Starting phenix.real_space_refine
on Wed Sep 17 10:06:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jbx_61329/09_2025/9jbx_61329.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jbx_61329/09_2025/9jbx_61329.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jbx_61329/09_2025/9jbx_61329.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jbx_61329/09_2025/9jbx_61329.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jbx_61329/09_2025/9jbx_61329.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jbx_61329/09_2025/9jbx_61329.cif"
  }
  resolution = 3.87
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.038
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      47      5.16       5
     C    5131      2.51       5
     N    1334      2.21       5
     O    1436      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7948
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1016, 7948
          Classifications: {'peptide': 1016}
          Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 962}
          Chain breaks: 1
  Time building chain proxies: 2.11, per 1000 atoms: 0.27
  Number of scatterers: 7948
  At special positions: 0
  Unit cell: (79.872, 94.016, 144.768, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      47     16.00
     O    1436      8.00
     N    1334      7.00
     C    5131      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 464.4 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1920

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 9 sheets defined
      49.7% alpha, 13.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 118 through 130
      removed outlier: 3.867A  pdb=" N   HIS A 123 " --> pdb=" O   HIS A 119 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ALA A 124 " --> pdb=" O   TRP A 120 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   HIS A 125 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 198
    Processing helix  chain 'A' and resid 199 through 206
    Processing helix  chain 'A' and resid 211 through 223
    Processing helix  chain 'A' and resid 233 through 243
      removed outlier: 3.690A  pdb=" N   THR A 243 " --> pdb=" O   LYS A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 260
    Processing helix  chain 'A' and resid 262 through 295
    Processing helix  chain 'A' and resid 349 through 354
    Processing helix  chain 'A' and resid 421 through 432
    Processing helix  chain 'A' and resid 441 through 468
    Processing helix  chain 'A' and resid 473 through 489
      removed outlier: 3.517A  pdb=" N   LEU A 477 " --> pdb=" O   ASN A 473 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   VAL A 489 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 510
      removed outlier: 3.831A  pdb=" N   LEU A 497 " --> pdb=" O   LEU A 493 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LYS A 510 " --> pdb=" O   ILE A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 525
    Processing helix  chain 'A' and resid 564 through 574
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'A' and resid 656 through 663
      removed outlier: 4.391A  pdb=" N   SER A 662 " --> pdb=" O   GLU A 658 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   MET A 663 " --> pdb=" O   THR A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 682
      removed outlier: 3.640A  pdb=" N   GLY A 682 " --> pdb=" O   ILE A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 704
      removed outlier: 3.762A  pdb=" N   ARG A 702 " --> pdb=" O   HIS A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 709
      removed outlier: 3.870A  pdb=" N   LEU A 709 " --> pdb=" O   ARG A 706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 738
      removed outlier: 4.009A  pdb=" N   LYS A 730 " --> pdb=" O   LYS A 726 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ALA A 731 " --> pdb=" O   ALA A 727 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL A 732 " --> pdb=" O   ASP A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 750 through 761
    Processing helix  chain 'A' and resid 800 through 807
    Processing helix  chain 'A' and resid 813 through 823
    Processing helix  chain 'A' and resid 823 through 831
      removed outlier: 4.114A  pdb=" N   LEU A 827 " --> pdb=" O   ASP A 823 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 832 through 834
      No H-bonds generated for 'chain 'A' and resid 832 through 834'
    Processing helix  chain 'A' and resid 841 through 855
    Processing helix  chain 'A' and resid 865 through 867
      No H-bonds generated for 'chain 'A' and resid 865 through 867'
    Processing helix  chain 'A' and resid 868 through 875
      removed outlier: 3.600A  pdb=" N   HIS A 874 " --> pdb=" O   GLY A 870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 952 through 958
      removed outlier: 3.779A  pdb=" N   ALA A 957 " --> pdb=" O   ASP A 953 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 967 through 1008
      removed outlier: 4.111A  pdb=" N   CYS A 971 " --> pdb=" O   ILE A 967 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU A1007 " --> pdb=" O   SER A1003 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1032
      removed outlier: 3.518A  pdb=" N   ALA A1017 " --> pdb=" O   SER A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1051 through 1078
      removed outlier: 3.721A  pdb=" N   ILE A1055 " --> pdb=" O   ASN A1051 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   SER A1068 " --> pdb=" O   VAL A1064 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1098 through 1119
      removed outlier: 3.884A  pdb=" N   TYR A1119 " --> pdb=" O   PHE A1115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1131 through 1151
    Processing helix  chain 'A' and resid 1153 through 1160
    Processing helix  chain 'A' and resid 1166 through 1195
      removed outlier: 4.330A  pdb=" N   VAL A1172 " --> pdb=" O   GLU A1168 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 141 through 144
      removed outlier: 3.574A  pdb=" N   VAL A 156 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   GLU A 154 " --> pdb=" O   VAL A 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 174
      removed outlier: 3.926A  pdb=" N   PHE A 172 " --> pdb=" O   TYR A 179 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   TYR A 179 " --> pdb=" O   PHE A 172 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 308 through 313
      removed outlier: 5.367A  pdb=" N   GLN A 302 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   SER A 324 " --> pdb=" O   GLN A 302 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   ILE A 322 " --> pdb=" O   TYR A 304 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 359 through 361
      removed outlier: 3.960A  pdb=" N   GLN A 359 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   VAL A 347 " --> pdb=" O   GLN A 359 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LYS A 361 " --> pdb=" O   CYS A 345 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   CYS A 345 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   ASP A 348 " --> pdb=" O   VAL A 390 " (cutoff:3.500A)
      removed outlier: 5.417A  pdb=" N   VAL A 390 " --> pdb=" O   ASP A 348 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 513 through 514
    Processing sheet with id=AA6, first strand: chain 'A' and resid 792 through 794
      removed outlier: 4.354A  pdb=" N   GLU A 783 " --> pdb=" O   GLN A 773 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   GLN A 773 " --> pdb=" O   GLU A 783 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   CYS A 810 " --> pdb=" O   LEU A 770 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LEU A 772 " --> pdb=" O   CYS A 810 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   THR A 812 " --> pdb=" O   LEU A 772 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   VAL A 836 " --> pdb=" O   LEU A 809 " (cutoff:3.500A)
      removed outlier: 8.411A  pdb=" N   PHE A 837 " --> pdb=" O   VAL A 743 " (cutoff:3.500A)
      removed outlier: 6.091A  pdb=" N   MET A 745 " --> pdb=" O   PHE A 837 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   CYS A 530 " --> pdb=" O   VAL A 744 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   ILE A 746 " --> pdb=" O   CYS A 530 " (cutoff:3.500A)
      removed outlier: 5.588A  pdb=" N   PHE A 532 " --> pdb=" O   ILE A 746 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   THR A 859 " --> pdb=" O   VAL A 877 " (cutoff:3.500A)
      removed outlier: 7.916A  pdb=" N   VAL A 879 " --> pdb=" O   THR A 859 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   MET A 861 " --> pdb=" O   VAL A 879 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 544 through 547
      removed outlier: 5.782A  pdb=" N   VAL A 545 " --> pdb=" O   SER A 722 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   SER A 722 " --> pdb=" O   VAL A 545 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   GLY A 547 " --> pdb=" O   VAL A 720 " (cutoff:3.500A)
      removed outlier: 5.214A  pdb=" N   PHE A 715 " --> pdb=" O   TYR A 690 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   TYR A 690 " --> pdb=" O   PHE A 715 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ALA A 687 " --> pdb=" O   GLY A 655 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   GLY A 655 " --> pdb=" O   ALA A 687 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ALA A 651 " --> pdb=" O   LYS A 691 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA A 637 " --> pdb=" O   ILE A 650 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   ARG A 632 " --> pdb=" O   PHE A 626 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   PHE A 626 " --> pdb=" O   ARG A 632 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   SER A 638 " --> pdb=" O   ILE A 620 " (cutoff:3.500A)
      removed outlier: 5.888A  pdb=" N   ILE A 620 " --> pdb=" O   SER A 638 " (cutoff:3.500A)
      removed outlier: 8.835A  pdb=" N   GLU A 640 " --> pdb=" O   LEU A 618 " (cutoff:3.500A)
      removed outlier: 8.478A  pdb=" N   LEU A 618 " --> pdb=" O   GLU A 640 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 544 through 547
      removed outlier: 5.782A  pdb=" N   VAL A 545 " --> pdb=" O   SER A 722 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   SER A 722 " --> pdb=" O   VAL A 545 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   GLY A 547 " --> pdb=" O   VAL A 720 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   PHE A 715 " --> pdb=" O   SER A 665 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 578 through 579
      removed outlier: 3.631A  pdb=" N   VAL A 586 " --> pdb=" O   MET A 578 " (cutoff:3.500A)

    405 hydrogen bonds defined for protein.
    1170 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: 1.59

  Time building geometry restraints manager: 1.04 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: 2546
        1.34 -     1.46: 1467
        1.46 -     1.58: 4042
        1.58 -     1.69: 1
        1.69 -     1.81: 69
  Bond restraints: 8125
  Sorted by residual:
  bond pdb=" CB  PRO A 395 "
       pdb=" CG  PRO A 395 "
    ideal  model  delta    sigma   weight residual
    1.492  1.593 -0.101 5.00e-02 4.00e+02 4.04e+00
  bond pdb=" CB  PRO A1045 "
       pdb=" CG  PRO A1045 "
    ideal  model  delta    sigma   weight residual
    1.492  1.566 -0.074 5.00e-02 4.00e+02 2.19e+00
  bond pdb=" CA  ALA A 958 "
       pdb=" C   ALA A 958 "
    ideal  model  delta    sigma   weight residual
    1.528  1.512  0.017 1.18e-02 7.18e+03 2.04e+00
  bond pdb=" CB  GLN A1020 "
       pdb=" CG  GLN A1020 "
    ideal  model  delta    sigma   weight residual
    1.520  1.480  0.040 3.00e-02 1.11e+03 1.74e+00
  bond pdb=" CA  LEU A1007 "
       pdb=" C   LEU A1007 "
    ideal  model  delta    sigma   weight residual
    1.523  1.507  0.016 1.35e-02 5.49e+03 1.36e+00
  ... (remaining 8120 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.97: 10919
        2.97 -     5.95: 100
        5.95 -     8.92: 4
        8.92 -    11.89: 0
       11.89 -    14.86: 1
  Bond angle restraints: 11024
  Sorted by residual:
  angle pdb=" C   ILE A 831 "
        pdb=" CA  ILE A 831 "
        pdb=" CB  ILE A 831 "
      ideal   model   delta    sigma   weight residual
     113.70  109.64    4.06 9.50e-01 1.11e+00 1.82e+01
  angle pdb=" CA  LEU A1005 "
        pdb=" CB  LEU A1005 "
        pdb=" CG  LEU A1005 "
      ideal   model   delta    sigma   weight residual
     116.30  101.44   14.86 3.50e+00 8.16e-02 1.80e+01
  angle pdb=" C   LEU A 543 "
        pdb=" CA  LEU A 543 "
        pdb=" CB  LEU A 543 "
      ideal   model   delta    sigma   weight residual
     115.79  111.16    4.63 1.19e+00 7.06e-01 1.51e+01
  angle pdb=" CA  TYR A1073 "
        pdb=" CB  TYR A1073 "
        pdb=" CG  TYR A1073 "
      ideal   model   delta    sigma   weight residual
     113.90  107.17    6.73 1.80e+00 3.09e-01 1.40e+01
  angle pdb=" CA  PRO A 395 "
        pdb=" N   PRO A 395 "
        pdb=" CD  PRO A 395 "
      ideal   model   delta    sigma   weight residual
     112.00  107.25    4.75 1.40e+00 5.10e-01 1.15e+01
  ... (remaining 11019 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4525
       17.98 -    35.97: 336
       35.97 -    53.95: 38
       53.95 -    71.94: 4
       71.94 -    89.92: 5
  Dihedral angle restraints: 4908
    sinusoidal: 1946
      harmonic: 2962
  Sorted by residual:
  dihedral pdb=" CA  PHE A1169 "
           pdb=" C   PHE A1169 "
           pdb=" N   LYS A1170 "
           pdb=" CA  LYS A1170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.69   25.31     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" CA  PRO A 518 "
           pdb=" C   PRO A 518 "
           pdb=" N   PHE A 519 "
           pdb=" CA  PHE A 519 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.76  -21.24     0      5.00e+00 4.00e-02 1.80e+01
  dihedral pdb=" CA  ARG A 520 "
           pdb=" C   ARG A 520 "
           pdb=" N   ILE A 521 "
           pdb=" CA  ILE A 521 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.71   19.29     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 4905 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 824
       0.034 -    0.069: 288
       0.069 -    0.103: 121
       0.103 -    0.138: 42
       0.138 -    0.172: 5
  Chirality restraints: 1280
  Sorted by residual:
  chirality pdb=" CB  ILE A 495 "
            pdb=" CA  ILE A 495 "
            pdb=" CG1 ILE A 495 "
            pdb=" CG2 ILE A 495 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.39e-01
  chirality pdb=" CA  ILE A1165 "
            pdb=" N   ILE A1165 "
            pdb=" C   ILE A1165 "
            pdb=" CB  ILE A1165 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.21e-01
  chirality pdb=" CA  GLU A 480 "
            pdb=" N   GLU A 480 "
            pdb=" C   GLU A 480 "
            pdb=" CB  GLU A 480 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.11e-01
  ... (remaining 1277 not shown)

  Planarity restraints: 1398
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A1044 "   -0.073 5.00e-02 4.00e+02   1.09e-01 1.89e+01
        pdb=" N   PRO A1045 "    0.188 5.00e-02 4.00e+02
        pdb=" CA  PRO A1045 "   -0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO A1045 "   -0.058 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 257 "    0.020 2.00e-02 2.50e+03   2.02e-02 1.02e+01
        pdb=" CG  TRP A 257 "   -0.055 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 257 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 257 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 257 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 257 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 257 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 257 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 257 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 257 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 394 "   -0.050 5.00e-02 4.00e+02   7.33e-02 8.60e+00
        pdb=" N   PRO A 395 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A 395 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 395 "   -0.041 5.00e-02 4.00e+02
  ... (remaining 1395 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.62: 80
        2.62 -     3.19: 7451
        3.19 -     3.76: 12235
        3.76 -     4.33: 15943
        4.33 -     4.90: 25839
  Nonbonded interactions: 61548
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 265 "
            pdb=" O   SER A1013 "
     model   vdw
     2.056 3.040
  nonbonded pdb=" O   ILE A1165 "
            pdb=" NZ  LYS A1170 "
     model   vdw
     2.105 3.120
  nonbonded pdb=" NH2 ARG A 436 "
            pdb=" OD1 ASN A 502 "
     model   vdw
     2.197 3.120
  nonbonded pdb=" ND2 ASN A 225 "
            pdb=" O   ILE A 317 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" OD2 ASP A 533 "
            pdb=" OG1 THR A 535 "
     model   vdw
     2.218 3.040
  ... (remaining 61543 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.890
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.820
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6790
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   0.101   8125  Z= 0.165
  Angle     :  0.703  14.864  11024  Z= 0.385
  Chirality :  0.044   0.172   1280
  Planarity :  0.006   0.109   1398
  Dihedral  : 12.224  89.921   2988
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 15.51
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.06 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.26), residues: 1012
  helix:  1.14 (0.24), residues: 455
  sheet:  0.26 (0.60), residues: 82
  loop :  0.01 (0.29), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 216 
 TYR   0.026   0.002   TYR A 265 
 PHE   0.029   0.002   PHE A1094 
 TRP   0.055   0.002   TRP A 257 
 HIS   0.009   0.001   HIS A 673 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 8125)
  covalent geometry    : angle       0.70272 (11024)
  hydrogen bonds       : bond        0.18281 (  404)
  hydrogen bonds       : angle       6.46532 ( 1170)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 CYS cc_start: 0.8493 (m) cc_final: 0.8205 (m)
REVERT: A  288 MET cc_start: 0.6117 (mmm) cc_final: 0.5375 (mmm)
REVERT: A  294 MET cc_start: 0.7250 (mpp) cc_final: 0.6923 (mpp)
REVERT: A  300 MET cc_start: 0.8372 (tmm) cc_final: 0.7892 (tmm)
REVERT: A  360 MET cc_start: 0.6853 (tpt) cc_final: 0.6118 (tpt)
REVERT: A  481 CYS cc_start: 0.8139 (m) cc_final: 0.7810 (m)
REVERT: A  498 SER cc_start: 0.8544 (m) cc_final: 0.8040 (p)
REVERT: A  511 LEU cc_start: 0.8836 (mp) cc_final: 0.8260 (mp)
REVERT: A  534 LYS cc_start: 0.8037 (pttp) cc_final: 0.7667 (pttp)
REVERT: A  578 MET cc_start: 0.6676 (ptp) cc_final: 0.6156 (ptp)
REVERT: A  622 GLN cc_start: 0.7043 (tm-30) cc_final: 0.6814 (tm-30)
REVERT: A  624 PHE cc_start: 0.7809 (m-10) cc_final: 0.7224 (m-10)
REVERT: A  663 MET cc_start: 0.7777 (mtm) cc_final: 0.7211 (mtm)
REVERT: A  677 GLU cc_start: 0.7391 (mp0) cc_final: 0.7038 (mp0)
REVERT: A  730 LYS cc_start: 0.8872 (ttmm) cc_final: 0.8400 (ttmm)
REVERT: A  747 THR cc_start: 0.7094 (t) cc_final: 0.6700 (t)
REVERT: A  755 CYS cc_start: 0.8312 (m) cc_final: 0.7905 (m)
REVERT: A  770 LEU cc_start: 0.8555 (mp) cc_final: 0.8247 (mp)
REVERT: A  818 HIS cc_start: 0.7830 (t70) cc_final: 0.7146 (t70)
REVERT: A  819 LEU cc_start: 0.8590 (mt) cc_final: 0.8209 (mt)
REVERT: A  844 GLN cc_start: 0.8303 (mp10) cc_final: 0.8075 (mp10)
REVERT: A  845 LYS cc_start: 0.8475 (mtmm) cc_final: 0.8052 (mtmm)
REVERT: A  853 LYS cc_start: 0.8781 (ttpp) cc_final: 0.8409 (ttpp)
REVERT: A  874 HIS cc_start: 0.8787 (m-70) cc_final: 0.8376 (m-70)
REVERT: A  975 LYS cc_start: 0.7955 (tptm) cc_final: 0.7436 (mtpt)
REVERT: A  978 ARG cc_start: 0.8187 (mtp85) cc_final: 0.7842 (mtp-110)
REVERT: A 1019 LEU cc_start: 0.8266 (tp) cc_final: 0.8027 (tp)
REVERT: A 1020 GLN cc_start: 0.8469 (pp30) cc_final: 0.8202 (pp30)
REVERT: A 1035 LYS cc_start: 0.8930 (mmpt) cc_final: 0.8633 (mmpt)
REVERT: A 1049 ILE cc_start: 0.8381 (tp) cc_final: 0.8160 (tp)
REVERT: A 1056 LEU cc_start: 0.8464 (tp) cc_final: 0.8251 (tp)
REVERT: A 1065 HIS cc_start: 0.8170 (m170) cc_final: 0.7929 (m170)
REVERT: A 1104 TYR cc_start: 0.7920 (t80) cc_final: 0.7669 (t80)
REVERT: A 1108 MET cc_start: 0.7922 (mmp) cc_final: 0.7526 (mmm)
REVERT: A 1110 MET cc_start: 0.7637 (mtt) cc_final: 0.7232 (mtt)
REVERT: A 1192 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7923 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.1027
  time to fit residues: 31.3375
Evaluate side-chains
  228 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.0030
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.1980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    9.9990
   chunk 100 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.5790

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

Flipped N/Q/H residues before XYZ refinement:
A 568 HIS
** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.179923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.144900 restraints weight = 16140.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.149975 restraints weight = 9144.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.153421 restraints weight = 5933.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.155620 restraints weight = 4250.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.157212 restraints weight = 3332.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.4136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6723
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8125  Z= 0.136
  Angle     :  0.643  17.894  11024  Z= 0.321
  Chirality :  0.044   0.148   1280
  Planarity :  0.005   0.070   1398
  Dihedral  :  4.214  20.398   1086
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.37 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 10.02 %
    Favored  : 89.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.26), residues: 1012
  helix:  1.30 (0.24), residues: 460
  sheet:  0.51 (0.52), residues: 98
  loop : -0.00 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 216 
 TYR   0.022   0.002   TYR A 181 
 PHE   0.020   0.002   PHE A 624 
 TRP   0.033   0.002   TRP A 257 
 HIS   0.008   0.001   HIS A 741 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8125)
  covalent geometry    : angle       0.64339 (11024)
  hydrogen bonds       : bond        0.04866 (  404)
  hydrogen bonds       : angle       5.11839 ( 1170)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 224
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 CYS cc_start: 0.8388 (m) cc_final: 0.8152 (m)
REVERT: A  288 MET cc_start: 0.5988 (mmm) cc_final: 0.5230 (mmm)
REVERT: A  477 LEU cc_start: 0.8122 (tp) cc_final: 0.7528 (tp)
REVERT: A  481 CYS cc_start: 0.8119 (m) cc_final: 0.7716 (m)
REVERT: A  498 SER cc_start: 0.8511 (m) cc_final: 0.8034 (p)
REVERT: A  534 LYS cc_start: 0.8153 (pttp) cc_final: 0.7733 (pttp)
REVERT: A  663 MET cc_start: 0.7784 (mtm) cc_final: 0.7181 (mtm)
REVERT: A  677 GLU cc_start: 0.7368 (mp0) cc_final: 0.6944 (mp0)
REVERT: A  730 LYS cc_start: 0.8830 (ttmm) cc_final: 0.8381 (ttmm)
REVERT: A  747 THR cc_start: 0.7026 (t) cc_final: 0.6679 (t)
REVERT: A  755 CYS cc_start: 0.8377 (m) cc_final: 0.7960 (m)
REVERT: A  818 HIS cc_start: 0.7772 (t70) cc_final: 0.7117 (t70)
REVERT: A  819 LEU cc_start: 0.8514 (mt) cc_final: 0.8168 (mt)
REVERT: A  844 GLN cc_start: 0.8349 (mp10) cc_final: 0.8118 (mp10)
REVERT: A  874 HIS cc_start: 0.8847 (m-70) cc_final: 0.8533 (m-70)
REVERT: A  975 LYS cc_start: 0.7949 (tptm) cc_final: 0.7498 (mtpt)
REVERT: A  978 ARG cc_start: 0.8163 (mtp85) cc_final: 0.7825 (mtp85)
REVERT: A 1019 LEU cc_start: 0.8126 (tp) cc_final: 0.7915 (tp)
REVERT: A 1035 LYS cc_start: 0.8925 (mmpt) cc_final: 0.8657 (mmmm)
REVERT: A 1065 HIS cc_start: 0.8233 (m170) cc_final: 0.7746 (m-70)
REVERT: A 1073 TYR cc_start: 0.8522 (t80) cc_final: 0.8025 (t80)
REVERT: A 1075 GLU cc_start: 0.7977 (tp30) cc_final: 0.7361 (tp30)
REVERT: A 1077 GLN cc_start: 0.8233 (tt0) cc_final: 0.7840 (tt0)
REVERT: A 1104 TYR cc_start: 0.7835 (t80) cc_final: 0.7605 (t80)
REVERT: A 1108 MET cc_start: 0.7922 (mmp) cc_final: 0.7370 (tpp)
REVERT: A 1110 MET cc_start: 0.7631 (mtt) cc_final: 0.7295 (mtt)
REVERT: A 1115 PHE cc_start: 0.8098 (m-80) cc_final: 0.7497 (m-80)
REVERT: A 1169 PHE cc_start: 0.6524 (m-80) cc_final: 0.5787 (m-80)
REVERT: A 1175 GLN cc_start: 0.7751 (mt0) cc_final: 0.7389 (mt0)
REVERT: A 1192 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7944 (tm-30)
  outliers start: 7
  outliers final: 5
  residues processed: 226
  average time/residue: 0.1115
  time to fit residues: 32.8741
Evaluate side-chains
  218 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 213
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  675 HIS
Chi-restraints excluded: chain A residue  855 LEU
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1070 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    0.0270
   chunk 1 optimal weight:    0.5980
   chunk 76 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 6 optimal weight:    0.3980
   chunk 19 optimal weight:    6.9990
   chunk 10 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0770
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.3596

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

Flipped N/Q/H residues before XYZ refinement:
A 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.181498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.146772 restraints weight = 15826.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.151938 restraints weight = 9036.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.154982 restraints weight = 5844.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.157507 restraints weight = 4308.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.159035 restraints weight = 3313.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.4155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6703
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8125  Z= 0.117
  Angle     :  0.602  14.885  11024  Z= 0.299
  Chirality :  0.042   0.145   1280
  Planarity :  0.005   0.059   1398
  Dihedral  :  4.098  18.426   1086
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.27 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 12.87 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.26), residues: 1012
  helix:  1.34 (0.24), residues: 462
  sheet:  0.50 (0.51), residues: 103
  loop : -0.01 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 216 
 TYR   0.014   0.001   TYR A 181 
 PHE   0.015   0.001   PHE A 450 
 TRP   0.021   0.002   TRP A 257 
 HIS   0.009   0.001   HIS A 741 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8125)
  covalent geometry    : angle       0.60159 (11024)
  hydrogen bonds       : bond        0.04395 (  404)
  hydrogen bonds       : angle       4.76634 ( 1170)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 216
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 CYS cc_start: 0.8353 (m) cc_final: 0.8148 (m)
REVERT: A  288 MET cc_start: 0.5963 (mmm) cc_final: 0.5270 (mmm)
REVERT: A  448 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8621 (tp)
REVERT: A  464 ILE cc_start: 0.7925 (mt) cc_final: 0.7597 (mm)
REVERT: A  481 CYS cc_start: 0.8169 (m) cc_final: 0.7747 (m)
REVERT: A  498 SER cc_start: 0.8478 (m) cc_final: 0.8000 (p)
REVERT: A  521 ILE cc_start: 0.8471 (mt) cc_final: 0.8241 (mt)
REVERT: A  534 LYS cc_start: 0.8094 (pttp) cc_final: 0.7408 (pttp)
REVERT: A  663 MET cc_start: 0.7777 (mtm) cc_final: 0.7194 (mtm)
REVERT: A  730 LYS cc_start: 0.8802 (ttmm) cc_final: 0.8347 (ttmm)
REVERT: A  747 THR cc_start: 0.6959 (t) cc_final: 0.6411 (t)
REVERT: A  749 ASP cc_start: 0.7794 (m-30) cc_final: 0.7172 (m-30)
REVERT: A  755 CYS cc_start: 0.8452 (m) cc_final: 0.8055 (m)
REVERT: A  818 HIS cc_start: 0.7799 (t70) cc_final: 0.7118 (t70)
REVERT: A  819 LEU cc_start: 0.8517 (mt) cc_final: 0.8169 (mt)
REVERT: A  844 GLN cc_start: 0.8355 (mp10) cc_final: 0.8101 (mp10)
REVERT: A  845 LYS cc_start: 0.8527 (mtmm) cc_final: 0.8100 (mtmm)
REVERT: A  874 HIS cc_start: 0.8801 (m-70) cc_final: 0.8522 (m-70)
REVERT: A  975 LYS cc_start: 0.7924 (tptm) cc_final: 0.7523 (mtpt)
REVERT: A  978 ARG cc_start: 0.8105 (mtp85) cc_final: 0.7818 (mtp85)
REVERT: A  986 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7255 (mm-40)
REVERT: A  994 ASN cc_start: 0.8355 (t0) cc_final: 0.8077 (t0)
REVERT: A  997 ILE cc_start: 0.8315 (mm) cc_final: 0.8041 (tp)
REVERT: A 1019 LEU cc_start: 0.8106 (tp) cc_final: 0.7861 (tp)
REVERT: A 1024 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8279 (mm)
REVERT: A 1027 CYS cc_start: 0.7899 (m) cc_final: 0.6981 (t)
REVERT: A 1035 LYS cc_start: 0.8918 (mmpt) cc_final: 0.8667 (mmmm)
REVERT: A 1063 PHE cc_start: 0.7424 (t80) cc_final: 0.7167 (t80)
REVERT: A 1065 HIS cc_start: 0.8229 (m170) cc_final: 0.7972 (m170)
REVERT: A 1073 TYR cc_start: 0.8455 (t80) cc_final: 0.7913 (t80)
REVERT: A 1075 GLU cc_start: 0.8037 (tp30) cc_final: 0.7369 (tp30)
REVERT: A 1077 GLN cc_start: 0.8228 (tt0) cc_final: 0.7842 (tt0)
REVERT: A 1079 ARG cc_start: 0.6758 (mtm180) cc_final: 0.5778 (mtt180)
REVERT: A 1103 VAL cc_start: 0.8513 (t) cc_final: 0.8199 (p)
REVERT: A 1112 MET cc_start: 0.6879 (tpt) cc_final: 0.6080 (tpt)
REVERT: A 1115 PHE cc_start: 0.8059 (m-80) cc_final: 0.6936 (m-10)
REVERT: A 1170 LYS cc_start: 0.8603 (mppt) cc_final: 0.7843 (mmtp)
REVERT: A 1175 GLN cc_start: 0.7728 (mt0) cc_final: 0.7456 (mt0)
REVERT: A 1192 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7957 (tm-30)
  outliers start: 11
  outliers final: 7
  residues processed: 219
  average time/residue: 0.1118
  time to fit residues: 32.0092
Evaluate side-chains
  219 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 210
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  675 HIS
Chi-restraints excluded: chain A residue  855 LEU
Chi-restraints excluded: chain A residue  971 CYS
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1059 MET
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1165 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:    0.0060
   chunk 56 optimal weight:    9.9990
   chunk 41 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 82 optimal weight:    0.7980
   chunk 70 optimal weight:    3.9990
   chunk 89 optimal weight:    0.3980
   chunk 10 optimal weight:    4.9990
   chunk 7 optimal weight:    0.3980
   chunk 93 optimal weight:    0.8980
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
A 225 ASN
** A1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.180917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.145662 restraints weight = 16360.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.150770 restraints weight = 9382.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.154338 restraints weight = 6156.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.156663 restraints weight = 4416.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.158323 restraints weight = 3450.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.4145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6722
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8125  Z= 0.111
  Angle     :  0.604  14.903  11024  Z= 0.294
  Chirality :  0.042   0.139   1280
  Planarity :  0.004   0.054   1398
  Dihedral  :  3.998  16.410   1086
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.98 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.92 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.26), residues: 1012
  helix:  1.41 (0.24), residues: 462
  sheet:  0.71 (0.52), residues: 100
  loop : -0.00 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 520 
 TYR   0.011   0.001   TYR A1053 
 PHE   0.013   0.001   PHE A 450 
 TRP   0.016   0.001   TRP A 257 
 HIS   0.010   0.001   HIS A 741 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 8125)
  covalent geometry    : angle       0.60375 (11024)
  hydrogen bonds       : bond        0.04057 (  404)
  hydrogen bonds       : angle       4.60598 ( 1170)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 216
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 CYS cc_start: 0.8393 (m) cc_final: 0.8118 (m)
REVERT: A  288 MET cc_start: 0.6036 (mmm) cc_final: 0.5369 (mmm)
REVERT: A  294 MET cc_start: 0.7865 (tpp) cc_final: 0.7487 (tpp)
REVERT: A  448 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8624 (tp)
REVERT: A  464 ILE cc_start: 0.7923 (mt) cc_final: 0.7575 (mm)
REVERT: A  473 ASN cc_start: 0.8609 (t0) cc_final: 0.8200 (t0)
REVERT: A  481 CYS cc_start: 0.8180 (m) cc_final: 0.7768 (m)
REVERT: A  498 SER cc_start: 0.8488 (m) cc_final: 0.8005 (p)
REVERT: A  520 ARG cc_start: 0.8102 (mpp80) cc_final: 0.7814 (mpp80)
REVERT: A  521 ILE cc_start: 0.8496 (mt) cc_final: 0.8261 (mt)
REVERT: A  534 LYS cc_start: 0.8027 (pttp) cc_final: 0.7160 (pttp)
REVERT: A  663 MET cc_start: 0.7804 (mtm) cc_final: 0.7226 (mtm)
REVERT: A  730 LYS cc_start: 0.8806 (ttmm) cc_final: 0.8352 (ttmm)
REVERT: A  747 THR cc_start: 0.6964 (t) cc_final: 0.6098 (t)
REVERT: A  749 ASP cc_start: 0.7828 (m-30) cc_final: 0.7104 (m-30)
REVERT: A  755 CYS cc_start: 0.8483 (m) cc_final: 0.8055 (m)
REVERT: A  759 GLN cc_start: 0.8471 (pp30) cc_final: 0.8147 (pp30)
REVERT: A  818 HIS cc_start: 0.7803 (t70) cc_final: 0.7119 (t70)
REVERT: A  819 LEU cc_start: 0.8529 (mt) cc_final: 0.8172 (mt)
REVERT: A  844 GLN cc_start: 0.8326 (mp10) cc_final: 0.8089 (mp10)
REVERT: A  858 VAL cc_start: 0.8055 (t) cc_final: 0.7752 (m)
REVERT: A  874 HIS cc_start: 0.8793 (m-70) cc_final: 0.8529 (m-70)
REVERT: A  975 LYS cc_start: 0.7916 (tptm) cc_final: 0.7359 (mttm)
REVERT: A  978 ARG cc_start: 0.8060 (mtp85) cc_final: 0.7774 (mtp85)
REVERT: A  986 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7350 (mm-40)
REVERT: A  997 ILE cc_start: 0.8363 (mm) cc_final: 0.8143 (tp)
REVERT: A 1011 LYS cc_start: 0.6838 (pttm) cc_final: 0.6530 (pttm)
REVERT: A 1019 LEU cc_start: 0.8021 (tp) cc_final: 0.7793 (tp)
REVERT: A 1027 CYS cc_start: 0.8006 (m) cc_final: 0.6931 (t)
REVERT: A 1035 LYS cc_start: 0.8905 (mmpt) cc_final: 0.8619 (mmmm)
REVERT: A 1063 PHE cc_start: 0.7453 (t80) cc_final: 0.7180 (t80)
REVERT: A 1065 HIS cc_start: 0.8239 (m170) cc_final: 0.7879 (m170)
REVERT: A 1073 TYR cc_start: 0.8395 (t80) cc_final: 0.7854 (t80)
REVERT: A 1075 GLU cc_start: 0.8053 (tp30) cc_final: 0.7243 (tp30)
REVERT: A 1077 GLN cc_start: 0.8238 (tt0) cc_final: 0.7901 (tt0)
REVERT: A 1103 VAL cc_start: 0.8476 (t) cc_final: 0.8154 (p)
REVERT: A 1108 MET cc_start: 0.7895 (mmm) cc_final: 0.7559 (tpp)
REVERT: A 1110 MET cc_start: 0.7805 (mtt) cc_final: 0.7256 (mtt)
REVERT: A 1115 PHE cc_start: 0.8076 (m-80) cc_final: 0.6893 (m-80)
REVERT: A 1170 LYS cc_start: 0.8620 (mppt) cc_final: 0.7864 (ttmm)
REVERT: A 1175 GLN cc_start: 0.7733 (mt0) cc_final: 0.7368 (mt0)
  outliers start: 16
  outliers final: 12
  residues processed: 222
  average time/residue: 0.1223
  time to fit residues: 34.9247
Evaluate side-chains
  216 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 203
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  480 GLU
Chi-restraints excluded: chain A residue  517 GLU
Chi-restraints excluded: chain A residue  675 HIS
Chi-restraints excluded: chain A residue  855 LEU
Chi-restraints excluded: chain A residue  971 CYS
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1059 MET
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1164 ASP
Chi-restraints excluded: chain A residue 1165 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 92 optimal weight:    6.9990
   chunk 68 optimal weight:    6.9990
   chunk 28 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0270
   chunk 38 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 52 optimal weight:    8.9990
   chunk 43 optimal weight:   30.0000
   chunk 45 optimal weight:    6.9990
   overall best weight:    1.5440

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

Flipped N/Q/H residues before XYZ refinement:
** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 773 GLN ** 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 = 0.4387 r_free = 0.4387 target = 0.178088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.142427 restraints weight = 16133.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.147419 restraints weight = 9243.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.150921 restraints weight = 6073.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.153200 restraints weight = 4377.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.154861 restraints weight = 3427.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.4094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6810
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8125  Z= 0.172
  Angle     :  0.636  17.997  11024  Z= 0.315
  Chirality :  0.043   0.142   1280
  Planarity :  0.005   0.052   1398
  Dihedral  :  4.112  16.333   1086
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.27 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.49 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.26), residues: 1012
  helix:  1.04 (0.24), residues: 486
  sheet:  0.35 (0.52), residues: 107
  loop :  0.08 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 292 
 TYR   0.014   0.001   TYR A1006 
 PHE   0.015   0.001   PHE A 222 
 TRP   0.010   0.001   TRP A 257 
 HIS   0.011   0.001   HIS A 741 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 8125)
  covalent geometry    : angle       0.63618 (11024)
  hydrogen bonds       : bond        0.04434 (  404)
  hydrogen bonds       : angle       4.64862 ( 1170)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 216
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 HIS cc_start: 0.2813 (OUTLIER) cc_final: 0.1133 (p90)
REVERT: A  170 LEU cc_start: 0.8447 (mt) cc_final: 0.8244 (mp)
REVERT: A  226 LYS cc_start: 0.7461 (mptt) cc_final: 0.7218 (mmtm)
REVERT: A  253 CYS cc_start: 0.8456 (m) cc_final: 0.8173 (m)
REVERT: A  263 TRP cc_start: 0.5439 (OUTLIER) cc_final: 0.5196 (t60)
REVERT: A  288 MET cc_start: 0.6173 (mmm) cc_final: 0.5486 (mmm)
REVERT: A  294 MET cc_start: 0.7831 (tpp) cc_final: 0.7429 (tpp)
REVERT: A  347 VAL cc_start: 0.7702 (OUTLIER) cc_final: 0.7045 (t)
REVERT: A  448 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8616 (tp)
REVERT: A  451 LEU cc_start: 0.8517 (mm) cc_final: 0.8310 (mm)
REVERT: A  464 ILE cc_start: 0.8032 (mt) cc_final: 0.7699 (mm)
REVERT: A  481 CYS cc_start: 0.8283 (m) cc_final: 0.7873 (m)
REVERT: A  498 SER cc_start: 0.8466 (m) cc_final: 0.7993 (p)
REVERT: A  534 LYS cc_start: 0.8073 (pttp) cc_final: 0.7473 (pttp)
REVERT: A  663 MET cc_start: 0.7865 (mtm) cc_final: 0.7288 (mtm)
REVERT: A  730 LYS cc_start: 0.8826 (ttmm) cc_final: 0.8390 (ttmm)
REVERT: A  755 CYS cc_start: 0.8483 (m) cc_final: 0.8126 (m)
REVERT: A  818 HIS cc_start: 0.7823 (t70) cc_final: 0.7147 (t70)
REVERT: A  819 LEU cc_start: 0.8559 (mt) cc_final: 0.8200 (mt)
REVERT: A  844 GLN cc_start: 0.8352 (mp10) cc_final: 0.8125 (mp10)
REVERT: A  845 LYS cc_start: 0.8621 (mtmm) cc_final: 0.8313 (mttt)
REVERT: A  858 VAL cc_start: 0.8075 (t) cc_final: 0.7738 (m)
REVERT: A  874 HIS cc_start: 0.8867 (m-70) cc_final: 0.8598 (m-70)
REVERT: A  975 LYS cc_start: 0.8008 (tptm) cc_final: 0.7507 (mmmm)
REVERT: A  978 ARG cc_start: 0.8152 (mtp85) cc_final: 0.7838 (mtp85)
REVERT: A  986 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7320 (mm-40)
REVERT: A 1011 LYS cc_start: 0.6987 (pttm) cc_final: 0.6709 (pttm)
REVERT: A 1027 CYS cc_start: 0.8096 (m) cc_final: 0.6812 (t)
REVERT: A 1035 LYS cc_start: 0.8933 (mmpt) cc_final: 0.8661 (mmmm)
REVERT: A 1056 LEU cc_start: 0.8435 (tp) cc_final: 0.8172 (tp)
REVERT: A 1065 HIS cc_start: 0.8245 (m170) cc_final: 0.7694 (m170)
REVERT: A 1073 TYR cc_start: 0.8423 (t80) cc_final: 0.7917 (t80)
REVERT: A 1075 GLU cc_start: 0.8082 (tp30) cc_final: 0.7374 (tp30)
REVERT: A 1077 GLN cc_start: 0.8208 (tt0) cc_final: 0.7915 (tt0)
REVERT: A 1095 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6831 (mt-10)
REVERT: A 1103 VAL cc_start: 0.8514 (t) cc_final: 0.8197 (p)
REVERT: A 1108 MET cc_start: 0.8000 (mmm) cc_final: 0.7188 (mmm)
REVERT: A 1110 MET cc_start: 0.7756 (mtt) cc_final: 0.7248 (mtt)
REVERT: A 1115 PHE cc_start: 0.8131 (m-80) cc_final: 0.6933 (m-80)
REVERT: A 1118 ASN cc_start: 0.8017 (m-40) cc_final: 0.7717 (m-40)
REVERT: A 1170 LYS cc_start: 0.8660 (mppt) cc_final: 0.7995 (mmtp)
REVERT: A 1175 GLN cc_start: 0.7791 (mt0) cc_final: 0.7425 (mt0)
  outliers start: 29
  outliers final: 19
  residues processed: 230
  average time/residue: 0.1105
  time to fit residues: 33.4254
Evaluate side-chains
  236 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 213
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 HIS
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  263 TRP
Chi-restraints excluded: chain A residue  265 TYR
Chi-restraints excluded: chain A residue  279 SER
Chi-restraints excluded: chain A residue  345 CYS
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  480 GLU
Chi-restraints excluded: chain A residue  517 GLU
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  675 HIS
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  807 TYR
Chi-restraints excluded: chain A residue  971 CYS
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue  996 LEU
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1059 MET
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1164 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 6 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 48 optimal weight:    7.9990
   chunk 93 optimal weight:    3.9990
   chunk 94 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   chunk 60 optimal weight:    0.3980
   chunk 37 optimal weight:    2.9990
   chunk 43 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:
A1002 GLN
A1100 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.176114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.140647 restraints weight = 15963.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.145782 restraints weight = 9108.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.149272 restraints weight = 5929.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.151693 restraints weight = 4248.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.152970 restraints weight = 3282.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.4078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6844
moved from start:          0.2780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8125  Z= 0.172
  Angle     :  0.619   9.075  11024  Z= 0.315
  Chirality :  0.044   0.140   1280
  Planarity :  0.004   0.049   1398
  Dihedral  :  4.221  16.274   1086
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.87 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.97 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.26), residues: 1012
  helix:  0.94 (0.24), residues: 478
  sheet:  0.06 (0.52), residues: 112
  loop :  0.14 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1079 
 TYR   0.012   0.001   TYR A 475 
 PHE   0.018   0.001   PHE A 276 
 TRP   0.014   0.002   TRP A 463 
 HIS   0.011   0.001   HIS A 741 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8125)
  covalent geometry    : angle       0.61905 (11024)
  hydrogen bonds       : bond        0.04539 (  404)
  hydrogen bonds       : angle       4.61904 ( 1170)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 218
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 HIS cc_start: 0.2744 (OUTLIER) cc_final: 0.1256 (t-90)
REVERT: A  253 CYS cc_start: 0.8451 (m) cc_final: 0.8170 (m)
REVERT: A  263 TRP cc_start: 0.5496 (OUTLIER) cc_final: 0.5225 (t60)
REVERT: A  288 MET cc_start: 0.6328 (mmm) cc_final: 0.5601 (mmm)
REVERT: A  294 MET cc_start: 0.7860 (tpp) cc_final: 0.7445 (tpp)
REVERT: A  344 ARG cc_start: 0.6813 (mtt180) cc_final: 0.6562 (mtt-85)
REVERT: A  347 VAL cc_start: 0.7764 (OUTLIER) cc_final: 0.7131 (t)
REVERT: A  448 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8717 (tp)
REVERT: A  464 ILE cc_start: 0.8026 (mt) cc_final: 0.7683 (mm)
REVERT: A  481 CYS cc_start: 0.8349 (m) cc_final: 0.8002 (m)
REVERT: A  483 LEU cc_start: 0.8288 (tp) cc_final: 0.8009 (tp)
REVERT: A  498 SER cc_start: 0.8532 (m) cc_final: 0.8029 (p)
REVERT: A  534 LYS cc_start: 0.8054 (pttp) cc_final: 0.7449 (pttp)
REVERT: A  663 MET cc_start: 0.7916 (mtm) cc_final: 0.7358 (mtm)
REVERT: A  730 LYS cc_start: 0.8811 (ttmm) cc_final: 0.8418 (ttmm)
REVERT: A  755 CYS cc_start: 0.8520 (m) cc_final: 0.8081 (m)
REVERT: A  759 GLN cc_start: 0.8524 (pp30) cc_final: 0.8246 (pp30)
REVERT: A  785 ARG cc_start: 0.6907 (mtm-85) cc_final: 0.6663 (mtm-85)
REVERT: A  818 HIS cc_start: 0.7854 (t70) cc_final: 0.7174 (t70)
REVERT: A  819 LEU cc_start: 0.8567 (mt) cc_final: 0.8207 (mt)
REVERT: A  826 GLN cc_start: 0.7794 (pm20) cc_final: 0.7532 (pm20)
REVERT: A  845 LYS cc_start: 0.8650 (mtmm) cc_final: 0.8321 (mttt)
REVERT: A  855 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8440 (mm)
REVERT: A  874 HIS cc_start: 0.8849 (m-70) cc_final: 0.8629 (m-70)
REVERT: A  975 LYS cc_start: 0.8045 (tptm) cc_final: 0.7474 (mtpt)
REVERT: A  978 ARG cc_start: 0.8194 (mtp85) cc_final: 0.7845 (mtp85)
REVERT: A  986 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7308 (mm110)
REVERT: A 1013 SER cc_start: 0.7716 (OUTLIER) cc_final: 0.7345 (p)
REVERT: A 1027 CYS cc_start: 0.8131 (m) cc_final: 0.6794 (t)
REVERT: A 1035 LYS cc_start: 0.8956 (mmpt) cc_final: 0.8733 (mmmm)
REVERT: A 1056 LEU cc_start: 0.8422 (tp) cc_final: 0.8117 (tp)
REVERT: A 1073 TYR cc_start: 0.8358 (t80) cc_final: 0.7821 (t80)
REVERT: A 1075 GLU cc_start: 0.8081 (tp30) cc_final: 0.7624 (tp30)
REVERT: A 1077 GLN cc_start: 0.8233 (tt0) cc_final: 0.7952 (tt0)
REVERT: A 1079 ARG cc_start: 0.7121 (mtm180) cc_final: 0.6237 (mtm180)
REVERT: A 1106 MET cc_start: 0.7483 (tpt) cc_final: 0.7086 (tpt)
REVERT: A 1108 MET cc_start: 0.7845 (mmm) cc_final: 0.6970 (tpp)
REVERT: A 1115 PHE cc_start: 0.8057 (m-80) cc_final: 0.6942 (m-80)
REVERT: A 1118 ASN cc_start: 0.8053 (m-40) cc_final: 0.7817 (m-40)
REVERT: A 1120 LYS cc_start: 0.8000 (tptp) cc_final: 0.7769 (tmtt)
REVERT: A 1170 LYS cc_start: 0.8656 (mtpt) cc_final: 0.7991 (mmtp)
REVERT: A 1175 GLN cc_start: 0.7858 (mt0) cc_final: 0.7495 (mt0)
  outliers start: 27
  outliers final: 17
  residues processed: 230
  average time/residue: 0.1067
  time to fit residues: 32.1205
Evaluate side-chains
  240 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 217
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 HIS
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  257 TRP
Chi-restraints excluded: chain A residue  263 TRP
Chi-restraints excluded: chain A residue  265 TYR
Chi-restraints excluded: chain A residue  345 CYS
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  517 GLU
Chi-restraints excluded: chain A residue  658 GLU
Chi-restraints excluded: chain A residue  675 HIS
Chi-restraints excluded: chain A residue  807 TYR
Chi-restraints excluded: chain A residue  855 LEU
Chi-restraints excluded: chain A residue  971 CYS
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1013 SER
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1059 MET
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1164 ASP
Chi-restraints excluded: chain A residue 1165 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 92 optimal weight:    1.9990
   chunk 43 optimal weight:   20.0000
   chunk 98 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 38 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0670
   chunk 79 optimal weight:    0.7980
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.6520

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

Flipped N/Q/H residues before XYZ refinement:
A 225 ASN
A 283 GLN
A 284 GLN
A 737 GLN
A 773 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.178565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.142380 restraints weight = 16048.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.147571 restraints weight = 9167.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.151139 restraints weight = 5967.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.153413 restraints weight = 4297.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.155199 restraints weight = 3381.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.4103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6802
moved from start:          0.3024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8125  Z= 0.120
  Angle     :  0.603   9.254  11024  Z= 0.304
  Chirality :  0.043   0.146   1280
  Planarity :  0.004   0.049   1398
  Dihedral  :  4.096  15.419   1086
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.17 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 18.11 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.26), residues: 1012
  helix:  1.09 (0.24), residues: 485
  sheet:  0.12 (0.52), residues: 112
  loop :  0.11 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 785 
 TYR   0.016   0.001   TYR A1006 
 PHE   0.023   0.001   PHE A 960 
 TRP   0.011   0.001   TRP A 463 
 HIS   0.011   0.001   HIS A 741 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8125)
  covalent geometry    : angle       0.60266 (11024)
  hydrogen bonds       : bond        0.04024 (  404)
  hydrogen bonds       : angle       4.45872 ( 1170)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 223
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 HIS cc_start: 0.2693 (OUTLIER) cc_final: 0.1067 (p90)
REVERT: A  207 ARG cc_start: 0.8484 (mmm160) cc_final: 0.8018 (mmp80)
REVERT: A  221 LYS cc_start: 0.7176 (ptpp) cc_final: 0.6613 (mtmm)
REVERT: A  253 CYS cc_start: 0.8399 (m) cc_final: 0.8134 (m)
REVERT: A  263 TRP cc_start: 0.5337 (OUTLIER) cc_final: 0.5123 (t60)
REVERT: A  288 MET cc_start: 0.6306 (mmm) cc_final: 0.5472 (mmm)
REVERT: A  294 MET cc_start: 0.7790 (tpp) cc_final: 0.7413 (tpp)
REVERT: A  347 VAL cc_start: 0.7565 (OUTLIER) cc_final: 0.6896 (t)
REVERT: A  448 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8695 (tp)
REVERT: A  464 ILE cc_start: 0.7984 (mt) cc_final: 0.7654 (mm)
REVERT: A  481 CYS cc_start: 0.8233 (m) cc_final: 0.7904 (m)
REVERT: A  483 LEU cc_start: 0.8223 (tp) cc_final: 0.7925 (tp)
REVERT: A  498 SER cc_start: 0.8489 (m) cc_final: 0.8042 (p)
REVERT: A  510 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8405 (tppt)
REVERT: A  534 LYS cc_start: 0.8065 (pttp) cc_final: 0.7482 (pttp)
REVERT: A  578 MET cc_start: 0.6369 (ptp) cc_final: 0.5849 (ptp)
REVERT: A  663 MET cc_start: 0.7933 (mtm) cc_final: 0.7336 (mtm)
REVERT: A  730 LYS cc_start: 0.8796 (ttmm) cc_final: 0.8400 (ttmm)
REVERT: A  755 CYS cc_start: 0.8550 (m) cc_final: 0.8175 (m)
REVERT: A  785 ARG cc_start: 0.7137 (mtm-85) cc_final: 0.6881 (mtm-85)
REVERT: A  818 HIS cc_start: 0.7771 (t70) cc_final: 0.7111 (t70)
REVERT: A  819 LEU cc_start: 0.8531 (mt) cc_final: 0.8166 (mt)
REVERT: A  845 LYS cc_start: 0.8621 (mtmm) cc_final: 0.8240 (mtmm)
REVERT: A  855 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8400 (mm)
REVERT: A  858 VAL cc_start: 0.8063 (t) cc_final: 0.7619 (m)
REVERT: A  874 HIS cc_start: 0.8780 (m-70) cc_final: 0.8281 (m-70)
REVERT: A  964 LEU cc_start: 0.7933 (mt) cc_final: 0.7666 (tp)
REVERT: A  975 LYS cc_start: 0.7955 (tptm) cc_final: 0.7255 (mmmt)
REVERT: A  978 ARG cc_start: 0.8118 (mtp85) cc_final: 0.7770 (mtp85)
REVERT: A  986 GLN cc_start: 0.7567 (mm-40) cc_final: 0.7186 (mm-40)
REVERT: A  991 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8300 (mm)
REVERT: A 1020 GLN cc_start: 0.8522 (pp30) cc_final: 0.8311 (pp30)
REVERT: A 1035 LYS cc_start: 0.8943 (mmpt) cc_final: 0.8722 (mmmm)
REVERT: A 1073 TYR cc_start: 0.8249 (t80) cc_final: 0.7679 (t80)
REVERT: A 1075 GLU cc_start: 0.8061 (tp30) cc_final: 0.7417 (tp30)
REVERT: A 1077 GLN cc_start: 0.8252 (tt0) cc_final: 0.7949 (tt0)
REVERT: A 1079 ARG cc_start: 0.7002 (mtm180) cc_final: 0.5697 (mtt90)
REVERT: A 1100 ASN cc_start: 0.8103 (m110) cc_final: 0.7871 (m110)
REVERT: A 1106 MET cc_start: 0.7402 (tpt) cc_final: 0.6895 (tpt)
REVERT: A 1115 PHE cc_start: 0.8046 (m-80) cc_final: 0.7565 (m-10)
REVERT: A 1118 ASN cc_start: 0.7992 (m-40) cc_final: 0.7682 (m-40)
REVERT: A 1125 MET cc_start: 0.7150 (ptp) cc_final: 0.6854 (ptp)
REVERT: A 1170 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8049 (ttmm)
REVERT: A 1175 GLN cc_start: 0.7790 (mt0) cc_final: 0.7418 (mt0)
  outliers start: 29
  outliers final: 18
  residues processed: 236
  average time/residue: 0.1089
  time to fit residues: 33.5315
Evaluate side-chains
  245 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 220
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 HIS
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  257 TRP
Chi-restraints excluded: chain A residue  263 TRP
Chi-restraints excluded: chain A residue  265 TYR
Chi-restraints excluded: chain A residue  345 CYS
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  510 LYS
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  675 HIS
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  807 TYR
Chi-restraints excluded: chain A residue  855 LEU
Chi-restraints excluded: chain A residue  971 CYS
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue  993 LEU
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1059 MET
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1164 ASP
Chi-restraints excluded: chain A residue 1165 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 49 optimal weight:   20.0000
   chunk 88 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 43 optimal weight:   30.0000
   chunk 27 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0040
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
A 225 ASN
A 283 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.178754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.143807 restraints weight = 16046.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.148883 restraints weight = 9098.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.152280 restraints weight = 5911.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.154635 restraints weight = 4257.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.156072 restraints weight = 3326.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.4112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6775
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8125  Z= 0.119
  Angle     :  0.610   8.920  11024  Z= 0.304
  Chirality :  0.043   0.146   1280
  Planarity :  0.004   0.049   1398
  Dihedral  :  4.028  15.354   1086
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.47 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 19.02 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.26), residues: 1012
  helix:  1.13 (0.24), residues: 484
  sheet:  0.05 (0.50), residues: 120
  loop :  0.15 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 292 
 TYR   0.016   0.001   TYR A1006 
 PHE   0.020   0.001   PHE A 960 
 TRP   0.011   0.001   TRP A 463 
 HIS   0.011   0.001   HIS A 741 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8125)
  covalent geometry    : angle       0.61010 (11024)
  hydrogen bonds       : bond        0.04019 (  404)
  hydrogen bonds       : angle       4.42683 ( 1170)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 225
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 HIS cc_start: 0.2727 (OUTLIER) cc_final: 0.1103 (p90)
REVERT: A  207 ARG cc_start: 0.8507 (mmm160) cc_final: 0.8095 (mmp80)
REVERT: A  226 LYS cc_start: 0.7344 (mptt) cc_final: 0.7115 (mmtt)
REVERT: A  253 CYS cc_start: 0.8379 (m) cc_final: 0.8101 (m)
REVERT: A  263 TRP cc_start: 0.5290 (OUTLIER) cc_final: 0.5075 (t60)
REVERT: A  288 MET cc_start: 0.6241 (mmm) cc_final: 0.5479 (mmm)
REVERT: A  294 MET cc_start: 0.7748 (tpp) cc_final: 0.7377 (tpp)
REVERT: A  308 LYS cc_start: 0.7371 (mmpt) cc_final: 0.7163 (mmpt)
REVERT: A  347 VAL cc_start: 0.7593 (OUTLIER) cc_final: 0.6914 (t)
REVERT: A  359 GLN cc_start: 0.5490 (mt0) cc_final: 0.5107 (mt0)
REVERT: A  448 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8705 (tp)
REVERT: A  451 LEU cc_start: 0.8446 (mm) cc_final: 0.8211 (mm)
REVERT: A  464 ILE cc_start: 0.7955 (mt) cc_final: 0.7604 (mm)
REVERT: A  481 CYS cc_start: 0.8173 (m) cc_final: 0.7842 (m)
REVERT: A  483 LEU cc_start: 0.8216 (tp) cc_final: 0.7914 (tp)
REVERT: A  498 SER cc_start: 0.8492 (m) cc_final: 0.8044 (p)
REVERT: A  510 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8371 (tppt)
REVERT: A  534 LYS cc_start: 0.8054 (pttp) cc_final: 0.7438 (pttp)
REVERT: A  578 MET cc_start: 0.6207 (ptp) cc_final: 0.5832 (ptp)
REVERT: A  622 GLN cc_start: 0.8619 (tp-100) cc_final: 0.8309 (tp-100)
REVERT: A  663 MET cc_start: 0.7896 (mtm) cc_final: 0.7325 (mtm)
REVERT: A  730 LYS cc_start: 0.8778 (ttmm) cc_final: 0.8382 (ttmm)
REVERT: A  755 CYS cc_start: 0.8496 (m) cc_final: 0.8103 (m)
REVERT: A  759 GLN cc_start: 0.8404 (pp30) cc_final: 0.8111 (pp30)
REVERT: A  785 ARG cc_start: 0.7065 (mtm-85) cc_final: 0.6651 (mtm-85)
REVERT: A  818 HIS cc_start: 0.7707 (t70) cc_final: 0.7067 (t70)
REVERT: A  819 LEU cc_start: 0.8550 (mt) cc_final: 0.8195 (mt)
REVERT: A  845 LYS cc_start: 0.8571 (mtmm) cc_final: 0.8232 (mtmm)
REVERT: A  855 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8386 (mm)
REVERT: A  858 VAL cc_start: 0.8088 (t) cc_final: 0.7739 (m)
REVERT: A  874 HIS cc_start: 0.8716 (m-70) cc_final: 0.8252 (m-70)
REVERT: A  964 LEU cc_start: 0.7936 (mt) cc_final: 0.7727 (tp)
REVERT: A  968 GLN cc_start: 0.8858 (mm110) cc_final: 0.8596 (mm110)
REVERT: A  975 LYS cc_start: 0.7944 (tptm) cc_final: 0.7279 (mmmt)
REVERT: A  978 ARG cc_start: 0.8076 (mtp85) cc_final: 0.7747 (mtp85)
REVERT: A  986 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7344 (mm110)
REVERT: A  987 MET cc_start: 0.7823 (tpp) cc_final: 0.7448 (tpp)
REVERT: A 1013 SER cc_start: 0.7630 (t) cc_final: 0.7278 (p)
REVERT: A 1020 GLN cc_start: 0.8480 (pp30) cc_final: 0.8079 (pp30)
REVERT: A 1073 TYR cc_start: 0.8174 (t80) cc_final: 0.7459 (t80)
REVERT: A 1075 GLU cc_start: 0.8012 (tp30) cc_final: 0.7496 (tp30)
REVERT: A 1077 GLN cc_start: 0.8197 (tt0) cc_final: 0.7695 (tt0)
REVERT: A 1079 ARG cc_start: 0.6970 (mtm180) cc_final: 0.5935 (mtm-85)
REVERT: A 1100 ASN cc_start: 0.8052 (m110) cc_final: 0.7764 (m110)
REVERT: A 1106 MET cc_start: 0.7391 (tpt) cc_final: 0.6894 (tpt)
REVERT: A 1115 PHE cc_start: 0.7994 (m-80) cc_final: 0.7539 (m-10)
REVERT: A 1118 ASN cc_start: 0.8030 (m-40) cc_final: 0.7668 (m-40)
REVERT: A 1125 MET cc_start: 0.6993 (ptp) cc_final: 0.6736 (ptp)
REVERT: A 1170 LYS cc_start: 0.8644 (mtpt) cc_final: 0.8046 (ttmm)
REVERT: A 1175 GLN cc_start: 0.7726 (mt0) cc_final: 0.7369 (mt0)
  outliers start: 32
  outliers final: 18
  residues processed: 239
  average time/residue: 0.1115
  time to fit residues: 34.5638
Evaluate side-chains
  238 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 214
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 HIS
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  257 TRP
Chi-restraints excluded: chain A residue  263 TRP
Chi-restraints excluded: chain A residue  265 TYR
Chi-restraints excluded: chain A residue  345 CYS
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  480 GLU
Chi-restraints excluded: chain A residue  510 LYS
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  675 HIS
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  807 TYR
Chi-restraints excluded: chain A residue  855 LEU
Chi-restraints excluded: chain A residue  971 CYS
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1164 ASP
Chi-restraints excluded: chain A residue 1165 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0060
   chunk 46 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 90 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0570
   chunk 20 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   overall best weight:    0.5714

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

Flipped N/Q/H residues before XYZ refinement:
A 225 ASN
A 283 GLN
A 737 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.178591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.144558 restraints weight = 16105.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.149644 restraints weight = 9162.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.153074 restraints weight = 5938.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.155232 restraints weight = 4243.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.156855 restraints weight = 3315.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6752
moved from start:          0.3257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8125  Z= 0.116
  Angle     :  0.631   9.584  11024  Z= 0.309
  Chirality :  0.043   0.164   1280
  Planarity :  0.004   0.049   1398
  Dihedral  :  3.997  15.217   1086
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.17 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 19.59 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.26), residues: 1012
  helix:  1.11 (0.24), residues: 484
  sheet: -0.34 (0.52), residues: 116
  loop :  0.14 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 292 
 TYR   0.017   0.001   TYR A1006 
 PHE   0.019   0.001   PHE A 960 
 TRP   0.012   0.001   TRP A 463 
 HIS   0.011   0.001   HIS A 741 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8125)
  covalent geometry    : angle       0.63090 (11024)
  hydrogen bonds       : bond        0.03958 (  404)
  hydrogen bonds       : angle       4.39008 ( 1170)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 218
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 HIS cc_start: 0.2897 (OUTLIER) cc_final: 0.1268 (p90)
REVERT: A  207 ARG cc_start: 0.8497 (mmm160) cc_final: 0.8122 (mmp80)
REVERT: A  221 LYS cc_start: 0.7155 (ptpp) cc_final: 0.6587 (mtmm)
REVERT: A  253 CYS cc_start: 0.8374 (m) cc_final: 0.8079 (m)
REVERT: A  263 TRP cc_start: 0.5252 (OUTLIER) cc_final: 0.5050 (t60)
REVERT: A  288 MET cc_start: 0.6176 (mmm) cc_final: 0.5429 (mmm)
REVERT: A  294 MET cc_start: 0.7683 (tpp) cc_final: 0.7316 (tpp)
REVERT: A  308 LYS cc_start: 0.7359 (mmpt) cc_final: 0.7151 (mmpt)
REVERT: A  347 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.6821 (t)
REVERT: A  359 GLN cc_start: 0.5336 (mt0) cc_final: 0.5088 (mt0)
REVERT: A  448 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8683 (tp)
REVERT: A  481 CYS cc_start: 0.8188 (m) cc_final: 0.7823 (m)
REVERT: A  483 LEU cc_start: 0.8191 (tp) cc_final: 0.7913 (tp)
REVERT: A  498 SER cc_start: 0.8459 (m) cc_final: 0.8024 (p)
REVERT: A  534 LYS cc_start: 0.8068 (pttp) cc_final: 0.7461 (pttp)
REVERT: A  578 MET cc_start: 0.6183 (ptp) cc_final: 0.5781 (ptp)
REVERT: A  663 MET cc_start: 0.7876 (mtm) cc_final: 0.7300 (mtm)
REVERT: A  730 LYS cc_start: 0.8760 (ttmm) cc_final: 0.8352 (ttmm)
REVERT: A  755 CYS cc_start: 0.8524 (m) cc_final: 0.8115 (m)
REVERT: A  759 GLN cc_start: 0.8400 (pp30) cc_final: 0.8063 (pp30)
REVERT: A  785 ARG cc_start: 0.6942 (mtm-85) cc_final: 0.6665 (mtm-85)
REVERT: A  818 HIS cc_start: 0.7701 (t70) cc_final: 0.7059 (t70)
REVERT: A  819 LEU cc_start: 0.8534 (mt) cc_final: 0.8174 (mt)
REVERT: A  845 LYS cc_start: 0.8570 (mtmm) cc_final: 0.8226 (mtmm)
REVERT: A  855 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8352 (mm)
REVERT: A  874 HIS cc_start: 0.8719 (m-70) cc_final: 0.8250 (m-70)
REVERT: A  963 LYS cc_start: 0.8297 (mttt) cc_final: 0.8082 (mttt)
REVERT: A  978 ARG cc_start: 0.8080 (mtp85) cc_final: 0.7828 (mtp85)
REVERT: A  986 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7170 (mm-40)
REVERT: A  987 MET cc_start: 0.7827 (tpp) cc_final: 0.7482 (tpp)
REVERT: A 1022 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7764 (mm)
REVERT: A 1035 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8566 (mmmm)
REVERT: A 1061 GLN cc_start: 0.7862 (mt0) cc_final: 0.7556 (mt0)
REVERT: A 1065 HIS cc_start: 0.8065 (m170) cc_final: 0.7836 (m170)
REVERT: A 1073 TYR cc_start: 0.8154 (t80) cc_final: 0.7813 (t80)
REVERT: A 1075 GLU cc_start: 0.8017 (tp30) cc_final: 0.7411 (tp30)
REVERT: A 1077 GLN cc_start: 0.8196 (tt0) cc_final: 0.7881 (tt0)
REVERT: A 1079 ARG cc_start: 0.6951 (mtm180) cc_final: 0.6004 (mtt180)
REVERT: A 1095 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6765 (mt-10)
REVERT: A 1100 ASN cc_start: 0.8058 (m110) cc_final: 0.7781 (m110)
REVERT: A 1106 MET cc_start: 0.7416 (tpt) cc_final: 0.6892 (tpt)
REVERT: A 1115 PHE cc_start: 0.7987 (m-80) cc_final: 0.7576 (m-10)
REVERT: A 1118 ASN cc_start: 0.7980 (m-40) cc_final: 0.7608 (m-40)
REVERT: A 1125 MET cc_start: 0.7018 (ptp) cc_final: 0.6761 (ptp)
REVERT: A 1170 LYS cc_start: 0.8632 (mtpt) cc_final: 0.8078 (ttmm)
REVERT: A 1175 GLN cc_start: 0.7732 (mt0) cc_final: 0.7342 (mt0)
  outliers start: 29
  outliers final: 18
  residues processed: 231
  average time/residue: 0.1113
  time to fit residues: 33.5028
Evaluate side-chains
  237 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 213
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 HIS
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  257 TRP
Chi-restraints excluded: chain A residue  263 TRP
Chi-restraints excluded: chain A residue  265 TYR
Chi-restraints excluded: chain A residue  345 CYS
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  480 GLU
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  675 HIS
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  807 TYR
Chi-restraints excluded: chain A residue  855 LEU
Chi-restraints excluded: chain A residue  971 CYS
Chi-restraints excluded: chain A residue 1013 SER
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1059 MET
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1165 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 58 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 2 optimal weight:    0.4980
   chunk 60 optimal weight:    9.9990
   chunk 48 optimal weight:    8.9990
   chunk 76 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 225 ASN
** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.175826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.141108 restraints weight = 16081.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.146166 restraints weight = 9083.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.149618 restraints weight = 5881.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.151854 restraints weight = 4197.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.153513 restraints weight = 3286.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.4079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6822
moved from start:          0.3395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8125  Z= 0.165
  Angle     :  0.678   9.855  11024  Z= 0.337
  Chirality :  0.045   0.219   1280
  Planarity :  0.004   0.048   1398
  Dihedral  :  4.140  15.787   1086
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.77 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 20.27 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.27), residues: 1012
  helix:  0.93 (0.24), residues: 485
  sheet: -0.15 (0.48), residues: 132
  loop :  0.17 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 680 
 TYR   0.024   0.001   TYR A1006 
 PHE   0.023   0.002   PHE A 450 
 TRP   0.015   0.002   TRP A 463 
 HIS   0.011   0.001   HIS A 741 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 8125)
  covalent geometry    : angle       0.67781 (11024)
  hydrogen bonds       : bond        0.04373 (  404)
  hydrogen bonds       : angle       4.50071 ( 1170)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 224
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 HIS cc_start: 0.2822 (OUTLIER) cc_final: 0.1252 (p-80)
REVERT: A  207 ARG cc_start: 0.8481 (mmm160) cc_final: 0.8136 (mmp80)
REVERT: A  253 CYS cc_start: 0.8448 (m) cc_final: 0.8129 (m)
REVERT: A  263 TRP cc_start: 0.5439 (OUTLIER) cc_final: 0.5174 (t60)
REVERT: A  288 MET cc_start: 0.6235 (mmm) cc_final: 0.5504 (mmm)
REVERT: A  294 MET cc_start: 0.7767 (tpp) cc_final: 0.7393 (tpp)
REVERT: A  347 VAL cc_start: 0.7791 (OUTLIER) cc_final: 0.7161 (t)
REVERT: A  359 GLN cc_start: 0.5492 (mt0) cc_final: 0.5274 (mt0)
REVERT: A  427 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7538 (tt)
REVERT: A  448 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8792 (tp)
REVERT: A  450 PHE cc_start: 0.8142 (t80) cc_final: 0.7905 (t80)
REVERT: A  481 CYS cc_start: 0.8274 (m) cc_final: 0.7926 (m)
REVERT: A  483 LEU cc_start: 0.8368 (tp) cc_final: 0.8088 (tp)
REVERT: A  498 SER cc_start: 0.8525 (m) cc_final: 0.8095 (p)
REVERT: A  510 LYS cc_start: 0.8795 (tppt) cc_final: 0.8471 (ttpt)
REVERT: A  534 LYS cc_start: 0.8146 (pttp) cc_final: 0.7562 (pttp)
REVERT: A  578 MET cc_start: 0.6261 (ptp) cc_final: 0.5854 (ptp)
REVERT: A  622 GLN cc_start: 0.8652 (tp-100) cc_final: 0.8343 (tp-100)
REVERT: A  663 MET cc_start: 0.7916 (mtm) cc_final: 0.7357 (mtm)
REVERT: A  730 LYS cc_start: 0.8814 (ttmm) cc_final: 0.8424 (ttmm)
REVERT: A  755 CYS cc_start: 0.8533 (m) cc_final: 0.8154 (m)
REVERT: A  759 GLN cc_start: 0.8494 (pp30) cc_final: 0.8222 (pp30)
REVERT: A  785 ARG cc_start: 0.6997 (mtm-85) cc_final: 0.6670 (mtm-85)
REVERT: A  818 HIS cc_start: 0.7756 (t70) cc_final: 0.7157 (t70)
REVERT: A  819 LEU cc_start: 0.8494 (mt) cc_final: 0.8136 (mt)
REVERT: A  845 LYS cc_start: 0.8612 (mtmm) cc_final: 0.8262 (mtmm)
REVERT: A  855 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8341 (mm)
REVERT: A  858 VAL cc_start: 0.8047 (t) cc_final: 0.7683 (p)
REVERT: A  874 HIS cc_start: 0.8754 (m-70) cc_final: 0.8283 (m-70)
REVERT: A  968 GLN cc_start: 0.8899 (mm110) cc_final: 0.8606 (mm110)
REVERT: A  986 GLN cc_start: 0.7555 (mm-40) cc_final: 0.7051 (mm-40)
REVERT: A  987 MET cc_start: 0.7841 (tpp) cc_final: 0.7540 (tpp)
REVERT: A 1013 SER cc_start: 0.7902 (OUTLIER) cc_final: 0.7518 (p)
REVERT: A 1035 LYS cc_start: 0.8930 (mmmm) cc_final: 0.8624 (mmmm)
REVERT: A 1056 LEU cc_start: 0.8355 (tp) cc_final: 0.8046 (tp)
REVERT: A 1073 TYR cc_start: 0.8190 (t80) cc_final: 0.7556 (t80)
REVERT: A 1075 GLU cc_start: 0.8061 (tp30) cc_final: 0.7175 (tp30)
REVERT: A 1077 GLN cc_start: 0.8233 (tt0) cc_final: 0.7668 (tt0)
REVERT: A 1079 ARG cc_start: 0.7074 (mtm180) cc_final: 0.5896 (mtt90)
REVERT: A 1095 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6838 (mt-10)
REVERT: A 1100 ASN cc_start: 0.8140 (m110) cc_final: 0.7827 (m110)
REVERT: A 1106 MET cc_start: 0.7481 (tpt) cc_final: 0.6974 (tpt)
REVERT: A 1108 MET cc_start: 0.7751 (mmm) cc_final: 0.7509 (tpp)
REVERT: A 1115 PHE cc_start: 0.8044 (m-80) cc_final: 0.7604 (m-80)
REVERT: A 1118 ASN cc_start: 0.7989 (m-40) cc_final: 0.7503 (m-40)
REVERT: A 1175 GLN cc_start: 0.7767 (mt0) cc_final: 0.7393 (mt0)
  outliers start: 26
  outliers final: 17
  residues processed: 236
  average time/residue: 0.1075
  time to fit residues: 33.2769
Evaluate side-chains
  248 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 224
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 HIS
Chi-restraints excluded: chain A residue  123 HIS
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  257 TRP
Chi-restraints excluded: chain A residue  263 TRP
Chi-restraints excluded: chain A residue  265 TYR
Chi-restraints excluded: chain A residue  345 CYS
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  480 GLU
Chi-restraints excluded: chain A residue  517 GLU
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  675 HIS
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  807 TYR
Chi-restraints excluded: chain A residue  855 LEU
Chi-restraints excluded: chain A residue  971 CYS
Chi-restraints excluded: chain A residue 1013 SER
Chi-restraints excluded: chain A residue 1022 LEU
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1070 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 74 optimal weight:   10.0000
   chunk 11 optimal weight:    0.0000
   chunk 2 optimal weight:    4.9990
   chunk 3 optimal weight:    6.9990
   chunk 48 optimal weight:    9.9990
   chunk 28 optimal weight:   20.0000
   chunk 86 optimal weight:    0.1980
   chunk 56 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.8390

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

Flipped N/Q/H residues before XYZ refinement:
A 225 ASN
** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 741 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.175234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.140187 restraints weight = 15973.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.145247 restraints weight = 9003.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.148577 restraints weight = 5826.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.150906 restraints weight = 4197.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.152413 restraints weight = 3282.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.4061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6872
moved from start:          0.3594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8125  Z= 0.195
  Angle     :  0.727  14.839  11024  Z= 0.365
  Chirality :  0.046   0.264   1280
  Planarity :  0.005   0.048   1398
  Dihedral  :  4.333  17.073   1086
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.36 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 20.27 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.26), residues: 1012
  helix:  0.78 (0.24), residues: 478
  sheet:  0.19 (0.50), residues: 122
  loop : -0.02 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 292 
 TYR   0.029   0.002   TYR A1006 
 PHE   0.024   0.002   PHE A 450 
 TRP   0.018   0.002   TRP A 463 
 HIS   0.011   0.001   HIS A 741 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 8125)
  covalent geometry    : angle       0.72676 (11024)
  hydrogen bonds       : bond        0.04836 (  404)
  hydrogen bonds       : angle       4.68541 ( 1170)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1748.86 seconds
wall clock time: 30 minutes 56.56 seconds (1856.56 seconds total)