 123 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 109 optimal weight:    9.9990
   chunk 65 optimal weight:    7.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 898 HIS
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 730 ASN
B 896 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.103859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.087288 restraints weight = 33440.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.088822 restraints weight = 21538.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.089710 restraints weight = 16166.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.2939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12066  Z= 0.145
  Angle     :  0.638   9.889  16328  Z= 0.328
  Chirality :  0.043   0.268   1794
  Planarity :  0.005   0.055   2044
  Dihedral  :  4.694  17.821   1584
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.22), residues: 1416
  helix:  0.88 (0.17), residues: 836
  sheet: -3.49 (0.83), residues: 24
  loop : -2.33 (0.25), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 760 
 HIS   0.006   0.001   HIS A 402 
 PHE   0.019   0.001   PHE B 499 
 TYR   0.019   0.001   TYR A 182 
 ARG   0.003   0.000   ARG A 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04222 (  652)
  hydrogen bonds       : angle       4.44243 ( 1926)
  SS BOND              : bond        0.00260 (    8)
  SS BOND              : angle       1.41432 (   16)
  covalent geometry    : bond        0.00320 (12058)
  covalent geometry    : angle       0.63668 (16312)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 1.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  500 MET cc_start: 0.8112 (mtp) cc_final: 0.7492 (mtm)
REVERT: A  508 VAL cc_start: 0.8745 (t) cc_final: 0.8484 (p)
REVERT: B  405 ASP cc_start: 0.8489 (t0) cc_final: 0.8256 (t70)
REVERT: B  500 MET cc_start: 0.8469 (mtm) cc_final: 0.8221 (mtm)
REVERT: B  535 ARG cc_start: 0.5960 (mmp-170) cc_final: 0.5503 (mmm160)
REVERT: B  760 TRP cc_start: 0.8215 (m100) cc_final: 0.7954 (m-90)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.2315
  time to fit residues: 59.3904
Evaluate side-chains
  127 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 38 optimal weight:   10.0000
   chunk 122 optimal weight:    0.5980
   chunk 41 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 141 optimal weight:    6.9990
   chunk 83 optimal weight:   10.0000
   chunk 89 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   overall best weight:    2.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 685 GLN
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 896 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.102224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.085572 restraints weight = 34135.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.086868 restraints weight = 22688.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.087900 restraints weight = 17538.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.3024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  12066  Z= 0.188
  Angle     :  0.674  10.282  16328  Z= 0.349
  Chirality :  0.045   0.303   1794
  Planarity :  0.005   0.053   2044
  Dihedral  :  4.818  17.467   1584
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.22), residues: 1416
  helix:  0.81 (0.17), residues: 834
  sheet: -3.48 (0.83), residues: 24
  loop : -2.30 (0.25), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 760 
 HIS   0.008   0.001   HIS A 402 
 PHE   0.020   0.002   PHE B 499 
 TYR   0.018   0.002   TYR B 436 
 ARG   0.006   0.000   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04429 (  652)
  hydrogen bonds       : angle       4.59173 ( 1926)
  SS BOND              : bond        0.00392 (    8)
  SS BOND              : angle       1.03186 (   16)
  covalent geometry    : bond        0.00429 (12058)
  covalent geometry    : angle       0.67378 (16312)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 1.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 TYR cc_start: 0.8576 (t80) cc_final: 0.8206 (t80)
REVERT: A  500 MET cc_start: 0.8171 (mtp) cc_final: 0.7494 (mtm)
REVERT: A  632 MET cc_start: 0.8736 (mmm) cc_final: 0.8458 (tpt)
REVERT: A  640 ILE cc_start: 0.8001 (pt) cc_final: 0.7768 (mm)
REVERT: B  405 ASP cc_start: 0.8504 (t0) cc_final: 0.7484 (p0)
REVERT: B  535 ARG cc_start: 0.5773 (mmp-170) cc_final: 0.5324 (mmm160)
REVERT: B  760 TRP cc_start: 0.8350 (m100) cc_final: 0.8131 (m-90)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.2220
  time to fit residues: 55.2831
Evaluate side-chains
  124 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 1.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 77 optimal weight:    3.9990
   chunk 20 optimal weight:    0.1980
   chunk 139 optimal weight:    0.8980
   chunk 13 optimal weight:    9.9990
   chunk 48 optimal weight:    9.9990
   chunk 81 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 110 optimal weight:    6.9990
   chunk 118 optimal weight:    9.9990
   overall best weight:    1.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 183 HIS
** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 730 ASN
** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 896 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.103360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.086720 restraints weight = 34320.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.088082 restraints weight = 22802.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.089097 restraints weight = 17425.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.3219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12066  Z= 0.152
  Angle     :  0.646   9.907  16328  Z= 0.332
  Chirality :  0.043   0.242   1794
  Planarity :  0.005   0.053   2044
  Dihedral  :  4.740  18.874   1584
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.22), residues: 1416
  helix:  0.84 (0.17), residues: 848
  sheet: -3.39 (0.85), residues: 24
  loop : -2.13 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 760 
 HIS   0.006   0.001   HIS B 402 
 PHE   0.022   0.001   PHE A 499 
 TYR   0.018   0.002   TYR B 436 
 ARG   0.006   0.000   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04277 (  652)
  hydrogen bonds       : angle       4.50995 ( 1926)
  SS BOND              : bond        0.00320 (    8)
  SS BOND              : angle       0.70731 (   16)
  covalent geometry    : bond        0.00340 (12058)
  covalent geometry    : angle       0.64558 (16312)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 1.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  500 MET cc_start: 0.8132 (mtp) cc_final: 0.7416 (mtm)
REVERT: A  508 VAL cc_start: 0.8878 (t) cc_final: 0.8629 (p)
REVERT: A  606 PHE cc_start: 0.7121 (m-80) cc_final: 0.6327 (t80)
REVERT: A  632 MET cc_start: 0.8692 (mmm) cc_final: 0.8253 (tpt)
REVERT: B  405 ASP cc_start: 0.8242 (t0) cc_final: 0.7461 (p0)
REVERT: B  535 ARG cc_start: 0.5805 (mmp-170) cc_final: 0.5370 (mmm160)
REVERT: B  660 MET cc_start: 0.4724 (mmp) cc_final: 0.4440 (mmp)
REVERT: B  760 TRP cc_start: 0.8433 (m100) cc_final: 0.7595 (m-90)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.2272
  time to fit residues: 55.4780
Evaluate side-chains
  124 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 11 optimal weight:    0.0060
   chunk 8 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 101 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0970
   chunk 137 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 122 optimal weight:    0.8980
   chunk 114 optimal weight:    3.9990
   chunk 74 optimal weight:    8.9990
   chunk 7 optimal weight:   10.0000
   overall best weight:    0.9796

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 375 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.105569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.089233 restraints weight = 33423.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.090761 restraints weight = 21973.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.091641 restraints weight = 16473.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.3503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12066  Z= 0.124
  Angle     :  0.616  10.027  16328  Z= 0.313
  Chirality :  0.042   0.239   1794
  Planarity :  0.005   0.053   2044
  Dihedral  :  4.551  17.251   1584
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.22), residues: 1416
  helix:  1.02 (0.17), residues: 850
  sheet: -3.22 (0.84), residues: 24
  loop : -2.00 (0.26), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.002   TRP A 760 
 HIS   0.004   0.001   HIS B 402 
 PHE   0.023   0.001   PHE A 499 
 TYR   0.022   0.001   TYR A 703 
 ARG   0.004   0.000   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04059 (  652)
  hydrogen bonds       : angle       4.40435 ( 1926)
  SS BOND              : bond        0.00253 (    8)
  SS BOND              : angle       0.65421 (   16)
  covalent geometry    : bond        0.00263 (12058)
  covalent geometry    : angle       0.61637 (16312)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 1.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  500 MET cc_start: 0.8073 (mtp) cc_final: 0.7355 (mtm)
REVERT: A  508 VAL cc_start: 0.8805 (t) cc_final: 0.8573 (p)
REVERT: A  606 PHE cc_start: 0.7115 (m-80) cc_final: 0.6352 (t80)
REVERT: B  508 VAL cc_start: 0.8820 (t) cc_final: 0.8584 (p)
REVERT: B  535 ARG cc_start: 0.5716 (mmp-170) cc_final: 0.5452 (mmp-170)
REVERT: B  660 MET cc_start: 0.4638 (mmp) cc_final: 0.4390 (mmp)
REVERT: B  760 TRP cc_start: 0.8292 (m100) cc_final: 0.7517 (m-90)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.2235
  time to fit residues: 61.4461
Evaluate side-chains
  139 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 127 optimal weight:    6.9990
   chunk 75 optimal weight:    7.9990
   chunk 89 optimal weight:    4.9990
   chunk 137 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 60 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9990
   chunk 30 optimal weight:    8.9990
   chunk 57 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 685 GLN
B 896 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.102775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.085894 restraints weight = 33768.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.087383 restraints weight = 22428.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.088246 restraints weight = 17022.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.3462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12066  Z= 0.189
  Angle     :  0.689   9.270  16328  Z= 0.355
  Chirality :  0.045   0.240   1794
  Planarity :  0.005   0.052   2044
  Dihedral  :  4.795  19.463   1584
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.77 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.22), residues: 1416
  helix:  0.77 (0.17), residues: 858
  sheet: -3.24 (0.85), residues: 24
  loop : -2.16 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP A 760 
 HIS   0.007   0.001   HIS A 402 
 PHE   0.021   0.002   PHE A 499 
 TYR   0.018   0.002   TYR B 331 
 ARG   0.004   0.000   ARG A 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04414 (  652)
  hydrogen bonds       : angle       4.50630 ( 1926)
  SS BOND              : bond        0.00409 (    8)
  SS BOND              : angle       1.89130 (   16)
  covalent geometry    : bond        0.00429 (12058)
  covalent geometry    : angle       0.68671 (16312)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 1.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  500 MET cc_start: 0.8172 (mtp) cc_final: 0.7383 (mtm)
REVERT: A  580 LEU cc_start: 0.8298 (tp) cc_final: 0.8089 (tt)
REVERT: B  535 ARG cc_start: 0.5835 (mmp-170) cc_final: 0.5377 (mmm160)
REVERT: B  760 TRP cc_start: 0.8465 (m100) cc_final: 0.7594 (m-90)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.2129
  time to fit residues: 55.0870
Evaluate side-chains
  128 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 1.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 79 optimal weight:    9.9990
   chunk 30 optimal weight:    0.8980
   chunk 31 optimal weight:    6.9990
   chunk 115 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 47 optimal weight:    8.9990
   chunk 113 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 117 optimal weight:    0.9980
   chunk 118 optimal weight:    2.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 284 HIS
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 896 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.105279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.088461 restraints weight = 33092.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.089820 restraints weight = 22401.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.090868 restraints weight = 17357.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.3657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12066  Z= 0.139
  Angle     :  0.647  10.763  16328  Z= 0.330
  Chirality :  0.043   0.242   1794
  Planarity :  0.005   0.052   2044
  Dihedral  :  4.666  17.792   1584
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.22), residues: 1416
  helix:  0.90 (0.17), residues: 858
  sheet: -3.07 (0.85), residues: 24
  loop : -1.97 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 760 
 HIS   0.005   0.001   HIS A 402 
 PHE   0.020   0.001   PHE A 499 
 TYR   0.016   0.001   TYR A 355 
 ARG   0.006   0.000   ARG B 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04162 (  652)
  hydrogen bonds       : angle       4.43673 ( 1926)
  SS BOND              : bond        0.00304 (    8)
  SS BOND              : angle       1.39122 (   16)
  covalent geometry    : bond        0.00304 (12058)
  covalent geometry    : angle       0.64558 (16312)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 1.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  500 MET cc_start: 0.7959 (mtp) cc_final: 0.7245 (mtm)
REVERT: A  508 VAL cc_start: 0.8779 (t) cc_final: 0.8505 (p)
REVERT: A  606 PHE cc_start: 0.7180 (m-80) cc_final: 0.6399 (t80)
REVERT: B  508 VAL cc_start: 0.8819 (t) cc_final: 0.8585 (p)
REVERT: B  535 ARG cc_start: 0.5791 (mmp-170) cc_final: 0.5359 (mmm160)
REVERT: B  760 TRP cc_start: 0.8355 (m100) cc_final: 0.7600 (m-90)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.2303
  time to fit residues: 59.8377
Evaluate side-chains
  134 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 90 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 93 optimal weight:    9.9990
   chunk 81 optimal weight:    3.9990
   chunk 61 optimal weight:   10.0000
   chunk 110 optimal weight:    3.9990
   chunk 137 optimal weight:    0.8980
   chunk 108 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 896 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.106716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.090166 restraints weight = 32876.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.091611 restraints weight = 21999.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.092667 restraints weight = 16828.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.3895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12066  Z= 0.125
  Angle     :  0.627   9.845  16328  Z= 0.318
  Chirality :  0.042   0.238   1794
  Planarity :  0.005   0.052   2044
  Dihedral  :  4.484  17.090   1584
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.22), residues: 1416
  helix:  1.07 (0.17), residues: 850
  sheet: -3.04 (0.85), residues: 24
  loop : -1.88 (0.27), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP A 760 
 HIS   0.003   0.001   HIS A 402 
 PHE   0.021   0.001   PHE A 499 
 TYR   0.020   0.001   TYR A 436 
 ARG   0.008   0.000   ARG A 437 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03955 (  652)
  hydrogen bonds       : angle       4.37928 ( 1926)
  SS BOND              : bond        0.00269 (    8)
  SS BOND              : angle       1.02013 (   16)
  covalent geometry    : bond        0.00267 (12058)
  covalent geometry    : angle       0.62666 (16312)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3485.13 seconds
wall clock time: 61 minutes 57.63 seconds (3717.63 seconds total)