Starting phenix.real_space_refine
on Mon Mar 11 09:36:40 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7s_31003/03_2024/7e7s_31003.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7s_31003/03_2024/7e7s_31003.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/7e7s_31003/03_2024/7e7s_31003.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7s_31003/03_2024/7e7s_31003.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7s_31003/03_2024/7e7s_31003.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7s_31003/03_2024/7e7s_31003.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=   0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     S      58      5.16       5
     C    5027      2.51       5
     N    1314      2.21       5
     O    1483      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ASP   59": "OD1" <-> "OD2"
    Residue "A GLU  121": "OE1" <-> "OE2"
    Residue "A GLU  125": "OE1" <-> "OE2"
    Residue "A TYR  295": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  394": "OE1" <-> "OE2"
    Residue "A GLU  439": "OE1" <-> "OE2"
    Residue "A PHE  483": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  518": "OE1" <-> "OE2"
    Residue "A ASP  694": "OD1" <-> "OD2"
    Residue "A TYR  867": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  882": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1040": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 7884
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1022, 7884
          Unusual residues: {' CA': 2}
          Classifications: {'peptide': 1020, 'undetermined': 2}
          Link IDs: {'PTRANS': 46, 'TRANS': 973, None: 2}
            Not linked:
              pdbres="SER A1042 "
              pdbres=" CA A4001 "
            Not linked:
              pdbres=" CA A4001 "
              pdbres=" CA A4002 "
          Chain breaks: 2
  Time building chain proxies: 4.79, per 1000 atoms: 0.61
  Number of scatterers: 7884
  At special positions: 0
  Unit cell: (78.435, 84.66, 150.645, 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      2     19.99
     S      58     16.00
     O    1483      8.00
     N    1314      7.00
     C    5027      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 875 " - pdb=" SG  CYS A 887 " 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: 3.03
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1910

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 7 sheets defined
      55.0% alpha, 14.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 7
      removed outlier: 3.599A  pdb=" N   THR A   6 " --> pdb=" O   ASN A   3 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LYS A   7 " --> pdb=" O   ALA A   4 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 3 through 7'
    Processing helix  chain 'A' and resid 8 through 17
    Processing helix  chain 'A' and resid 25 through 36
      removed outlier: 3.588A  pdb=" N   GLU A  34 " --> pdb=" O   LYS A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 57
    Processing helix  chain 'A' and resid 59 through 76
    Processing helix  chain 'A' and resid 88 through 123
      removed outlier: 3.509A  pdb=" N   PHE A  92 " --> pdb=" O   PHE A  88 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ILE A  94 " --> pdb=" O   GLU A  90 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   ILE A  97 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLU A 121 " --> pdb=" O   GLU A 117 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLU A 123 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 145
      No H-bonds generated for 'chain 'A' and resid 143 through 145'
    Processing helix  chain 'A' and resid 177 through 182
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.976A  pdb=" N   ASN A 229 " --> pdb=" O   THR A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 274
    Processing helix  chain 'A' and resid 275 through 280
      removed outlier: 3.748A  pdb=" N   HIS A 278 " --> pdb=" O   ASN A 275 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   ASN A 280 " --> pdb=" O   GLY A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 285
    Processing helix  chain 'A' and resid 287 through 307
      removed outlier: 3.631A  pdb=" N   PHE A 296 " --> pdb=" O   ALA A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 329
    Processing helix  chain 'A' and resid 337 through 342
      removed outlier: 3.690A  pdb=" N   THR A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 345
      No H-bonds generated for 'chain 'A' and resid 343 through 345'
    Processing helix  chain 'A' and resid 407 through 420
      removed outlier: 3.745A  pdb=" N   VAL A 411 " --> pdb=" O   TYR A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 453
    Processing helix  chain 'A' and resid 463 through 468
      removed outlier: 4.106A  pdb=" N   ALA A 468 " --> pdb=" O   LYS A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 478
    Processing helix  chain 'A' and resid 516 through 523
    Processing helix  chain 'A' and resid 537 through 554
      removed outlier: 3.622A  pdb=" N   GLN A 542 " --> pdb=" O   SER A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 586
      removed outlier: 3.859A  pdb=" N   PHE A 583 " --> pdb=" O   ASP A 579 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   LYS A 585 " --> pdb=" O   ALA A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 616
    Processing helix  chain 'A' and resid 627 through 639
    Processing helix  chain 'A' and resid 654 through 659
    Processing helix  chain 'A' and resid 661 through 672
      removed outlier: 3.502A  pdb=" N   ASN A 671 " --> pdb=" O   ASP A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 693
      removed outlier: 3.868A  pdb=" N   LYS A 683 " --> pdb=" O   GLU A 679 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   SER A 684 " --> pdb=" O   PRO A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 705
      No H-bonds generated for 'chain 'A' and resid 703 through 705'
    Processing helix  chain 'A' and resid 706 through 713
    Processing helix  chain 'A' and resid 723 through 729
      removed outlier: 3.639A  pdb=" N   LYS A 727 " --> pdb=" O   THR A 723 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 781
      removed outlier: 3.705A  pdb=" N   VAL A 743 " --> pdb=" O   PHE A 739 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLY A 769 " --> pdb=" O   SER A 765 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ILE A 774 " --> pdb=" O   GLU A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 800
      removed outlier: 3.676A  pdb=" N   GLY A 800 " --> pdb=" O   LEU A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 805
    Processing helix  chain 'A' and resid 806 through 809
    Processing helix  chain 'A' and resid 829 through 858
      removed outlier: 3.557A  pdb=" N   TRP A 854 " --> pdb=" O   ALA A 850 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   PHE A 855 " --> pdb=" O   ALA A 851 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ALA A 858 " --> pdb=" O   TRP A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 871
    Processing helix  chain 'A' and resid 872 through 875
    Processing helix  chain 'A' and resid 886 through 891
    Processing helix  chain 'A' and resid 892 through 913
      removed outlier: 4.425A  pdb=" N   MET A 896 " --> pdb=" O   SER A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 914 through 916
      No H-bonds generated for 'chain 'A' and resid 914 through 916'
    Processing helix  chain 'A' and resid 925 through 928
    Processing helix  chain 'A' and resid 929 through 946
    Processing helix  chain 'A' and resid 952 through 957
    Processing helix  chain 'A' and resid 962 through 974
      removed outlier: 3.621A  pdb=" N   MET A 968 " --> pdb=" O   THR A 964 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 990
      removed outlier: 3.632A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1030
      Proline residue:  A1024  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 129
    Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 153
      removed outlier: 6.861A  pdb=" N   MET A 220 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   ASP A 162 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ILE A 163 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LEU A 208 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 176
      removed outlier: 6.552A  pdb=" N   ARG A 174 " --> pdb=" O   ALA A 215 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ASN A 213 " --> pdb=" O   ASP A 176 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 651 through 653
      removed outlier: 8.069A  pdb=" N   PHE A 675 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   MET A 622 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   VAL A 347 " --> pdb=" O   ALA A 698 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   THR A 700 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   CYS A 349 " --> pdb=" O   THR A 700 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   THR A 697 " --> pdb=" O   ILE A 715 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   ILE A 717 " --> pdb=" O   THR A 697 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   MET A 699 " --> pdb=" O   ILE A 717 " (cutoff:3.500A)
      removed outlier: 8.171A  pdb=" N   MET A 719 " --> pdb=" O   MET A 699 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LEU A 734 " --> pdb=" O   ALA A 718 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396
      removed outlier: 7.446A  pdb=" N   THR A 376 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   VAL A 372 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 368 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ARG A 365 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.034A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 15.946A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 7.411A  pdb=" N   LEU A 563 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 4.853A  pdb=" N   CYS A 595 " --> pdb=" O   LEU A 561 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   LEU A 561 " --> pdb=" O   CYS A 595 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   GLY A 597 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   ARG A 559 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY A 515 " --> pdb=" O   ALA A 562 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ALA A 564 " --> pdb=" O   VAL A 513 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   THR A 499 " --> pdb=" O   LYS A 481 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   LYS A 481 " --> pdb=" O   THR A 499 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 395 through 396
      removed outlier: 7.446A  pdb=" N   THR A 376 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   VAL A 372 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 368 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ARG A 365 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.034A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 15.946A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   CYS A 524 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   PHE A 592 " --> pdb=" O   CYS A 524 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   HIS A 526 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   GLY A 594 " --> pdb=" O   HIS A 526 " (cutoff:3.500A)
      removed outlier: 9.299A  pdb=" N   ARG A 528 " --> pdb=" O   GLY A 594 " (cutoff:3.500A)
      removed outlier: 13.026A  pdb=" N   VAL A 596 " --> pdb=" O   ARG A 528 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 424 through 428

    413 hydrogen bonds defined for protein.
    1185 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.82

  Time building geometry restraints manager: 3.31 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2577
        1.34 -     1.46: 1658
        1.46 -     1.58: 3706
        1.58 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 8031
  Sorted by residual:
  bond pdb=" CA  VAL A 529 "
       pdb=" CB  VAL A 529 "
    ideal  model  delta    sigma   weight residual
    1.540  1.530  0.010 1.36e-02 5.41e+03 5.72e-01
  bond pdb=" CG  LEU A 806 "
       pdb=" CD1 LEU A 806 "
    ideal  model  delta    sigma   weight residual
    1.521  1.498  0.023 3.30e-02 9.18e+02 4.87e-01
  bond pdb=" N   PRO A 819 "
       pdb=" CA  PRO A 819 "
    ideal  model  delta    sigma   weight residual
    1.457  1.466 -0.009 1.31e-02 5.83e+03 4.68e-01
  bond pdb=" C   PRO A 819 "
       pdb=" O   PRO A 819 "
    ideal  model  delta    sigma   weight residual
    1.246  1.240  0.005 8.50e-03 1.38e+04 4.18e-01
  bond pdb=" CG  PRO A 312 "
       pdb=" CD  PRO A 312 "
    ideal  model  delta    sigma   weight residual
    1.503  1.481  0.022 3.40e-02 8.65e+02 4.14e-01
  ... (remaining 8026 not shown)

  Histogram of bond angle deviations from ideal:
       99.97 -   106.79: 239
      106.79 -   113.60: 4553
      113.60 -   120.41: 2910
      120.41 -   127.22: 3113
      127.22 -   134.03: 84
  Bond angle restraints: 10899
  Sorted by residual:
  angle pdb=" CB  MET A 908 "
        pdb=" CG  MET A 908 "
        pdb=" SD  MET A 908 "
      ideal   model   delta    sigma   weight residual
     112.70  121.00   -8.30 3.00e+00 1.11e-01 7.65e+00
  angle pdb=" N   ILE A 232 "
        pdb=" CA  ILE A 232 "
        pdb=" C   ILE A 232 "
      ideal   model   delta    sigma   weight residual
     113.07  109.43    3.64 1.36e+00 5.41e-01 7.18e+00
  angle pdb=" C   VAL A 223 "
        pdb=" N   VAL A 224 "
        pdb=" CA  VAL A 224 "
      ideal   model   delta    sigma   weight residual
     122.66  120.19    2.47 9.70e-01 1.06e+00 6.46e+00
  angle pdb=" CB  LYS A 541 "
        pdb=" CG  LYS A 541 "
        pdb=" CD  LYS A 541 "
      ideal   model   delta    sigma   weight residual
     111.30  116.95   -5.65 2.30e+00 1.89e-01 6.04e+00
  angle pdb=" N   LEU A 952 "
        pdb=" CA  LEU A 952 "
        pdb=" C   LEU A 952 "
      ideal   model   delta    sigma   weight residual
     109.81  115.21   -5.40 2.21e+00 2.05e-01 5.98e+00
  ... (remaining 10894 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 4353
       17.73 -    35.45: 426
       35.45 -    53.18: 64
       53.18 -    70.91: 17
       70.91 -    88.63: 8
  Dihedral angle restraints: 4868
    sinusoidal: 1922
      harmonic: 2946
  Sorted by residual:
  dihedral pdb=" CA  VAL A 949 "
           pdb=" C   VAL A 949 "
           pdb=" N   GLU A 950 "
           pdb=" CA  GLU A 950 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.07  -22.93     0      5.00e+00 4.00e-02 2.10e+01
  dihedral pdb=" CA  ASP A1038 "
           pdb=" CB  ASP A1038 "
           pdb=" CG  ASP A1038 "
           pdb=" OD1 ASP A1038 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.97   58.97     1      2.00e+01 2.50e-03 1.16e+01
  dihedral pdb=" CB  GLU A  79 "
           pdb=" CG  GLU A  79 "
           pdb=" CD  GLU A  79 "
           pdb=" OE1 GLU A  79 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.63  -88.63     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 4865 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 919
       0.036 -    0.072: 256
       0.072 -    0.108: 85
       0.108 -    0.144: 18
       0.144 -    0.180: 1
  Chirality restraints: 1279
  Sorted by residual:
  chirality pdb=" CB  ILE A 150 "
            pdb=" CA  ILE A 150 "
            pdb=" CG1 ILE A 150 "
            pdb=" CG2 ILE A 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 8.07e-01
  chirality pdb=" CA  ILE A 527 "
            pdb=" N   ILE A 527 "
            pdb=" C   ILE A 527 "
            pdb=" CB  ILE A 527 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.37e-01
  chirality pdb=" CA  PRO A 788 "
            pdb=" N   PRO A 788 "
            pdb=" C   PRO A 788 "
            pdb=" CB  PRO A 788 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 3.96e-01
  ... (remaining 1276 not shown)

  Planarity restraints: 1389
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 400 "    0.035 5.00e-02 4.00e+02   5.36e-02 4.59e+00
        pdb=" N   PRO A 401 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 401 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 401 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 247 "   -0.030 5.00e-02 4.00e+02   4.58e-02 3.35e+00
        pdb=" N   PRO A 248 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 248 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 248 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 892 "   -0.025 5.00e-02 4.00e+02   3.87e-02 2.39e+00
        pdb=" N   PRO A 893 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 893 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 893 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1386 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 222
        2.71 -     3.26: 8253
        3.26 -     3.81: 12642
        3.81 -     4.35: 15906
        4.35 -     4.90: 26753
  Nonbonded interactions: 63776
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 879 "
            pdb=" OD1 ASP A 881 "
     model   vdw
     2.166 2.520
  nonbonded pdb=" O   ILE A 307 "
            pdb=" OE1 GLU A 309 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" NH2 ARG A 619 "
            pdb=" O   CYS A 669 "
     model   vdw
     2.264 2.520
  nonbonded pdb=" O   PHE A 209 "
            pdb=" OG1 THR A 212 "
     model   vdw
     2.284 2.440
  nonbonded pdb=" OG  SER A  38 "
            pdb=" O   LYS A 143 "
     model   vdw
     2.296 2.440
  ... (remaining 63771 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.200
  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:          1.410
  Check model and map are aligned:         0.110
  Set scattering table:                    0.080
  Process input model:                     25.160
  Find NCS groups from input model:        0.190
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8031  Z= 0.171
  Angle     :  0.496   8.299  10899  Z= 0.261
  Chirality :  0.040   0.180   1279
  Planarity :  0.004   0.054   1389
  Dihedral  : 14.410  88.632   2955
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  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: -0.13 (0.26), residues: 1014
  helix:  0.30 (0.23), residues: 482
  sheet: -1.14 (0.48), residues: 109
  loop : -0.03 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 272 
 HIS   0.001   0.000   HIS A 396 
 PHE   0.014   0.001   PHE A1040 
 TYR   0.008   0.001   TYR A 842 
 ARG   0.004   0.000   ARG A 134 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.969 
Fit side-chains
REVERT: A  126 MET cc_start: 0.7479 (mmm) cc_final: 0.7023 (tmm)
REVERT: A  399 ASP cc_start: 0.6887 (t70) cc_final: 0.6640 (t70)
REVERT: A  568 ASN cc_start: 0.7578 (t0) cc_final: 0.7082 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1995
  time to fit residues: 29.1339
Evaluate side-chains
  81 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 52 optimal weight:    9.9990
   chunk 41 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0570
   chunk 48 optimal weight:   10.0000
   chunk 59 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0770
   overall best weight:    0.7860

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

Flipped N/Q/H residues before XYZ refinement:
A 275 ASN
A 403 ASN
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 913 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8031  Z= 0.183
  Angle     :  0.526   7.083  10899  Z= 0.275
  Chirality :  0.042   0.164   1279
  Planarity :  0.004   0.045   1389
  Dihedral  :  3.821  22.431   1078
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  6.76 %
    Favored  : 92.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.27), residues: 1014
  helix:  1.32 (0.23), residues: 501
  sheet: -1.16 (0.46), residues: 105
  loop : -0.04 (0.33), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 682 
 PHE   0.009   0.001   PHE A 367 
 TYR   0.016   0.001   TYR A 842 
 ARG   0.002   0.000   ARG A 673 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 96
  time to evaluate  : 0.921 
Fit side-chains
REVERT: A  482 GLU cc_start: 0.6950 (mp0) cc_final: 0.6216 (mp0)
REVERT: A  568 ASN cc_start: 0.7681 (t0) cc_final: 0.7279 (p0)
  outliers start: 3
  outliers final: 2
  residues processed: 97
  average time/residue: 0.1908
  time to fit residues: 26.0390
Evaluate side-chains
  84 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 82
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  437 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0020
   chunk 100 optimal weight:    5.9990
   chunk 82 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 91 optimal weight:    0.6980
   overall best weight:    0.8792

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

Flipped N/Q/H residues before XYZ refinement:
A 275 ASN
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8031  Z= 0.180
  Angle     :  0.496   5.997  10899  Z= 0.255
  Chirality :  0.041   0.139   1279
  Planarity :  0.004   0.044   1389
  Dihedral  :  3.810  23.460   1078
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 10.42 %
    Favored  : 89.00 %
  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:  0.94 (0.27), residues: 1014
  helix:  1.59 (0.24), residues: 501
  sheet: -0.96 (0.47), residues: 105
  loop : -0.04 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 682 
 PHE   0.012   0.001   PHE A1040 
 TYR   0.016   0.001   TYR A 842 
 ARG   0.003   0.000   ARG A 134 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.856 
Fit side-chains
REVERT: A  482 GLU cc_start: 0.6777 (mp0) cc_final: 0.6147 (mp0)
REVERT: A  553 SER cc_start: 0.8414 (t) cc_final: 0.8158 (p)
REVERT: A  568 ASN cc_start: 0.7548 (t0) cc_final: 0.7220 (p0)
REVERT: A  585 LYS cc_start: 0.7837 (ptpp) cc_final: 0.7564 (pttp)
REVERT: A  586 TYR cc_start: 0.6584 (m-10) cc_final: 0.6250 (m-80)
REVERT: A  898 MET cc_start: 0.8808 (mmm) cc_final: 0.8549 (mmm)
  outliers start: 5
  outliers final: 2
  residues processed: 97
  average time/residue: 0.2136
  time to fit residues: 29.1781
Evaluate side-chains
  92 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  663 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 98 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8031  Z= 0.209
  Angle     :  0.499   6.514  10899  Z= 0.254
  Chirality :  0.041   0.157   1279
  Planarity :  0.004   0.045   1389
  Dihedral  :  3.810  24.206   1078
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 12.49 %
    Favored  : 86.48 %
  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:  1.03 (0.27), residues: 1014
  helix:  1.67 (0.23), residues: 501
  sheet: -0.79 (0.52), residues: 87
  loop : -0.10 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 278 
 PHE   0.010   0.001   PHE A1040 
 TYR   0.018   0.001   TYR A 842 
 ARG   0.003   0.000   ARG A 134 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.866 
Fit side-chains
REVERT: A  482 GLU cc_start: 0.6607 (mp0) cc_final: 0.6207 (mp0)
REVERT: A  537 THR cc_start: 0.7998 (p) cc_final: 0.7798 (p)
REVERT: A  568 ASN cc_start: 0.7510 (t0) cc_final: 0.7198 (p0)
REVERT: A  585 LYS cc_start: 0.7855 (ptpp) cc_final: 0.7577 (pttp)
REVERT: A  586 TYR cc_start: 0.6745 (m-10) cc_final: 0.6400 (m-80)
REVERT: A  763 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8582 (mp)
  outliers start: 9
  outliers final: 6
  residues processed: 98
  average time/residue: 0.2065
  time to fit residues: 27.9376
Evaluate side-chains
  98 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  663 SER
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  978 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 40 optimal weight:   20.0000
   chunk 84 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 50 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 24 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 19 optimal weight:    8.9990
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8031  Z= 0.238
  Angle     :  0.514   6.861  10899  Z= 0.260
  Chirality :  0.042   0.140   1279
  Planarity :  0.004   0.047   1389
  Dihedral  :  3.867  24.676   1078
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 13.52 %
    Favored  : 85.22 %
  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:  1.00 (0.27), residues: 1014
  helix:  1.66 (0.23), residues: 501
  sheet: -0.82 (0.52), residues: 87
  loop : -0.13 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 107 
 HIS   0.001   0.001   HIS A 566 
 PHE   0.009   0.001   PHE A  78 
 TYR   0.019   0.002   TYR A 842 
 ARG   0.004   0.000   ARG A 134 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.948 
Fit side-chains
REVERT: A  150 ILE cc_start: 0.5251 (OUTLIER) cc_final: 0.5021 (tp)
REVERT: A  482 GLU cc_start: 0.6598 (mp0) cc_final: 0.6198 (mp0)
REVERT: A  549 ARG cc_start: 0.7459 (mtt90) cc_final: 0.6873 (mtm110)
REVERT: A  568 ASN cc_start: 0.7396 (t0) cc_final: 0.7109 (p0)
REVERT: A  585 LYS cc_start: 0.7850 (ptpp) cc_final: 0.7584 (pttp)
REVERT: A  763 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8581 (mp)
  outliers start: 11
  outliers final: 6
  residues processed: 104
  average time/residue: 0.2009
  time to fit residues: 28.8451
Evaluate side-chains
  101 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  661 ASN
Chi-restraints excluded: chain A residue  663 SER
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  978 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:   30.0000
   chunk 24 optimal weight:    3.9990
   chunk 98 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 45 optimal weight:    9.9990
   chunk 8 optimal weight:    0.0970
   chunk 32 optimal weight:    1.9990
   chunk 51 optimal weight:    9.9990
   chunk 95 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 56 optimal weight:    9.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8031  Z= 0.264
  Angle     :  0.527   7.330  10899  Z= 0.268
  Chirality :  0.043   0.136   1279
  Planarity :  0.004   0.047   1389
  Dihedral  :  3.935  24.944   1078
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 13.86 %
    Favored  : 84.54 %
  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:  0.97 (0.27), residues: 1014
  helix:  1.63 (0.24), residues: 501
  sheet: -0.83 (0.52), residues: 87
  loop : -0.15 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 107 
 HIS   0.001   0.001   HIS A 566 
 PHE   0.010   0.001   PHE A  78 
 TYR   0.019   0.002   TYR A 842 
 ARG   0.004   0.000   ARG A 134 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.843 
Fit side-chains
REVERT: A  150 ILE cc_start: 0.5212 (OUTLIER) cc_final: 0.4981 (tp)
REVERT: A  467 ARG cc_start: 0.7800 (tpp-160) cc_final: 0.7556 (tpp80)
REVERT: A  482 GLU cc_start: 0.6769 (mp0) cc_final: 0.6315 (mp0)
REVERT: A  549 ARG cc_start: 0.7408 (mtt90) cc_final: 0.6802 (mtm110)
REVERT: A  568 ASN cc_start: 0.7382 (t0) cc_final: 0.7102 (p0)
REVERT: A  585 LYS cc_start: 0.7861 (ptpp) cc_final: 0.7591 (pttp)
REVERT: A  763 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8597 (mp)
  outliers start: 14
  outliers final: 8
  residues processed: 105
  average time/residue: 0.2274
  time to fit residues: 32.7198
Evaluate side-chains
  106 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  661 ASN
Chi-restraints excluded: chain A residue  663 SER
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  978 LEU
Chi-restraints excluded: chain A residue 1023 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 83 optimal weight:    0.7980
   chunk 98 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 45 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 58 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8031  Z= 0.212
  Angle     :  0.513   7.709  10899  Z= 0.259
  Chirality :  0.041   0.137   1279
  Planarity :  0.004   0.047   1389
  Dihedral  :  3.884  24.279   1078
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 14.55 %
    Favored  : 83.73 %
  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 (0.27), residues: 1014
  helix:  1.70 (0.24), residues: 501
  sheet: -0.78 (0.51), residues: 87
  loop : -0.13 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 396 
 PHE   0.010   0.001   PHE A 367 
 TYR   0.017   0.002   TYR A 842 
 ARG   0.004   0.000   ARG A 134 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.948 
Fit side-chains
REVERT: A   59 ASP cc_start: 0.8107 (t0) cc_final: 0.7539 (t0)
REVERT: A  150 ILE cc_start: 0.5178 (OUTLIER) cc_final: 0.4954 (tp)
REVERT: A  467 ARG cc_start: 0.7808 (tpp-160) cc_final: 0.7578 (tpp80)
REVERT: A  482 GLU cc_start: 0.6597 (mp0) cc_final: 0.6214 (mp0)
REVERT: A  549 ARG cc_start: 0.7431 (mtt90) cc_final: 0.6830 (mtm110)
REVERT: A  568 ASN cc_start: 0.7429 (t0) cc_final: 0.7192 (p0)
REVERT: A  585 LYS cc_start: 0.7854 (ptpp) cc_final: 0.7592 (pttp)
REVERT: A  586 TYR cc_start: 0.6761 (m-10) cc_final: 0.6542 (m-10)
REVERT: A  763 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8618 (mp)
  outliers start: 15
  outliers final: 10
  residues processed: 107
  average time/residue: 0.2172
  time to fit residues: 31.9172
Evaluate side-chains
  109 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  661 ASN
Chi-restraints excluded: chain A residue  663 SER
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  978 LEU
Chi-restraints excluded: chain A residue 1023 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    0.0050
   chunk 62 optimal weight:    0.7980
   chunk 66 optimal weight:    0.1980
   chunk 48 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   chunk 94 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8031  Z= 0.150
  Angle     :  0.496   8.006  10899  Z= 0.248
  Chirality :  0.041   0.173   1279
  Planarity :  0.003   0.046   1389
  Dihedral  :  3.773  22.952   1078
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 15.01 %
    Favored  : 83.62 %
  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:  1.23 (0.27), residues: 1014
  helix:  1.90 (0.24), residues: 500
  sheet: -0.68 (0.56), residues: 77
  loop : -0.11 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 793 
 HIS   0.001   0.000   HIS A 396 
 PHE   0.009   0.001   PHE A 985 
 TYR   0.014   0.001   TYR A 842 
 ARG   0.003   0.000   ARG A 134 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.890 
Fit side-chains
REVERT: A   59 ASP cc_start: 0.8028 (t0) cc_final: 0.7518 (t0)
REVERT: A  482 GLU cc_start: 0.6581 (mp0) cc_final: 0.6194 (mp0)
REVERT: A  585 LYS cc_start: 0.7809 (ptpp) cc_final: 0.7556 (pttp)
REVERT: A  763 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8611 (mp)
  outliers start: 12
  outliers final: 7
  residues processed: 106
  average time/residue: 0.1946
  time to fit residues: 28.9937
Evaluate side-chains
  103 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  661 ASN
Chi-restraints excluded: chain A residue  663 SER
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  978 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0770
   chunk 86 optimal weight:    0.7980
   chunk 91 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9980
   chunk 96 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8031  Z= 0.163
  Angle     :  0.500   8.519  10899  Z= 0.251
  Chirality :  0.041   0.180   1279
  Planarity :  0.004   0.047   1389
  Dihedral  :  3.740  23.264   1078
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 15.35 %
    Favored  : 83.39 %
  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:  1.29 (0.27), residues: 1014
  helix:  1.95 (0.24), residues: 500
  sheet: -0.60 (0.56), residues: 77
  loop : -0.10 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A 396 
 PHE   0.010   0.001   PHE A 367 
 TYR   0.016   0.001   TYR A 842 
 ARG   0.004   0.000   ARG A 134 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.957 
Fit side-chains
REVERT: A   59 ASP cc_start: 0.8018 (t0) cc_final: 0.7558 (t0)
REVERT: A  150 ILE cc_start: 0.5103 (OUTLIER) cc_final: 0.4864 (tp)
REVERT: A  467 ARG cc_start: 0.7877 (tpp-160) cc_final: 0.7641 (tpp80)
REVERT: A  482 GLU cc_start: 0.6572 (mp0) cc_final: 0.6192 (mp0)
REVERT: A  549 ARG cc_start: 0.7443 (mtt90) cc_final: 0.6815 (mtm110)
REVERT: A  585 LYS cc_start: 0.7807 (ptpp) cc_final: 0.7564 (pttp)
REVERT: A  763 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8677 (mp)
  outliers start: 11
  outliers final: 8
  residues processed: 106
  average time/residue: 0.2261
  time to fit residues: 32.4393
Evaluate side-chains
  109 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  661 ASN
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  978 LEU
Chi-restraints excluded: chain A residue 1023 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    5.9990
   chunk 93 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9980
   chunk 8 optimal weight:    0.3980
   chunk 62 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   chunk 64 optimal weight:    7.9990
   chunk 86 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8031  Z= 0.163
  Angle     :  0.507   8.741  10899  Z= 0.251
  Chirality :  0.041   0.179   1279
  Planarity :  0.004   0.047   1389
  Dihedral  :  3.716  23.297   1078
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 15.81 %
    Favored  : 82.82 %
  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:  1.33 (0.27), residues: 1014
  helix:  1.99 (0.23), residues: 500
  sheet: -0.47 (0.58), residues: 77
  loop : -0.10 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A 396 
 PHE   0.009   0.001   PHE A 367 
 TYR   0.015   0.001   TYR A 842 
 ARG   0.008   0.000   ARG A 655 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 GLU cc_start: 0.7476 (pp20) cc_final: 0.7220 (pp20)
REVERT: A   59 ASP cc_start: 0.8008 (t0) cc_final: 0.7505 (t0)
REVERT: A  150 ILE cc_start: 0.5092 (OUTLIER) cc_final: 0.4853 (tp)
REVERT: A  239 MET cc_start: 0.4407 (mmm) cc_final: 0.4202 (mmm)
REVERT: A  326 MET cc_start: 0.7155 (mmp) cc_final: 0.6941 (mmp)
REVERT: A  549 ARG cc_start: 0.7378 (mtt90) cc_final: 0.6749 (mtm110)
REVERT: A  568 ASN cc_start: 0.7500 (m-40) cc_final: 0.7232 (p0)
REVERT: A  575 MET cc_start: 0.7006 (mmp) cc_final: 0.5490 (tmm)
REVERT: A  585 LYS cc_start: 0.7803 (ptpp) cc_final: 0.7562 (pttp)
REVERT: A  763 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8626 (mp)
  outliers start: 12
  outliers final: 9
  residues processed: 108
  average time/residue: 0.2130
  time to fit residues: 31.5579
Evaluate side-chains
  109 residues out of total 873 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  661 ASN
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  978 LEU
Chi-restraints excluded: chain A residue 1023 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:   20.0000
   chunk 81 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    8.9990
   chunk 71 optimal weight:    0.9980
   chunk 4 optimal weight:    0.1980
   chunk 58 optimal weight:    5.9990
   chunk 92 optimal weight:    0.0770
   chunk 54 optimal weight:    4.9990
   overall best weight:    0.5540

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

Flipped N/Q/H residues before XYZ refinement:
** A 421 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 = 0.4043 r_free = 0.4043 target = 0.181638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.108206 restraints weight = 8368.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 2.03
r_work: 0.3016 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2880 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8031  Z= 0.148
  Angle     :  0.500   8.599  10899  Z= 0.248
  Chirality :  0.041   0.176   1279
  Planarity :  0.004   0.047   1389
  Dihedral  :  3.671  22.848   1078
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 16.04 %
    Favored  : 82.70 %
  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:  1.44 (0.27), residues: 1014
  helix:  2.08 (0.24), residues: 498
  sheet: -0.33 (0.58), residues: 77
  loop : -0.06 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 793 
 HIS   0.001   0.000   HIS A 396 
 PHE   0.014   0.001   PHE A1040 
 TYR   0.016   0.001   TYR A 407 
 ARG   0.007   0.000   ARG A 655 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1884.09 seconds
wall clock time: 34 minutes 52.91 seconds (2092.91 seconds total)