Starting phenix.real_space_refine
on Tue Feb 13 12:57:38 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/02_2024/7rav_24387_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/02_2024/7rav_24387.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/02_2024/7rav_24387.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/02_2024/7rav_24387.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/02_2024/7rav_24387_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/02_2024/7rav_24387_updated.pdb"
  }
  resolution = 3.3
  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=   0.001 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 40 atoms to isotropic.
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
     P       3      5.49       5
     S      39      5.16       5
     C    3976      2.51       5
     N    1046      2.21       5
     O    1151      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   60": "OE1" <-> "OE2"
    Residue "A PHE   73": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  158": "OE1" <-> "OE2"
    Residue "A GLU  159": "OE1" <-> "OE2"
    Residue "A PHE  166": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  168": "OD1" <-> "OD2"
    Residue "A GLU  208": "OE1" <-> "OE2"
    Residue "A GLU  216": "OE1" <-> "OE2"
    Residue "A ASP  272": "OD1" <-> "OD2"
    Residue "A GLU  279": "OE1" <-> "OE2"
    Residue "A GLU  471": "OE1" <-> "OE2"
    Residue "A ASP  551": "OD1" <-> "OD2"
    Residue "A ASP  588": "OD1" <-> "OD2"
    Residue "A TYR  605": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  628": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  629": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  631": "OD1" <-> "OD2"
    Residue "A ASP  634": "OD1" <-> "OD2"
    Residue "A PHE  644": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  706": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  748": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  751": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  764": "OD1" <-> "OD2"
    Residue "A TYR  795": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 6215
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6215
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 774, 6215
          Unusual residues: {'ATP': 1}
          Classifications: {'peptide': 773, 'undetermined': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 746, None: 1}
            Not linked:
              pdbres="ARG A 915 "
              pdbres="ATP A1501 "
          Chain breaks: 3
  Time building chain proxies: 3.94, per 1000 atoms: 0.63
  Number of scatterers: 6215
  At special positions: 0
  Unit cell: (74.858, 78.0662, 133.675, 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)
     S      39     16.00
     P       3     15.00
     O    1151      8.00
     N    1046      7.00
     C    3976      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 100 " - pdb=" SG  CYS A 124 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 224 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 2.43
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1460

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      34 helices and 3 sheets defined
      40.1% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 69
      removed outlier: 4.092A  pdb=" N   THR A  69 " --> pdb=" O   THR A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 84
    Processing helix  chain 'A' and resid 113 through 120
    Processing helix  chain 'A' and resid 160 through 164
    Processing helix  chain 'A' and resid 178 through 184
      removed outlier: 3.826A  pdb=" N   ALA A 184 " --> pdb=" O   VAL A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 220
    Processing helix  chain 'A' and resid 225 through 230
    Processing helix  chain 'A' and resid 235 through 239
    Processing helix  chain 'A' and resid 275 through 281
      removed outlier: 4.022A  pdb=" N   LEU A 280 " --> pdb=" O   ALA A 276 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ARG A 281 " --> pdb=" O   ASN A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 300
    Processing helix  chain 'A' and resid 333 through 339
    Processing helix  chain 'A' and resid 343 through 349
    Processing helix  chain 'A' and resid 402 through 417
    Processing helix  chain 'A' and resid 455 through 461
      removed outlier: 3.711A  pdb=" N   PHE A 459 " --> pdb=" O   ILE A 455 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   SER A 460 " --> pdb=" O   PRO A 456 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ASN A 461 " --> pdb=" O   GLU A 457 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 455 through 461'
    Processing helix  chain 'A' and resid 476 through 488
    Processing helix  chain 'A' and resid 493 through 497
      removed outlier: 3.803A  pdb=" N   ARG A 497 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 520
    Processing helix  chain 'A' and resid 532 through 541
    Processing helix  chain 'A' and resid 556 through 558
      No H-bonds generated for 'chain 'A' and resid 556 through 558'
    Processing helix  chain 'A' and resid 561 through 568
    Processing helix  chain 'A' and resid 604 through 614
    Processing helix  chain 'A' and resid 620 through 629
    Processing helix  chain 'A' and resid 642 through 653
    Processing helix  chain 'A' and resid 663 through 703
      removed outlier: 3.880A  pdb=" N   LYS A 680 " --> pdb=" O   SER A 676 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   ALA A 681 " --> pdb=" O   LEU A 677 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   THR A 682 " --> pdb=" O   LYS A 678 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   GLU A 684 " --> pdb=" O   LYS A 680 " (cutoff:3.500A)
      Proline residue:  A 685  - end of helix
      removed outlier: 3.916A  pdb=" N   LEU A 696 " --> pdb=" O   SER A 692 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ALA A 697 " --> pdb=" O   CYS A 693 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   PHE A 702 " --> pdb=" O   LEU A 698 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   SER A 703 " --> pdb=" O   THR A 699 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 716
      removed outlier: 3.749A  pdb=" N   ALA A 714 " --> pdb=" O   SER A 710 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLU A 715 " --> pdb=" O   ASP A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 724 through 727
    Processing helix  chain 'A' and resid 746 through 762
    Processing helix  chain 'A' and resid 766 through 777
      removed outlier: 4.432A  pdb=" N   LEU A 771 " --> pdb=" O   GLU A 767 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   GLY A 772 " --> pdb=" O   ASP A 768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 787
    Processing helix  chain 'A' and resid 793 through 796
      No H-bonds generated for 'chain 'A' and resid 793 through 796'
    Processing helix  chain 'A' and resid 802 through 815
      Proline residue:  A 806  - end of helix
      removed outlier: 3.835A  pdb=" N   LEU A 815 " --> pdb=" O   HIS A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 858 through 877
      removed outlier: 3.993A  pdb=" N   THR A 877 " --> pdb=" O   TYR A 873 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 881 through 886
      removed outlier: 4.224A  pdb=" N   ILE A 885 " --> pdb=" O   CYS A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 911 through 913
      No H-bonds generated for 'chain 'A' and resid 911 through 913'
    Processing sheet with id=  A, first strand: chain 'A' and resid 86 through 88
    Processing sheet with id=  B, first strand: chain 'A' and resid 186 through 188
    Processing sheet with id=  C, first strand: chain 'A' and resid 466 through 468
      removed outlier: 6.813A  pdb=" N   LEU A 500 " --> pdb=" O   LEU A 547 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   LEU A 549 " --> pdb=" O   LEU A 500 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   PHE A 502 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   ASP A 551 " --> pdb=" O   PHE A 502 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   LEU A 504 " --> pdb=" O   ASP A 551 " (cutoff:3.500A)

    168 hydrogen bonds defined for protein.
    444 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: 1.53

  Time building geometry restraints manager: 2.63 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: 1961
        1.34 -     1.46: 1377
        1.46 -     1.58: 2962
        1.58 -     1.70: 5
        1.70 -     1.83: 52
  Bond restraints: 6357
  Sorted by residual:
  bond pdb=" C4  ATP A1501 "
       pdb=" C5  ATP A1501 "
    ideal  model  delta    sigma   weight residual
    1.388  1.467 -0.079 1.00e-02 1.00e+04 6.24e+01
  bond pdb=" C5  ATP A1501 "
       pdb=" C6  ATP A1501 "
    ideal  model  delta    sigma   weight residual
    1.409  1.478 -0.069 1.00e-02 1.00e+04 4.79e+01
  bond pdb=" C8  ATP A1501 "
       pdb=" N7  ATP A1501 "
    ideal  model  delta    sigma   weight residual
    1.310  1.356 -0.046 1.00e-02 1.00e+04 2.11e+01
  bond pdb=" C5  ATP A1501 "
       pdb=" N7  ATP A1501 "
    ideal  model  delta    sigma   weight residual
    1.387  1.342  0.045 1.00e-02 1.00e+04 2.01e+01
  bond pdb=" C4  ATP A1501 "
       pdb=" N9  ATP A1501 "
    ideal  model  delta    sigma   weight residual
    1.374  1.331  0.043 1.00e-02 1.00e+04 1.89e+01
  ... (remaining 6352 not shown)

  Histogram of bond angle deviations from ideal:
       99.15 -   106.53: 158
      106.53 -   113.91: 3493
      113.91 -   121.28: 3388
      121.28 -   128.66: 1506
      128.66 -   136.04: 48
  Bond angle restraints: 8593
  Sorted by residual:
  angle pdb=" PB  ATP A1501 "
        pdb=" O3B ATP A1501 "
        pdb=" PG  ATP A1501 "
      ideal   model   delta    sigma   weight residual
     139.87  119.24   20.63 1.00e+00 1.00e+00 4.26e+02
  angle pdb=" PA  ATP A1501 "
        pdb=" O3A ATP A1501 "
        pdb=" PB  ATP A1501 "
      ideal   model   delta    sigma   weight residual
     136.83  118.98   17.85 1.00e+00 1.00e+00 3.19e+02
  angle pdb=" N   GLY A 175 "
        pdb=" CA  GLY A 175 "
        pdb=" C   GLY A 175 "
      ideal   model   delta    sigma   weight residual
     112.73  100.90   11.83 1.20e+00 6.94e-01 9.72e+01
  angle pdb=" C5  ATP A1501 "
        pdb=" C4  ATP A1501 "
        pdb=" N3  ATP A1501 "
      ideal   model   delta    sigma   weight residual
     126.80  118.66    8.14 1.00e+00 1.00e+00 6.62e+01
  angle pdb=" N3  ATP A1501 "
        pdb=" C4  ATP A1501 "
        pdb=" N9  ATP A1501 "
      ideal   model   delta    sigma   weight residual
     127.04  134.79   -7.75 1.15e+00 7.59e-01 4.56e+01
  ... (remaining 8588 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 3348
       17.97 -    35.93: 371
       35.93 -    53.90: 71
       53.90 -    71.86: 15
       71.86 -    89.83: 11
  Dihedral angle restraints: 3816
    sinusoidal: 1559
      harmonic: 2257
  Sorted by residual:
  dihedral pdb=" CB  CYS A 100 "
           pdb=" SG  CYS A 100 "
           pdb=" SG  CYS A 124 "
           pdb=" CB  CYS A 124 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   48.56   44.44     1      1.00e+01 1.00e-02 2.75e+01
  dihedral pdb=" CA  HIS A 157 "
           pdb=" C   HIS A 157 "
           pdb=" N   GLU A 158 "
           pdb=" CA  GLU A 158 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.55  -25.45     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  ILE A 135 "
           pdb=" C   ILE A 135 "
           pdb=" N   GLY A 136 "
           pdb=" CA  GLY A 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.40   23.60     0      5.00e+00 4.00e-02 2.23e+01
  ... (remaining 3813 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 756
       0.058 -    0.117: 170
       0.117 -    0.175: 18
       0.175 -    0.233: 2
       0.233 -    0.292: 1
  Chirality restraints: 947
  Sorted by residual:
  chirality pdb=" CA  PRO A 340 "
            pdb=" N   PRO A 340 "
            pdb=" C   PRO A 340 "
            pdb=" CB  PRO A 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.43    0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CA  HIS A 174 "
            pdb=" N   HIS A 174 "
            pdb=" C   HIS A 174 "
            pdb=" CB  HIS A 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.05e-01
  chirality pdb=" CA  GLN A 766 "
            pdb=" N   GLN A 766 "
            pdb=" C   GLN A 766 "
            pdb=" CB  GLN A 766 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.68e-01
  ... (remaining 944 not shown)

  Planarity restraints: 1089
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 339 "    0.061 5.00e-02 4.00e+02   9.20e-02 1.36e+01
        pdb=" N   PRO A 340 "   -0.159 5.00e-02 4.00e+02
        pdb=" CA  PRO A 340 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A 340 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 492 "   -0.038 5.00e-02 4.00e+02   5.85e-02 5.48e+00
        pdb=" N   PRO A 493 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A 493 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 493 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 330 "    0.037 5.00e-02 4.00e+02   5.58e-02 4.97e+00
        pdb=" N   PRO A 331 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 331 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 331 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1086 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1072
        2.76 -     3.29: 6549
        3.29 -     3.83: 9935
        3.83 -     4.36: 11671
        4.36 -     4.90: 18886
  Nonbonded interactions: 48113
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 172 "
            pdb=" NH2 ARG A 261 "
     model   vdw
     2.224 2.520
  nonbonded pdb=" NZ  LYS A 723 "
            pdb=" OG1 THR A 725 "
     model   vdw
     2.224 2.520
  nonbonded pdb=" NH1 ARG A 314 "
            pdb=" O   THR A 430 "
     model   vdw
     2.242 2.520
  nonbonded pdb=" OG  SER A 554 "
            pdb=" OG  SER A 558 "
     model   vdw
     2.247 2.440
  nonbonded pdb=" O   ASN A 900 "
            pdb=" ND2 ASN A 900 "
     model   vdw
     2.248 2.520
  ... (remaining 48108 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          3.690
  Check model and map are aligned:         0.090
  Set scattering table:                    0.050
  Process input model:                     20.630
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
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      :  0.004   0.079   6357  Z= 0.275
  Angle     :  0.930  20.628   8593  Z= 0.590
  Chirality :  0.049   0.292    947
  Planarity :  0.005   0.092   1089
  Dihedral  : 15.924  89.826   2350
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 16.68
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 16.73 %
    Favored  : 82.88 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  0.44 %
    Favored  : 98.39 %
  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: -3.36 (0.29), residues: 765
  helix: -0.98 (0.29), residues: 313
  sheet: -1.74 (0.75), residues: 37
  loop : -3.46 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 220 
 HIS   0.006   0.001   HIS A 582 
 PHE   0.027   0.002   PHE A 859 
 TYR   0.037   0.002   TYR A 496 
 ARG   0.008   0.001   ARG A  74 

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 683 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 225
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7514 (tpp) cc_final: 0.7266 (tpp)
REVERT: A   57 MET cc_start: 0.7615 (ptp) cc_final: 0.7405 (ptp)
REVERT: A  148 MET cc_start: 0.6317 (tmm) cc_final: 0.6110 (tmm)
REVERT: A  160 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7252 (tm-30)
REVERT: A  164 GLU cc_start: 0.7523 (pp20) cc_final: 0.7231 (pp20)
REVERT: A  167 GLU cc_start: 0.7299 (mp0) cc_final: 0.6992 (mp0)
REVERT: A  332 MET cc_start: 0.5342 (pmm) cc_final: 0.5045 (pmm)
REVERT: A  408 ARG cc_start: 0.7768 (tmm-80) cc_final: 0.7230 (tmm-80)
REVERT: A  443 LYS cc_start: 0.8249 (mtmm) cc_final: 0.7908 (mtmm)
REVERT: A  535 LEU cc_start: 0.8699 (tp) cc_final: 0.8470 (tp)
REVERT: A  551 ASP cc_start: 0.7114 (t70) cc_final: 0.6681 (t0)
REVERT: A  598 GLU cc_start: 0.6899 (tt0) cc_final: 0.6650 (tt0)
REVERT: A  630 ILE cc_start: 0.8585 (tp) cc_final: 0.8332 (tp)
REVERT: A  651 ASP cc_start: 0.7321 (t0) cc_final: 0.7087 (t0)
REVERT: A  812 LEU cc_start: 0.8393 (mt) cc_final: 0.8094 (mt)
REVERT: A  814 GLN cc_start: 0.7762 (pp30) cc_final: 0.7405 (pp30)
REVERT: A  865 LEU cc_start: 0.8483 (mm) cc_final: 0.8281 (mm)
REVERT: A  867 LEU cc_start: 0.8955 (pp) cc_final: 0.8365 (pp)
REVERT: A  869 LEU cc_start: 0.8422 (mm) cc_final: 0.8213 (mm)
REVERT: A  871 PHE cc_start: 0.7230 (m-80) cc_final: 0.6856 (m-80)
  outliers start: 8
  outliers final: 0
  residues processed: 228
  average time/residue: 0.2120
  time to fit residues: 61.0146
Evaluate side-chains
  198 residues out of total 683 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 31 optimal weight:    0.3980
   chunk 60 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 206 ASN
A 570 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.1328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6357  Z= 0.271
  Angle     :  0.756   9.530   8593  Z= 0.394
  Chirality :  0.047   0.176    947
  Planarity :  0.005   0.050   1089
  Dihedral  :  7.903  85.352    871
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 16.19
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 17.25 %
    Favored  : 82.48 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 14.49 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    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: -3.14 (0.30), residues: 765
  helix: -0.68 (0.30), residues: 330
  sheet: -1.78 (0.69), residues: 42
  loop : -3.53 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 220 
 HIS   0.005   0.001   HIS A 253 
 PHE   0.055   0.002   PHE A 792 
 TYR   0.044   0.003   TYR A 496 
 ARG   0.006   0.001   ARG A 585 

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 683 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 214
  time to evaluate  : 0.794 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7520 (tpp) cc_final: 0.7195 (tpp)
REVERT: A   57 MET cc_start: 0.7759 (ptp) cc_final: 0.7524 (ptp)
REVERT: A  138 TYR cc_start: 0.7232 (t80) cc_final: 0.6871 (t80)
REVERT: A  148 MET cc_start: 0.6434 (tmm) cc_final: 0.6158 (tmm)
REVERT: A  160 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7291 (tm-30)
REVERT: A  167 GLU cc_start: 0.7403 (mp0) cc_final: 0.7114 (mp0)
REVERT: A  332 MET cc_start: 0.5460 (pmm) cc_final: 0.5112 (pmm)
REVERT: A  408 ARG cc_start: 0.7742 (tmm-80) cc_final: 0.7198 (tmm-80)
REVERT: A  443 LYS cc_start: 0.8379 (mtmm) cc_final: 0.7925 (mtmm)
REVERT: A  454 THR cc_start: 0.8353 (p) cc_final: 0.8047 (t)
REVERT: A  455 ILE cc_start: 0.8500 (mm) cc_final: 0.8036 (tp)
REVERT: A  457 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7904 (tm-30)
REVERT: A  535 LEU cc_start: 0.8782 (tp) cc_final: 0.8530 (tp)
REVERT: A  551 ASP cc_start: 0.7038 (t70) cc_final: 0.6676 (t70)
REVERT: A  590 ARG cc_start: 0.7600 (tpp-160) cc_final: 0.7297 (tpp-160)
REVERT: A  598 GLU cc_start: 0.6945 (tt0) cc_final: 0.6671 (tt0)
REVERT: A  630 ILE cc_start: 0.8687 (tp) cc_final: 0.8357 (tp)
REVERT: A  766 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7744 (pp30)
REVERT: A  812 LEU cc_start: 0.8438 (mt) cc_final: 0.8099 (mt)
REVERT: A  814 GLN cc_start: 0.7899 (pp30) cc_final: 0.7508 (pp30)
REVERT: A  865 LEU cc_start: 0.8511 (mm) cc_final: 0.8285 (mm)
REVERT: A  867 LEU cc_start: 0.8942 (pp) cc_final: 0.8387 (pp)
REVERT: A  869 LEU cc_start: 0.8498 (mm) cc_final: 0.8285 (mm)
REVERT: A  871 PHE cc_start: 0.7378 (m-80) cc_final: 0.6909 (m-80)
REVERT: A  873 TYR cc_start: 0.7344 (t80) cc_final: 0.6929 (t80)
  outliers start: 11
  outliers final: 9
  residues processed: 219
  average time/residue: 0.2232
  time to fit residues: 61.3871
Evaluate side-chains
  211 residues out of total 683 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 202
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  126 PHE
Chi-restraints excluded: chain A residue  174 HIS
Chi-restraints excluded: chain A residue  206 ASN
Chi-restraints excluded: chain A residue  405 GLU
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  596 SER
Chi-restraints excluded: chain A residue  624 LYS
Chi-restraints excluded: chain A residue  771 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 19 optimal weight:    0.3980
   chunk 70 optimal weight:    0.4980
   chunk 75 optimal weight:    0.5980
   chunk 62 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 570 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
moved from start:          0.1646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6357  Z= 0.225
  Angle     :  0.706   8.973   8593  Z= 0.366
  Chirality :  0.045   0.170    947
  Planarity :  0.005   0.047   1089
  Dihedral  :  7.654  82.622    871
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 16.60 %
    Favored  : 83.14 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 20.35 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.01 (0.30), residues: 765
  helix: -0.44 (0.31), residues: 322
  sheet: -1.65 (0.74), residues: 37
  loop : -3.53 (0.28), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 220 
 HIS   0.005   0.001   HIS A 811 
 PHE   0.036   0.002   PHE A 792 
 TYR   0.025   0.002   TYR A 496 
 ARG   0.005   0.001   ARG A  92 

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 683 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 202
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7512 (tpp) cc_final: 0.7221 (tpp)
REVERT: A   57 MET cc_start: 0.7779 (ptp) cc_final: 0.7536 (ptp)
REVERT: A  138 TYR cc_start: 0.7164 (t80) cc_final: 0.6772 (t80)
REVERT: A  148 MET cc_start: 0.6419 (tmm) cc_final: 0.6103 (tmm)
REVERT: A  160 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7321 (tm-30)
REVERT: A  164 GLU cc_start: 0.7626 (pp20) cc_final: 0.7356 (pp20)
REVERT: A  167 GLU cc_start: 0.7372 (mp0) cc_final: 0.6991 (mp0)
REVERT: A  206 ASN cc_start: 0.8236 (m-40) cc_final: 0.7732 (m-40)
REVERT: A  208 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6725 (mm-30)
REVERT: A  226 PHE cc_start: 0.8623 (t80) cc_final: 0.8210 (t80)
REVERT: A  282 MET cc_start: 0.6412 (tpt) cc_final: 0.6210 (tpt)
REVERT: A  332 MET cc_start: 0.5457 (pmm) cc_final: 0.5088 (pmm)
REVERT: A  408 ARG cc_start: 0.7698 (tmm-80) cc_final: 0.7200 (tmm-80)
REVERT: A  454 THR cc_start: 0.8290 (p) cc_final: 0.8077 (t)
REVERT: A  457 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7820 (tm-30)
REVERT: A  535 LEU cc_start: 0.8691 (tp) cc_final: 0.8436 (tp)
REVERT: A  551 ASP cc_start: 0.7009 (t70) cc_final: 0.6672 (t70)
REVERT: A  585 ARG cc_start: 0.8395 (mmm-85) cc_final: 0.8158 (mmm-85)
REVERT: A  630 ILE cc_start: 0.8669 (tp) cc_final: 0.8341 (tp)
REVERT: A  709 ASN cc_start: 0.7565 (p0) cc_final: 0.6896 (p0)
REVERT: A  712 ASP cc_start: 0.8118 (m-30) cc_final: 0.7833 (m-30)
REVERT: A  766 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7705 (pp30)
REVERT: A  812 LEU cc_start: 0.8352 (mt) cc_final: 0.8038 (mt)
REVERT: A  814 GLN cc_start: 0.7943 (pp30) cc_final: 0.7557 (pp30)
REVERT: A  865 LEU cc_start: 0.8486 (mm) cc_final: 0.8252 (mm)
REVERT: A  867 LEU cc_start: 0.8920 (pp) cc_final: 0.8386 (pp)
REVERT: A  871 PHE cc_start: 0.7382 (m-80) cc_final: 0.6896 (m-80)
REVERT: A  873 TYR cc_start: 0.7376 (t80) cc_final: 0.6918 (t80)
  outliers start: 11
  outliers final: 6
  residues processed: 206
  average time/residue: 0.2103
  time to fit residues: 54.8515
Evaluate side-chains
  208 residues out of total 683 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 202
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 HIS
Chi-restraints excluded: chain A residue  405 GLU
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  624 LYS
Chi-restraints excluded: chain A residue  691 SER
Chi-restraints excluded: chain A residue  705 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 61 optimal weight:    0.1980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 206 ASN
** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 570 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6357  Z= 0.228
  Angle     :  0.698   9.098   8593  Z= 0.362
  Chirality :  0.046   0.194    947
  Planarity :  0.004   0.047   1089
  Dihedral  :  7.511  76.276    871
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 15.71
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 16.99 %
    Favored  : 82.88 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 21.52 %
    Favored  : 75.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.96 (0.30), residues: 765
  helix: -0.35 (0.31), residues: 320
  sheet: -1.69 (0.73), residues: 37
  loop : -3.53 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 220 
 HIS   0.004   0.001   HIS A 582 
 PHE   0.030   0.002   PHE A 792 
 TYR   0.021   0.002   TYR A 903 
 ARG   0.012   0.001   ARG A  92 

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 683 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 211
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7533 (tpp) cc_final: 0.7210 (tpp)
REVERT: A  138 TYR cc_start: 0.7268 (t80) cc_final: 0.6809 (t80)
REVERT: A  148 MET cc_start: 0.6430 (tmm) cc_final: 0.6113 (tmm)
REVERT: A  160 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7336 (tm-30)
REVERT: A  282 MET cc_start: 0.6476 (tpt) cc_final: 0.6250 (tpt)
REVERT: A  332 MET cc_start: 0.5543 (pmm) cc_final: 0.5161 (pmm)
REVERT: A  408 ARG cc_start: 0.7708 (tmm-80) cc_final: 0.7227 (tmm-80)
REVERT: A  542 LEU cc_start: 0.8595 (mt) cc_final: 0.8265 (mp)
REVERT: A  551 ASP cc_start: 0.7013 (t70) cc_final: 0.6593 (t0)
REVERT: A  590 ARG cc_start: 0.7629 (tpp-160) cc_final: 0.7361 (tpp80)
REVERT: A  628 TYR cc_start: 0.7396 (t80) cc_final: 0.6816 (t80)
REVERT: A  630 ILE cc_start: 0.8679 (tp) cc_final: 0.8363 (tp)
REVERT: A  723 LYS cc_start: 0.8008 (tmtt) cc_final: 0.7667 (tmtt)
REVERT: A  766 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8173 (tm-30)
REVERT: A  812 LEU cc_start: 0.8353 (mt) cc_final: 0.8026 (mt)
REVERT: A  814 GLN cc_start: 0.7963 (pp30) cc_final: 0.7547 (pp30)
REVERT: A  865 LEU cc_start: 0.8499 (mm) cc_final: 0.8283 (mm)
REVERT: A  867 LEU cc_start: 0.8917 (pp) cc_final: 0.8384 (pp)
REVERT: A  871 PHE cc_start: 0.7382 (m-80) cc_final: 0.6947 (m-80)
REVERT: A  873 TYR cc_start: 0.7420 (t80) cc_final: 0.6979 (t80)
  outliers start: 20
  outliers final: 11
  residues processed: 218
  average time/residue: 0.2185
  time to fit residues: 60.3569
Evaluate side-chains
  210 residues out of total 683 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 199
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 MET
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  405 GLU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  705 CYS
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  911 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 63 optimal weight:    0.0070
   chunk 51 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
A 206 ASN
** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 570 ASN
A 606 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7074
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6357  Z= 0.230
  Angle     :  0.712   8.815   8593  Z= 0.365
  Chirality :  0.046   0.213    947
  Planarity :  0.004   0.047   1089
  Dihedral  :  7.397  73.478    871
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 16.03
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 16.73 %
    Favored  : 83.14 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 22.40 %
    Favored  : 73.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.89 (0.30), residues: 765
  helix: -0.31 (0.31), residues: 321
  sheet: -1.70 (0.71), residues: 37
  loop : -3.48 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 220 
 HIS   0.004   0.001   HIS A 582 
 PHE   0.026   0.001   PHE A 792 
 TYR   0.021   0.002   TYR A 903 
 ARG   0.005   0.001   ARG A 417 

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 683 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 208
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7551 (tpp) cc_final: 0.7250 (tpp)
REVERT: A  138 TYR cc_start: 0.7325 (t80) cc_final: 0.6933 (t80)
REVERT: A  148 MET cc_start: 0.6381 (tmm) cc_final: 0.6102 (tmm)
REVERT: A  160 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7350 (tm-30)
REVERT: A  164 GLU cc_start: 0.7888 (pp20) cc_final: 0.7649 (pp20)
REVERT: A  167 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7493 (mm-30)
REVERT: A  208 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6782 (mm-30)
REVERT: A  282 MET cc_start: 0.6476 (tpt) cc_final: 0.6251 (tpt)
REVERT: A  332 MET cc_start: 0.5563 (pmm) cc_final: 0.5171 (pmm)
REVERT: A  408 ARG cc_start: 0.7717 (tmm-80) cc_final: 0.7337 (tmm-80)
REVERT: A  457 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7889 (tm-30)
REVERT: A  532 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7494 (mm-30)
REVERT: A  541 GLN cc_start: 0.7901 (pt0) cc_final: 0.7644 (pt0)
REVERT: A  542 LEU cc_start: 0.8535 (mt) cc_final: 0.8240 (mp)
REVERT: A  551 ASP cc_start: 0.6934 (t70) cc_final: 0.6632 (t70)
REVERT: A  630 ILE cc_start: 0.8650 (tp) cc_final: 0.8338 (tp)
REVERT: A  723 LYS cc_start: 0.8022 (tmtt) cc_final: 0.7694 (tmtt)
REVERT: A  766 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8108 (tm-30)
REVERT: A  778 GLN cc_start: 0.7777 (mp10) cc_final: 0.7468 (mp10)
REVERT: A  812 LEU cc_start: 0.8343 (mt) cc_final: 0.8010 (mt)
REVERT: A  814 GLN cc_start: 0.7960 (pp30) cc_final: 0.7521 (pp30)
REVERT: A  865 LEU cc_start: 0.8511 (mm) cc_final: 0.8185 (mt)
REVERT: A  867 LEU cc_start: 0.8917 (pp) cc_final: 0.8403 (pp)
REVERT: A  871 PHE cc_start: 0.7404 (m-80) cc_final: 0.6973 (m-80)
REVERT: A  873 TYR cc_start: 0.7406 (t80) cc_final: 0.6982 (t80)
  outliers start: 25
  outliers final: 20
  residues processed: 219
  average time/residue: 0.2200
  time to fit residues: 61.5350
Evaluate side-chains
  220 residues out of total 683 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 200
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 MET
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  174 HIS
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  405 GLU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  596 SER
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  624 LYS
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  691 SER
Chi-restraints excluded: chain A residue  705 CYS
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  911 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0570
   chunk 43 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0370
   chunk 74 optimal weight:    0.5980
   chunk 61 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0870
   chunk 6 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.2954

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 517 ASN
A 570 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7025
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6357  Z= 0.176
  Angle     :  0.686   9.267   8593  Z= 0.352
  Chirality :  0.045   0.290    947
  Planarity :  0.004   0.045   1089
  Dihedral  :  7.121  74.284    871
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 14.77 %
    Favored  : 85.10 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 24.16 %
    Favored  : 72.91 %
  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: -2.78 (0.30), residues: 765
  helix: -0.24 (0.31), residues: 319
  sheet: -1.64 (0.71), residues: 37
  loop : -3.39 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 220 
 HIS   0.005   0.001   HIS A 444 
 PHE   0.025   0.001   PHE A 792 
 TYR   0.020   0.002   TYR A 903 
 ARG   0.011   0.001   ARG A  92 

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 683 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 202
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7557 (tpp) cc_final: 0.7308 (tpp)
REVERT: A  148 MET cc_start: 0.6297 (tmm) cc_final: 0.6050 (tmm)
REVERT: A  160 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7313 (tm-30)
REVERT: A  208 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6830 (mm-30)
REVERT: A  282 MET cc_start: 0.6458 (tpt) cc_final: 0.6247 (tpt)
REVERT: A  332 MET cc_start: 0.5496 (pmm) cc_final: 0.5107 (pmm)
REVERT: A  408 ARG cc_start: 0.7599 (tmm-80) cc_final: 0.7257 (tmm-80)
REVERT: A  441 ILE cc_start: 0.8198 (mp) cc_final: 0.7994 (pt)
REVERT: A  443 LYS cc_start: 0.8573 (mtmm) cc_final: 0.8182 (mtmm)
REVERT: A  457 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7802 (tm-30)
REVERT: A  532 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7472 (mm-30)
REVERT: A  541 GLN cc_start: 0.7859 (pt0) cc_final: 0.7646 (pt0)
REVERT: A  551 ASP cc_start: 0.6941 (t70) cc_final: 0.6538 (t0)
REVERT: A  628 TYR cc_start: 0.7313 (t80) cc_final: 0.6706 (t80)
REVERT: A  630 ILE cc_start: 0.8608 (tp) cc_final: 0.8299 (tp)
REVERT: A  695 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7592 (tm-30)
REVERT: A  723 LYS cc_start: 0.8140 (tmtt) cc_final: 0.7762 (tmtt)
REVERT: A  747 LEU cc_start: 0.8258 (mm) cc_final: 0.8053 (mm)
REVERT: A  766 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8013 (tm-30)
REVERT: A  776 LEU cc_start: 0.8257 (tp) cc_final: 0.8030 (tp)
REVERT: A  812 LEU cc_start: 0.8353 (mt) cc_final: 0.8016 (mt)
REVERT: A  814 GLN cc_start: 0.7922 (pp30) cc_final: 0.7476 (pp30)
REVERT: A  863 HIS cc_start: 0.7255 (m90) cc_final: 0.6581 (m90)
REVERT: A  865 LEU cc_start: 0.8533 (mm) cc_final: 0.8217 (mt)
REVERT: A  867 LEU cc_start: 0.8932 (pp) cc_final: 0.8430 (pp)
REVERT: A  871 PHE cc_start: 0.7361 (m-80) cc_final: 0.6955 (m-80)
REVERT: A  873 TYR cc_start: 0.7371 (t80) cc_final: 0.6972 (t80)
  outliers start: 20
  outliers final: 17
  residues processed: 209
  average time/residue: 0.2496
  time to fit residues: 65.5734
Evaluate side-chains
  212 residues out of total 683 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 195
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 MET
Chi-restraints excluded: chain A residue  174 HIS
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  405 GLU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  596 SER
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  624 LYS
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  911 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0770
   chunk 62 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0980
   chunk 74 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0770
   chunk 29 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.4500

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 570 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6357  Z= 0.205
  Angle     :  0.709  12.229   8593  Z= 0.363
  Chirality :  0.046   0.328    947
  Planarity :  0.004   0.043   1089
  Dihedral  :  7.065  71.157    871
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 16.60
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 14.90 %
    Favored  : 84.97 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 25.92 %
    Favored  : 71.16 %
  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: -2.78 (0.30), residues: 765
  helix: -0.19 (0.31), residues: 315
  sheet: -1.68 (0.69), residues: 37
  loop : -3.39 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 220 
 HIS   0.002   0.001   HIS A 582 
 PHE   0.017   0.001   PHE A 629 
 TYR   0.020   0.002   TYR A 903 
 ARG   0.006   0.001   ARG A  92 

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 683 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 196
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7552 (tpp) cc_final: 0.7318 (tpp)
REVERT: A  148 MET cc_start: 0.6217 (tmm) cc_final: 0.5998 (tmm)
REVERT: A  160 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7323 (tm-30)
REVERT: A  226 PHE cc_start: 0.8570 (t80) cc_final: 0.8197 (t80)
REVERT: A  262 GLU cc_start: 0.7161 (pm20) cc_final: 0.6697 (pm20)
REVERT: A  282 MET cc_start: 0.6502 (tpt) cc_final: 0.6282 (tpt)
REVERT: A  332 MET cc_start: 0.5463 (pmm) cc_final: 0.5084 (pmm)
REVERT: A  408 ARG cc_start: 0.7654 (tmm-80) cc_final: 0.7269 (tmm-80)
REVERT: A  409 ASP cc_start: 0.7459 (t0) cc_final: 0.7160 (t0)
REVERT: A  457 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7804 (tm-30)
REVERT: A  532 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7452 (mm-30)
REVERT: A  551 ASP cc_start: 0.6925 (t70) cc_final: 0.6597 (t70)
REVERT: A  585 ARG cc_start: 0.8426 (mmm-85) cc_final: 0.8151 (mmm-85)
REVERT: A  628 TYR cc_start: 0.7354 (t80) cc_final: 0.6855 (t80)
REVERT: A  630 ILE cc_start: 0.8588 (tp) cc_final: 0.8291 (tp)
REVERT: A  695 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7530 (tm-30)
REVERT: A  712 ASP cc_start: 0.8190 (m-30) cc_final: 0.7962 (m-30)
REVERT: A  723 LYS cc_start: 0.8175 (tmtt) cc_final: 0.7778 (tmtt)
REVERT: A  747 LEU cc_start: 0.8271 (mm) cc_final: 0.8060 (mm)
REVERT: A  766 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8216 (tm-30)
REVERT: A  812 LEU cc_start: 0.8350 (mt) cc_final: 0.8030 (mt)
REVERT: A  814 GLN cc_start: 0.7951 (pp30) cc_final: 0.7486 (pp30)
REVERT: A  863 HIS cc_start: 0.7300 (m90) cc_final: 0.6585 (m90)
REVERT: A  865 LEU cc_start: 0.8565 (mm) cc_final: 0.8255 (mt)
REVERT: A  867 LEU cc_start: 0.8952 (pp) cc_final: 0.8466 (pp)
REVERT: A  871 PHE cc_start: 0.7379 (m-80) cc_final: 0.6978 (m-80)
REVERT: A  873 TYR cc_start: 0.7356 (t80) cc_final: 0.6954 (t80)
  outliers start: 20
  outliers final: 17
  residues processed: 202
  average time/residue: 0.2132
  time to fit residues: 54.2030
Evaluate side-chains
  213 residues out of total 683 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 196
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 MET
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  174 HIS
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  405 GLU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  570 ASN
Chi-restraints excluded: chain A residue  596 SER
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  624 LYS
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  911 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 22 optimal weight:    0.0270
   chunk 14 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 58 optimal weight:    0.7980
   chunk 67 optimal weight:    0.4980
   chunk 71 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 570 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7046
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6357  Z= 0.217
  Angle     :  0.712  13.077   8593  Z= 0.365
  Chirality :  0.047   0.356    947
  Planarity :  0.004   0.042   1089
  Dihedral  :  7.064  69.806    871
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 17.00
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 15.95 %
    Favored  : 83.92 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 26.06 %
    Favored  : 70.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.77 (0.30), residues: 765
  helix: -0.20 (0.31), residues: 316
  sheet: -1.67 (0.69), residues: 37
  loop : -3.39 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 220 
 HIS   0.002   0.001   HIS A 582 
 PHE   0.017   0.001   PHE A 629 
 TYR   0.018   0.002   TYR A 903 
 ARG   0.007   0.001   ARG A  92 

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 683 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 195
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7547 (tpp) cc_final: 0.7317 (tpp)
REVERT: A  148 MET cc_start: 0.6207 (tmm) cc_final: 0.5955 (tmm)
REVERT: A  160 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7241 (tm-30)
REVERT: A  226 PHE cc_start: 0.8573 (t80) cc_final: 0.8202 (t80)
REVERT: A  282 MET cc_start: 0.6518 (tpt) cc_final: 0.6294 (tpt)
REVERT: A  332 MET cc_start: 0.5469 (pmm) cc_final: 0.5080 (pmm)
REVERT: A  408 ARG cc_start: 0.7657 (tmm-80) cc_final: 0.7280 (tmm-80)
REVERT: A  409 ASP cc_start: 0.7457 (t0) cc_final: 0.7143 (t0)
REVERT: A  457 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7779 (tm-30)
REVERT: A  532 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7450 (mm-30)
REVERT: A  542 LEU cc_start: 0.8516 (mt) cc_final: 0.8216 (mp)
REVERT: A  551 ASP cc_start: 0.6924 (t70) cc_final: 0.6600 (t70)
REVERT: A  585 ARG cc_start: 0.8438 (mmm-85) cc_final: 0.8176 (mmm-85)
REVERT: A  628 TYR cc_start: 0.7362 (t80) cc_final: 0.6849 (t80)
REVERT: A  630 ILE cc_start: 0.8604 (tp) cc_final: 0.8305 (tp)
REVERT: A  695 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7459 (tm-30)
REVERT: A  712 ASP cc_start: 0.8182 (m-30) cc_final: 0.7943 (m-30)
REVERT: A  723 LYS cc_start: 0.8179 (tmtt) cc_final: 0.7802 (tmtt)
REVERT: A  747 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8079 (mm)
REVERT: A  766 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8244 (tm-30)
REVERT: A  776 LEU cc_start: 0.8339 (tp) cc_final: 0.8131 (tp)
REVERT: A  812 LEU cc_start: 0.8353 (mt) cc_final: 0.8030 (mt)
REVERT: A  814 GLN cc_start: 0.7951 (pp30) cc_final: 0.7471 (pp30)
REVERT: A  863 HIS cc_start: 0.7356 (m90) cc_final: 0.6741 (m90)
REVERT: A  865 LEU cc_start: 0.8576 (mm) cc_final: 0.8262 (mt)
REVERT: A  867 LEU cc_start: 0.8966 (pp) cc_final: 0.8489 (pp)
REVERT: A  871 PHE cc_start: 0.7377 (m-80) cc_final: 0.6979 (m-80)
REVERT: A  873 TYR cc_start: 0.7321 (t80) cc_final: 0.6935 (t80)
  outliers start: 22
  outliers final: 17
  residues processed: 204
  average time/residue: 0.2225
  time to fit residues: 57.7344
Evaluate side-chains
  214 residues out of total 683 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 196
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 MET
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  174 HIS
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  405 GLU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  596 SER
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  624 LYS
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  747 LEU
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  911 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 71 optimal weight:    0.0060
   chunk 41 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 62 optimal weight:    0.4980
   chunk 65 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6357  Z= 0.231
  Angle     :  0.729  13.323   8593  Z= 0.371
  Chirality :  0.048   0.358    947
  Planarity :  0.004   0.041   1089
  Dihedral  :  7.101  68.554    871
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 17.81
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 15.82 %
    Favored  : 84.05 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 26.79 %
    Favored  : 70.28 %
  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: -2.79 (0.30), residues: 765
  helix: -0.21 (0.31), residues: 316
  sheet: -1.59 (0.71), residues: 37
  loop : -3.40 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 220 
 HIS   0.002   0.001   HIS A 432 
 PHE   0.016   0.001   PHE A 629 
 TYR   0.019   0.002   TYR A 605 
 ARG   0.007   0.001   ARG A  92 

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 683 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 200
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7532 (tpp) cc_final: 0.7310 (tpp)
REVERT: A  148 MET cc_start: 0.6216 (tmm) cc_final: 0.5947 (tmm)
REVERT: A  150 ARG cc_start: 0.6945 (ptp-110) cc_final: 0.6594 (ptp-110)
REVERT: A  158 GLU cc_start: 0.7422 (tp30) cc_final: 0.7177 (tp30)
REVERT: A  160 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7256 (tm-30)
REVERT: A  172 TYR cc_start: 0.7008 (m-80) cc_final: 0.6692 (m-80)
REVERT: A  226 PHE cc_start: 0.8570 (t80) cc_final: 0.8201 (t80)
REVERT: A  282 MET cc_start: 0.6540 (tpt) cc_final: 0.6304 (tpt)
REVERT: A  332 MET cc_start: 0.5486 (pmm) cc_final: 0.5098 (pmm)
REVERT: A  408 ARG cc_start: 0.7664 (tmm-80) cc_final: 0.7275 (tmm-80)
REVERT: A  409 ASP cc_start: 0.7470 (t0) cc_final: 0.7204 (t0)
REVERT: A  457 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7753 (tm-30)
REVERT: A  532 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7436 (mm-30)
REVERT: A  542 LEU cc_start: 0.8525 (mt) cc_final: 0.8235 (mp)
REVERT: A  551 ASP cc_start: 0.6933 (t70) cc_final: 0.6633 (t70)
REVERT: A  585 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.8202 (mmm-85)
REVERT: A  630 ILE cc_start: 0.8614 (tp) cc_final: 0.8308 (tp)
REVERT: A  695 GLN cc_start: 0.7805 (tm-30) cc_final: 0.7530 (tm-30)
REVERT: A  723 LYS cc_start: 0.8198 (tmtt) cc_final: 0.7847 (tmtt)
REVERT: A  747 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8092 (mm)
REVERT: A  812 LEU cc_start: 0.8366 (mt) cc_final: 0.8052 (mt)
REVERT: A  814 GLN cc_start: 0.7959 (pp30) cc_final: 0.7479 (pp30)
REVERT: A  863 HIS cc_start: 0.7344 (m90) cc_final: 0.6784 (m90)
REVERT: A  865 LEU cc_start: 0.8572 (mm) cc_final: 0.8265 (mt)
REVERT: A  867 LEU cc_start: 0.8979 (pp) cc_final: 0.8506 (pp)
REVERT: A  871 PHE cc_start: 0.7438 (m-80) cc_final: 0.7042 (m-80)
REVERT: A  873 TYR cc_start: 0.7277 (t80) cc_final: 0.6851 (t80)
  outliers start: 20
  outliers final: 18
  residues processed: 208
  average time/residue: 0.2174
  time to fit residues: 56.9948
Evaluate side-chains
  216 residues out of total 683 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 197
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 MET
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  174 HIS
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  405 GLU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  596 SER
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  691 SER
Chi-restraints excluded: chain A residue  705 CYS
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  747 LEU
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  911 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 34 optimal weight:    0.4980
   chunk 50 optimal weight:    0.6980
   chunk 76 optimal weight:    0.6980
   chunk 70 optimal weight:    0.5980
   chunk 61 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0870
   chunk 47 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 48 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7042
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6357  Z= 0.213
  Angle     :  0.730  13.822   8593  Z= 0.371
  Chirality :  0.047   0.376    947
  Planarity :  0.004   0.045   1089
  Dihedral  :  7.038  69.307    871
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 16.76
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 15.82 %
    Favored  : 84.05 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 27.09 %
    Favored  : 69.84 %
  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: -2.76 (0.30), residues: 765
  helix: -0.15 (0.31), residues: 314
  sheet: -1.63 (0.71), residues: 37
  loop : -3.41 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 220 
 HIS   0.002   0.001   HIS A 248 
 PHE   0.016   0.001   PHE A 629 
 TYR   0.018   0.002   TYR A 605 
 ARG   0.007   0.001   ARG A 141 

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 683 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 194
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7523 (tpp) cc_final: 0.7305 (tpp)
REVERT: A  148 MET cc_start: 0.6172 (tmm) cc_final: 0.5902 (tmm)
REVERT: A  150 ARG cc_start: 0.6925 (ptp-110) cc_final: 0.6594 (ptp-110)
REVERT: A  158 GLU cc_start: 0.7355 (tp30) cc_final: 0.7098 (tp30)
REVERT: A  160 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7251 (tm-30)
REVERT: A  172 TYR cc_start: 0.7107 (m-80) cc_final: 0.6801 (m-80)
REVERT: A  226 PHE cc_start: 0.8543 (t80) cc_final: 0.8185 (t80)
REVERT: A  282 MET cc_start: 0.6538 (tpt) cc_final: 0.6306 (tpt)
REVERT: A  332 MET cc_start: 0.5450 (pmm) cc_final: 0.5066 (pmm)
REVERT: A  408 ARG cc_start: 0.7654 (tmm-80) cc_final: 0.7219 (tmm-80)
REVERT: A  409 ASP cc_start: 0.7464 (t0) cc_final: 0.7212 (t0)
REVERT: A  457 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7744 (tm-30)
REVERT: A  532 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7417 (mm-30)
REVERT: A  542 LEU cc_start: 0.8522 (mt) cc_final: 0.8235 (mp)
REVERT: A  551 ASP cc_start: 0.6929 (t70) cc_final: 0.6617 (t70)
REVERT: A  585 ARG cc_start: 0.8499 (mmm-85) cc_final: 0.8241 (mmm-85)
REVERT: A  628 TYR cc_start: 0.7363 (t80) cc_final: 0.6819 (t80)
REVERT: A  630 ILE cc_start: 0.8614 (tp) cc_final: 0.8291 (tp)
REVERT: A  695 GLN cc_start: 0.7794 (tm-30) cc_final: 0.7508 (tm-30)
REVERT: A  712 ASP cc_start: 0.8138 (m-30) cc_final: 0.7875 (m-30)
REVERT: A  723 LYS cc_start: 0.8189 (tmtt) cc_final: 0.7806 (tmtt)
REVERT: A  812 LEU cc_start: 0.8357 (mt) cc_final: 0.8041 (mt)
REVERT: A  814 GLN cc_start: 0.7941 (pp30) cc_final: 0.7449 (pp30)
REVERT: A  863 HIS cc_start: 0.7342 (m90) cc_final: 0.6753 (m90)
REVERT: A  865 LEU cc_start: 0.8559 (mm) cc_final: 0.8254 (mt)
REVERT: A  867 LEU cc_start: 0.8985 (pp) cc_final: 0.8523 (pp)
REVERT: A  871 PHE cc_start: 0.7418 (m-80) cc_final: 0.7045 (m-80)
REVERT: A  873 TYR cc_start: 0.7243 (t80) cc_final: 0.6826 (t80)
  outliers start: 21
  outliers final: 16
  residues processed: 205
  average time/residue: 0.2091
  time to fit residues: 54.3627
Evaluate side-chains
  208 residues out of total 683 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 192
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 MET
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  174 HIS
Chi-restraints excluded: chain A residue  405 GLU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  596 SER
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  705 CYS
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  911 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0270
   chunk 25 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 7 optimal weight:    0.4980
   chunk 11 optimal weight:    0.5980
   chunk 53 optimal weight:    0.1980
   chunk 3 optimal weight:    0.0270
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.2696

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.158809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.141331 restraints weight = 10251.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3902 rms_B_bonded: 3.61
r_work: 0.3755 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.2710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6357  Z= 0.191
  Angle     :  0.726  13.576   8593  Z= 0.368
  Chirality :  0.046   0.372    947
  Planarity :  0.004   0.040   1089
  Dihedral  :  6.875  70.328    871
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 15.46
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 15.16 %
    Favored  : 84.71 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 28.11 %
    Favored  : 69.84 %
  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: -2.66 (0.30), residues: 765
  helix: -0.09 (0.31), residues: 314
  sheet: -1.63 (0.70), residues: 37
  loop : -3.31 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 220 
 HIS   0.003   0.001   HIS A 582 
 PHE   0.016   0.001   PHE A 629 
 TYR   0.017   0.001   TYR A 903 
 ARG   0.007   0.001   ARG A  92 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1934.08 seconds
wall clock time: 35 minutes 37.62 seconds (2137.62 seconds total)