Starting phenix.real_space_refine
on Wed Sep 17 15:38:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vxa_43615/09_2025/8vxa_43615.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vxa_43615/09_2025/8vxa_43615.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vxa_43615/09_2025/8vxa_43615.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vxa_43615/09_2025/8vxa_43615.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vxa_43615/09_2025/8vxa_43615.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vxa_43615/09_2025/8vxa_43615.map"
  }
  resolution = 2.79
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      24      5.49       5
     S      27      5.16       5
     C    5877      2.51       5
     N    1685      2.21       5
     O    1818      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 9431
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 284
          Classifications: {'DNA': 14}
          Link IDs: {'rna3p': 13}
    Chain: "C"
      Number of atoms: 201
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 201
          Classifications: {'DNA': 10}
          Link IDs: {'rna3p': 9}
    Chain: "A"
      Number of atoms: 8946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1139, 8946
          Classifications: {'peptide': 1139}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 4, 'PTRANS': 45, 'TRANS': 1089}
          Chain breaks: 1
  Time building chain proxies: 2.29, per 1000 atoms: 0.24
  Number of scatterers: 9431
  At special positions: 0
  Unit cell: (89.2, 92.545, 112.615, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     P      24     15.00
     O    1818      8.00
     N    1685      7.00
     C    5877      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: 0.99
  Conformation dependent library (CDL) restraints added in 348.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2120

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 3 sheets defined
      60.2% alpha, 7.5% beta
      6 base pairs and 18 stacking pairs defined.
    Time for finding SS restraints: 1.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 16
    Processing helix  chain 'A' and resid 23 through 33
    Processing helix  chain 'A' and resid 50 through 72
    Processing helix  chain 'A' and resid 75 through 95
      removed outlier: 3.735A  pdb=" N   ALA A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ILE A  81 " --> pdb=" O   ALA A  77 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA A  93 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 118
    Processing helix  chain 'A' and resid 120 through 129
    Processing helix  chain 'A' and resid 138 through 150
    Processing helix  chain 'A' and resid 151 through 166
      removed outlier: 3.842A  pdb=" N   ASP A 157 " --> pdb=" O   ARG A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 224
    Processing helix  chain 'A' and resid 225 through 247
      removed outlier: 3.883A  pdb=" N   LEU A 229 " --> pdb=" O   GLU A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 267
      removed outlier: 3.859A  pdb=" N   HIS A 260 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 274
    Processing helix  chain 'A' and resid 285 through 299
    Processing helix  chain 'A' and resid 311 through 319
      removed outlier: 4.220A  pdb=" N   VAL A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 348
      removed outlier: 3.960A  pdb=" N   ILE A 338 " --> pdb=" O   GLY A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 375
      removed outlier: 3.504A  pdb=" N   ALA A 368 " --> pdb=" O   ALA A 364 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   THR A 369 " --> pdb=" O   GLN A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 401
      removed outlier: 4.537A  pdb=" N   ASP A 396 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 418
      removed outlier: 3.636A  pdb=" N   ALA A 414 " --> pdb=" O   LYS A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 423
    Processing helix  chain 'A' and resid 439 through 454
    Processing helix  chain 'A' and resid 457 through 461
    Processing helix  chain 'A' and resid 475 through 483
    Processing helix  chain 'A' and resid 553 through 567
    Processing helix  chain 'A' and resid 578 through 580
      No H-bonds generated for 'chain 'A' and resid 578 through 580'
    Processing helix  chain 'A' and resid 581 through 595
      removed outlier: 3.811A  pdb=" N   PHE A 585 " --> pdb=" O   SER A 581 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ALA A 586 " --> pdb=" O   VAL A 582 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLU A 587 " --> pdb=" O   GLU A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 608
    Processing helix  chain 'A' and resid 609 through 618
      removed outlier: 3.686A  pdb=" N   GLU A 618 " --> pdb=" O   SER A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 632
      removed outlier: 3.517A  pdb=" N   LEU A 632 " --> pdb=" O   ALA A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 655
    Processing helix  chain 'A' and resid 665 through 668
    Processing helix  chain 'A' and resid 691 through 700
    Processing helix  chain 'A' and resid 720 through 733
    Processing helix  chain 'A' and resid 742 through 760
      removed outlier: 4.069A  pdb=" N   ARG A 754 " --> pdb=" O   VAL A 750 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   MET A 755 " --> pdb=" O   LEU A 751 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 762 through 773
    Processing helix  chain 'A' and resid 786 through 813
    Processing helix  chain 'A' and resid 818 through 820
      No H-bonds generated for 'chain 'A' and resid 818 through 820'
    Processing helix  chain 'A' and resid 821 through 830
    Processing helix  chain 'A' and resid 833 through 840
    Processing helix  chain 'A' and resid 844 through 865
      removed outlier: 3.821A  pdb=" N   LYS A 852 " --> pdb=" O   ARG A 848 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ARG A 865 " --> pdb=" O   TYR A 861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 867 through 878
    Processing helix  chain 'A' and resid 880 through 890
    Processing helix  chain 'A' and resid 890 through 907
      removed outlier: 4.403A  pdb=" N   GLN A 896 " --> pdb=" O   ALA A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 911 through 925
      removed outlier: 4.064A  pdb=" N   ILE A 917 " --> pdb=" O   ALA A 913 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 938 through 949
    Processing helix  chain 'A' and resid 951 through 955
      removed outlier: 3.601A  pdb=" N   VAL A 955 " --> pdb=" O   MET A 952 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 959 through 971
    Processing helix  chain 'A' and resid 973 through 990
    Processing helix  chain 'A' and resid 993 through 1002
      removed outlier: 3.863A  pdb=" N   THR A 998 " --> pdb=" O   GLY A 994 " (cutoff:3.500A)
      removed outlier: 4.816A  pdb=" N   THR A 999 " --> pdb=" O   ASP A 995 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU A1000 " --> pdb=" O   THR A 996 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1007 through 1015
      removed outlier: 3.762A  pdb=" N   ALA A1011 " --> pdb=" O   PHE A1007 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL A1012 " --> pdb=" O   ALA A1008 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1018 through 1028
      removed outlier: 3.727A  pdb=" N   GLY A1028 " --> pdb=" O   LEU A1024 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1031 through 1043
    Processing helix  chain 'A' and resid 1048 through 1058
    Processing helix  chain 'A' and resid 1058 through 1067
      removed outlier: 3.767A  pdb=" N   ILE A1062 " --> pdb=" O   SER A1058 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1075 through 1086
      removed outlier: 3.740A  pdb=" N   LEU A1080 " --> pdb=" O   ARG A1076 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   GLU A1081 " --> pdb=" O   VAL A1077 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   PHE A1082 " --> pdb=" O   MET A1078 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 381 through 383
      removed outlier: 3.657A  pdb=" N   VAL A 405 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   PHE A 428 " --> pdb=" O   VAL A 464 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   LEU A 466 " --> pdb=" O   PHE A 428 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   PHE A 430 " --> pdb=" O   LEU A 466 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   LEU A 325 " --> pdb=" O   CYS A 465 " (cutoff:3.500A)
      removed outlier: 7.885A  pdb=" N   SER A 467 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   VAL A 327 " --> pdb=" O   SER A 467 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 525 through 531
      removed outlier: 4.845A  pdb=" N   TRP A 525 " --> pdb=" O   LEU A 517 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   LEU A 517 " --> pdb=" O   TRP A 525 " (cutoff:3.500A)
      removed outlier: 5.557A  pdb=" N   SER A 527 " --> pdb=" O   LEU A 515 " (cutoff:3.500A)
      removed outlier: 4.886A  pdb=" N   LEU A 515 " --> pdb=" O   SER A 527 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   GLY A 513 " --> pdb=" O   PHE A 529 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ARG A 500 " --> pdb=" O   GLY A 711 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   VAL A 713 " --> pdb=" O   ARG A 500 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   GLN A 502 " --> pdb=" O   VAL A 713 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   TYR A 715 " --> pdb=" O   GLN A 502 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   GLY A 504 " --> pdb=" O   TYR A 715 " (cutoff:3.500A)
      removed outlier: 7.358A  pdb=" N   ILE A 717 " --> pdb=" O   GLY A 504 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   VAL A 506 " --> pdb=" O   ILE A 717 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   VAL A 572 " --> pdb=" O   THR A 661 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   SER A 663 " --> pdb=" O   VAL A 572 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   ILE A 574 " --> pdb=" O   SER A 663 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1097 through 1102
      removed outlier: 3.623A  pdb=" N   TYR A1099 " --> pdb=" O   PHE A1163 " (cutoff:3.500A)
      removed outlier: 8.617A  pdb=" N   LEU A1150 " --> pdb=" O   LEU A1118 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   LEU A1118 " --> pdb=" O   LEU A1150 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   VAL A1152 " --> pdb=" O   LEU A1116 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   HIS A1125 " --> pdb=" O   ILE A1138 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   GLY A1136 " --> pdb=" O   VAL A1127 " (cutoff:3.500A)

    484 hydrogen bonds defined for protein.
    1422 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      15 hydrogen bonds
      30 hydrogen bond angles
      0 basepair planarities
      6 basepair parallelities
      18 stacking parallelities
  Total time for adding SS restraints: 1.99

  Time building geometry restraints manager: 1.24 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2848
        1.33 -     1.45: 1445
        1.45 -     1.57: 5278
        1.57 -     1.69: 46
        1.69 -     1.80: 46
  Bond restraints: 9663
  Sorted by residual:
  bond pdb=" C3'  DC C   6 "
       pdb=" O3'  DC C   6 "
    ideal  model  delta    sigma   weight residual
    1.422  1.458 -0.036 3.00e-02 1.11e+03 1.48e+00
  bond pdb=" C3'  DT C   5 "
       pdb=" O3'  DT C   5 "
    ideal  model  delta    sigma   weight residual
    1.422  1.456 -0.034 3.00e-02 1.11e+03 1.29e+00
  bond pdb=" CG1 ILE A 566 "
       pdb=" CD1 ILE A 566 "
    ideal  model  delta    sigma   weight residual
    1.513  1.472  0.041 3.90e-02 6.57e+02 1.09e+00
  bond pdb=" CB  GLU A 980 "
       pdb=" CG  GLU A 980 "
    ideal  model  delta    sigma   weight residual
    1.520  1.489  0.031 3.00e-02 1.11e+03 1.06e+00
  bond pdb=" CA  ILE A 388 "
       pdb=" CB  ILE A 388 "
    ideal  model  delta    sigma   weight residual
    1.550  1.540  0.010 1.03e-02 9.43e+03 9.97e-01
  ... (remaining 9658 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 13040
        1.94 -     3.88: 165
        3.88 -     5.82: 13
        5.82 -     7.76: 0
        7.76 -     9.70: 1
  Bond angle restraints: 13219
  Sorted by residual:
  angle pdb=" N   GLY A 760 "
        pdb=" CA  GLY A 760 "
        pdb=" C   GLY A 760 "
      ideal   model   delta    sigma   weight residual
     110.58  114.65   -4.07 1.35e+00 5.49e-01 9.11e+00
  angle pdb=" C   GLU A 768 "
        pdb=" N   TYR A 769 "
        pdb=" CA  TYR A 769 "
      ideal   model   delta    sigma   weight residual
     120.44  124.14   -3.70 1.30e+00 5.92e-01 8.12e+00
  angle pdb=" CA  LEU A1135 "
        pdb=" CB  LEU A1135 "
        pdb=" CG  LEU A1135 "
      ideal   model   delta    sigma   weight residual
     116.30  126.00   -9.70 3.50e+00 8.16e-02 7.69e+00
  angle pdb=" N   LEU A 427 "
        pdb=" CA  LEU A 427 "
        pdb=" C   LEU A 427 "
      ideal   model   delta    sigma   weight residual
     108.32  111.93   -3.61 1.64e+00 3.72e-01 4.84e+00
  angle pdb=" C3'  DT C   5 "
        pdb=" O3'  DT C   5 "
        pdb=" P    DC C   6 "
      ideal   model   delta    sigma   weight residual
     120.20  123.36   -3.16 1.50e+00 4.44e-01 4.45e+00
  ... (remaining 13214 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.73: 5401
       25.73 -    51.47: 305
       51.47 -    77.20: 46
       77.20 -   102.94: 5
      102.94 -   128.67: 1
  Dihedral angle restraints: 5758
    sinusoidal: 2477
      harmonic: 3281
  Sorted by residual:
  dihedral pdb=" C4'  DC C   6 "
           pdb=" C3'  DC C   6 "
           pdb=" O3'  DC C   6 "
           pdb=" P    DC C   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   91.33  128.67     1      3.50e+01 8.16e-04 1.27e+01
  dihedral pdb=" CA  ILE A 662 "
           pdb=" C   ILE A 662 "
           pdb=" N   SER A 663 "
           pdb=" CA  SER A 663 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.70  -17.30     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  ASN A 672 "
           pdb=" C   ASN A 672 "
           pdb=" N   LEU A 673 "
           pdb=" CA  LEU A 673 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.14   16.86     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 5755 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 887
       0.027 -    0.054: 395
       0.054 -    0.082: 129
       0.082 -    0.109: 74
       0.109 -    0.136: 16
  Chirality restraints: 1501
  Sorted by residual:
  chirality pdb=" CA  ILE A 817 "
            pdb=" N   ILE A 817 "
            pdb=" C   ILE A 817 "
            pdb=" CB  ILE A 817 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  chirality pdb=" CA  ILE A 381 "
            pdb=" N   ILE A 381 "
            pdb=" C   ILE A 381 "
            pdb=" CB  ILE A 381 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.92e-01
  chirality pdb=" CA  VAL A 526 "
            pdb=" N   VAL A 526 "
            pdb=" C   VAL A 526 "
            pdb=" CB  VAL A 526 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.70e-01
  ... (remaining 1498 not shown)

  Planarity restraints: 1638
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  35 "    0.025 2.00e-02 2.50e+03   2.15e-02 1.15e+01
        pdb=" CG  TRP A  35 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  35 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  35 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  35 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  35 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  35 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  35 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  35 "    0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  35 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 563 "   -0.012 2.00e-02 2.50e+03   1.27e-02 4.06e+00
        pdb=" CG  TRP A 563 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 563 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 563 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 563 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 563 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 563 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 563 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 563 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 563 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 375 "   -0.028 5.00e-02 4.00e+02   4.26e-02 2.91e+00
        pdb=" N   PRO A 376 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 376 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 376 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1635 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 946
        2.74 -     3.28: 9537
        3.28 -     3.82: 16768
        3.82 -     4.36: 19865
        4.36 -     4.90: 32995
  Nonbonded interactions: 80111
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 395 "
            pdb=" OH  TYR A1003 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OG1 THR A 357 "
            pdb=" OG  SER A 363 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OE1 GLU A 304 "
            pdb=" NH2 ARG A 337 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" NH1 ARG A 454 "
            pdb=" O   ASP A 828 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" NH2 ARG A 685 "
            pdb=" OE1 GLU A 694 "
     model   vdw
     2.275 3.120
  ... (remaining 80106 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.790
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:7.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6920
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   0.041   9663  Z= 0.156
  Angle     :  0.532   9.703  13219  Z= 0.294
  Chirality :  0.039   0.136   1501
  Planarity :  0.004   0.043   1638
  Dihedral  : 15.673 128.673   3638
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.60 (0.25), residues: 1135
  helix:  1.12 (0.21), residues: 626
  sheet:  0.12 (0.64), residues: 79
  loop : -0.54 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 165 
 TYR   0.013   0.001   TYR A 445 
 PHE   0.023   0.002   PHE A 413 
 TRP   0.057   0.002   TRP A  35 
 HIS   0.004   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 9663)
  covalent geometry    : angle       0.53181 (13219)
  hydrogen bonds       : bond        0.15970 (  499)
  hydrogen bonds       : angle       5.91833 ( 1452)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 PHE cc_start: 0.8083 (t80) cc_final: 0.7798 (t80)
REVERT: A  153 ARG cc_start: 0.7431 (ttm-80) cc_final: 0.7157 (mtt180)
REVERT: A  264 ASP cc_start: 0.7024 (p0) cc_final: 0.6809 (p0)
REVERT: A  322 ASN cc_start: 0.7133 (t0) cc_final: 0.6886 (t0)
REVERT: A  382 SER cc_start: 0.7641 (m) cc_final: 0.7420 (t)
REVERT: A  383 MET cc_start: 0.7155 (ttt) cc_final: 0.6864 (ttp)
REVERT: A  472 ASP cc_start: 0.6824 (m-30) cc_final: 0.6347 (m-30)
REVERT: A  548 LYS cc_start: 0.7909 (mtmm) cc_final: 0.7468 (mtmm)
REVERT: A  649 ILE cc_start: 0.7968 (tt) cc_final: 0.7610 (pt)
REVERT: A  709 VAL cc_start: 0.8683 (p) cc_final: 0.8418 (t)
REVERT: A  764 LYS cc_start: 0.6737 (tptt) cc_final: 0.6404 (tptt)
REVERT: A  819 ASP cc_start: 0.6905 (t70) cc_final: 0.6683 (t0)
REVERT: A  831 GLN cc_start: 0.7262 (tp-100) cc_final: 0.6985 (mm-40)
REVERT: A 1169 ASP cc_start: 0.7219 (t0) cc_final: 0.6970 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 0.6543
  time to fit residues: 166.3815
Evaluate side-chains
  194 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0010
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
A 495 ASN
A 669 GLN
A 686 ASN
A 772 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.159053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.142258 restraints weight = 12370.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3839 rms_B_bonded: 1.69
r_work: 0.3734 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3590 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9663  Z= 0.174
  Angle     :  0.571  10.060  13219  Z= 0.306
  Chirality :  0.042   0.152   1501
  Planarity :  0.005   0.050   1638
  Dihedral  : 15.076 134.210   1522
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 10.23 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.58 (0.25), residues: 1135
  helix:  1.20 (0.20), residues: 639
  sheet: -0.51 (0.63), residues: 77
  loop : -0.62 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 454 
 TYR   0.014   0.002   TYR A 125 
 PHE   0.023   0.002   PHE A 413 
 TRP   0.031   0.002   TRP A  35 
 HIS   0.005   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 9663)
  covalent geometry    : angle       0.57081 (13219)
  hydrogen bonds       : bond        0.04285 (  499)
  hydrogen bonds       : angle       4.75248 ( 1452)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 209
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A   94 ILE cc_start: 0.7634 (pt) cc_final: 0.7350 (pp)
REVERT: A  235 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6879 (tppt)
REVERT: A  264 ASP cc_start: 0.7438 (p0) cc_final: 0.7170 (p0)
REVERT: A  322 ASN cc_start: 0.7761 (t0) cc_final: 0.7507 (t0)
REVERT: A  328 SER cc_start: 0.8428 (t) cc_final: 0.8187 (p)
REVERT: A  440 GLU cc_start: 0.7472 (pt0) cc_final: 0.7253 (pt0)
REVERT: A  470 LEU cc_start: 0.7972 (mt) cc_final: 0.7717 (mt)
REVERT: A  493 LYS cc_start: 0.8246 (tppp) cc_final: 0.7932 (tttm)
REVERT: A  552 SER cc_start: 0.8514 (t) cc_final: 0.8278 (p)
REVERT: A  649 ILE cc_start: 0.8201 (tt) cc_final: 0.7691 (pt)
REVERT: A  672 ASN cc_start: 0.8028 (t0) cc_final: 0.7757 (t0)
REVERT: A  701 ARG cc_start: 0.8220 (mmt180) cc_final: 0.7970 (mmt180)
REVERT: A  709 VAL cc_start: 0.8929 (p) cc_final: 0.8655 (t)
REVERT: A  715 TYR cc_start: 0.8381 (t80) cc_final: 0.8136 (t80)
REVERT: A  740 MET cc_start: 0.8374 (mmm) cc_final: 0.7786 (mmm)
REVERT: A  814 GLU cc_start: 0.6955 (tp30) cc_final: 0.6538 (tp30)
REVERT: A  819 ASP cc_start: 0.7568 (t70) cc_final: 0.7309 (t0)
REVERT: A  831 GLN cc_start: 0.7778 (tp-100) cc_final: 0.7524 (mm-40)
REVERT: A  836 GLN cc_start: 0.8082 (tt0) cc_final: 0.7846 (tt0)
REVERT: A  864 GLN cc_start: 0.7924 (tt0) cc_final: 0.7717 (tt0)
REVERT: A 1018 SER cc_start: 0.7958 (m) cc_final: 0.7665 (t)
REVERT: A 1029 PHE cc_start: 0.6653 (OUTLIER) cc_final: 0.5662 (m-80)
REVERT: A 1160 ARG cc_start: 0.7112 (mtm-85) cc_final: 0.6814 (mtm180)
REVERT: A 1169 ASP cc_start: 0.7341 (t0) cc_final: 0.7016 (t70)
  outliers start: 23
  outliers final: 11
  residues processed: 219
  average time/residue: 0.6730
  time to fit residues: 156.3288
Evaluate side-chains
  207 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 194
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue  235 LYS
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  399 ARG
Chi-restraints excluded: chain A residue  442 GLU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  669 GLN
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  735 THR
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue 1029 PHE
Chi-restraints excluded: chain A residue 1121 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 75 optimal weight:    0.6980
   chunk 85 optimal weight:    0.5980
   chunk 94 optimal weight:    0.7980
   chunk 93 optimal weight:    0.2980
   chunk 114 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 136 ASN
A 260 HIS
A 495 ASN
A 772 ASN
A 815 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.158684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.141662 restraints weight = 12355.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3828 rms_B_bonded: 1.68
r_work: 0.3722 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3582 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9663  Z= 0.170
  Angle     :  0.548   9.948  13219  Z= 0.294
  Chirality :  0.041   0.158   1501
  Planarity :  0.005   0.049   1638
  Dihedral  : 15.082 134.819   1522
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 14.56 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.62 (0.25), residues: 1135
  helix:  1.21 (0.20), residues: 639
  sheet: -0.51 (0.62), residues: 76
  loop : -0.57 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 758 
 TYR   0.013   0.002   TYR A 125 
 PHE   0.020   0.002   PHE A 413 
 TRP   0.024   0.002   TRP A  35 
 HIS   0.005   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 9663)
  covalent geometry    : angle       0.54783 (13219)
  hydrogen bonds       : bond        0.03973 (  499)
  hydrogen bonds       : angle       4.60368 ( 1452)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 202
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A   94 ILE cc_start: 0.7695 (pt) cc_final: 0.7414 (pp)
REVERT: A  210 TYR cc_start: 0.8051 (t80) cc_final: 0.7609 (t80)
REVERT: A  211 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.5382 (mmm)
REVERT: A  235 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6921 (tppt)
REVERT: A  264 ASP cc_start: 0.7501 (p0) cc_final: 0.7154 (p0)
REVERT: A  322 ASN cc_start: 0.7799 (t0) cc_final: 0.7545 (t0)
REVERT: A  328 SER cc_start: 0.8434 (t) cc_final: 0.8199 (p)
REVERT: A  400 GLN cc_start: 0.7674 (mp10) cc_final: 0.7347 (mp10)
REVERT: A  432 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7130 (mm-30)
REVERT: A  445 TYR cc_start: 0.8425 (t80) cc_final: 0.8069 (t80)
REVERT: A  470 LEU cc_start: 0.7917 (mt) cc_final: 0.7656 (mt)
REVERT: A  493 LYS cc_start: 0.8242 (tppp) cc_final: 0.7967 (tttm)
REVERT: A  649 ILE cc_start: 0.8201 (tt) cc_final: 0.7706 (pt)
REVERT: A  672 ASN cc_start: 0.7978 (t0) cc_final: 0.7716 (t0)
REVERT: A  709 VAL cc_start: 0.8967 (p) cc_final: 0.8678 (t)
REVERT: A  740 MET cc_start: 0.8383 (mmm) cc_final: 0.7851 (mmm)
REVERT: A  779 PHE cc_start: 0.8343 (t80) cc_final: 0.8001 (t80)
REVERT: A  814 GLU cc_start: 0.6851 (tp30) cc_final: 0.6544 (tp30)
REVERT: A  819 ASP cc_start: 0.7558 (t70) cc_final: 0.7292 (t0)
REVERT: A  831 GLN cc_start: 0.7777 (tp-100) cc_final: 0.7527 (mm-40)
REVERT: A  836 GLN cc_start: 0.8055 (tt0) cc_final: 0.7799 (tt0)
REVERT: A  864 GLN cc_start: 0.7897 (tt0) cc_final: 0.7691 (tt0)
REVERT: A 1018 SER cc_start: 0.8028 (m) cc_final: 0.7742 (t)
REVERT: A 1029 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.5682 (m-80)
REVERT: A 1169 ASP cc_start: 0.7377 (t0) cc_final: 0.7051 (t70)
  outliers start: 25
  outliers final: 14
  residues processed: 214
  average time/residue: 0.6523
  time to fit residues: 148.3789
Evaluate side-chains
  207 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 190
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  235 LYS
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  442 GLU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  735 THR
Chi-restraints excluded: chain A residue  759 LEU
Chi-restraints excluded: chain A residue  781 GLU
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1029 PHE
Chi-restraints excluded: chain A residue 1121 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 33 optimal weight:    0.0980
   chunk 106 optimal weight:    0.0570
   chunk 93 optimal weight:    0.4980
   chunk 4 optimal weight:    0.4980
   chunk 42 optimal weight:    0.5980
   chunk 28 optimal weight:    0.4980
   chunk 58 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 80 optimal weight:    0.5980
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.3298

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

Flipped N/Q/H residues before XYZ refinement:
A 136 ASN
A1125 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.160215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.143494 restraints weight = 12543.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 1.67
r_work: 0.3751 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3613 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9663  Z= 0.129
  Angle     :  0.509   9.136  13219  Z= 0.274
  Chirality :  0.039   0.151   1501
  Planarity :  0.004   0.044   1638
  Dihedral  : 15.022 134.730   1522
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 16.24 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.85 (0.25), residues: 1135
  helix:  1.45 (0.20), residues: 640
  sheet: -0.76 (0.60), residues: 86
  loop : -0.48 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 758 
 TYR   0.013   0.001   TYR A 445 
 PHE   0.009   0.001   PHE A 293 
 TRP   0.018   0.002   TRP A  35 
 HIS   0.006   0.001   HIS A1125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9663)
  covalent geometry    : angle       0.50854 (13219)
  hydrogen bonds       : bond        0.03477 (  499)
  hydrogen bonds       : angle       4.40597 ( 1452)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 208
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 ILE cc_start: 0.7663 (pt) cc_final: 0.7389 (pp)
REVERT: A  210 TYR cc_start: 0.8052 (t80) cc_final: 0.7587 (t80)
REVERT: A  211 MET cc_start: 0.6115 (OUTLIER) cc_final: 0.5316 (mmm)
REVERT: A  264 ASP cc_start: 0.7491 (p0) cc_final: 0.7180 (p0)
REVERT: A  312 ARG cc_start: 0.7910 (mpp80) cc_final: 0.7647 (mtm-85)
REVERT: A  322 ASN cc_start: 0.7592 (t0) cc_final: 0.7344 (t0)
REVERT: A  328 SER cc_start: 0.8373 (t) cc_final: 0.8145 (p)
REVERT: A  400 GLN cc_start: 0.7689 (mp10) cc_final: 0.7387 (mp10)
REVERT: A  432 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7097 (mm-30)
REVERT: A  445 TYR cc_start: 0.8403 (t80) cc_final: 0.8079 (t80)
REVERT: A  649 ILE cc_start: 0.8271 (tt) cc_final: 0.8052 (mp)
REVERT: A  709 VAL cc_start: 0.8967 (p) cc_final: 0.8670 (t)
REVERT: A  740 MET cc_start: 0.8382 (mmm) cc_final: 0.7839 (mmm)
REVERT: A  779 PHE cc_start: 0.8294 (t80) cc_final: 0.7879 (t80)
REVERT: A  814 GLU cc_start: 0.6659 (tp30) cc_final: 0.6420 (tp30)
REVERT: A  819 ASP cc_start: 0.7428 (t70) cc_final: 0.7170 (t0)
REVERT: A  831 GLN cc_start: 0.7828 (tp-100) cc_final: 0.7588 (mm-40)
REVERT: A  836 GLN cc_start: 0.8075 (tt0) cc_final: 0.7815 (tt0)
REVERT: A  897 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7418 (mm)
REVERT: A 1018 SER cc_start: 0.7924 (m) cc_final: 0.7722 (t)
REVERT: A 1029 PHE cc_start: 0.6729 (OUTLIER) cc_final: 0.5710 (m-80)
REVERT: A 1102 MET cc_start: 0.6256 (tpp) cc_final: 0.6031 (tpp)
REVERT: A 1162 MET cc_start: 0.7228 (tmm) cc_final: 0.6966 (tpt)
REVERT: A 1169 ASP cc_start: 0.7288 (t0) cc_final: 0.7080 (t70)
  outliers start: 27
  outliers final: 13
  residues processed: 221
  average time/residue: 0.6281
  time to fit residues: 147.6684
Evaluate side-chains
  216 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 200
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  395 GLU
Chi-restraints excluded: chain A residue  399 ARG
Chi-restraints excluded: chain A residue  442 GLU
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  735 THR
Chi-restraints excluded: chain A residue  759 LEU
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1029 PHE
Chi-restraints excluded: chain A residue 1121 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 52 optimal weight:    0.4980
   chunk 75 optimal weight:    0.6980
   chunk 41 optimal weight:    0.2980
   chunk 22 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 112 optimal weight:    3.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 136 ASN
A 772 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.158221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.141556 restraints weight = 12444.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3814 rms_B_bonded: 1.65
r_work: 0.3709 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3568 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9663  Z= 0.184
  Angle     :  0.554   9.689  13219  Z= 0.297
  Chirality :  0.041   0.164   1501
  Planarity :  0.005   0.045   1638
  Dihedral  : 15.060 135.019   1522
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 17.30 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.84 (0.25), residues: 1135
  helix:  1.40 (0.20), residues: 638
  sheet: -0.56 (0.55), residues: 97
  loop : -0.44 (0.32), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 758 
 TYR   0.011   0.002   TYR A 217 
 PHE   0.021   0.002   PHE A 966 
 TRP   0.019   0.002   TRP A  35 
 HIS   0.004   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 9663)
  covalent geometry    : angle       0.55360 (13219)
  hydrogen bonds       : bond        0.03798 (  499)
  hydrogen bonds       : angle       4.46673 ( 1452)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 208
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 ILE cc_start: 0.7734 (pt) cc_final: 0.7446 (pp)
REVERT: A  210 TYR cc_start: 0.8048 (t80) cc_final: 0.7644 (t80)
REVERT: A  211 MET cc_start: 0.6044 (OUTLIER) cc_final: 0.5324 (mmm)
REVERT: A  264 ASP cc_start: 0.7468 (p0) cc_final: 0.7146 (p0)
REVERT: A  312 ARG cc_start: 0.7920 (mpp80) cc_final: 0.7669 (mtm-85)
REVERT: A  322 ASN cc_start: 0.7600 (t0) cc_final: 0.7368 (t0)
REVERT: A  328 SER cc_start: 0.8374 (t) cc_final: 0.8047 (p)
REVERT: A  432 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7103 (mm-30)
REVERT: A  649 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8020 (mp)
REVERT: A  709 VAL cc_start: 0.8975 (p) cc_final: 0.8685 (t)
REVERT: A  740 MET cc_start: 0.8419 (mmm) cc_final: 0.7918 (mmm)
REVERT: A  802 SER cc_start: 0.8226 (t) cc_final: 0.7843 (p)
REVERT: A  814 GLU cc_start: 0.6719 (tp30) cc_final: 0.6512 (tp30)
REVERT: A  819 ASP cc_start: 0.7526 (t70) cc_final: 0.7265 (t0)
REVERT: A  831 GLN cc_start: 0.7826 (tp-100) cc_final: 0.7621 (mm-40)
REVERT: A  979 MET cc_start: 0.8258 (mtm) cc_final: 0.7998 (mtm)
REVERT: A  989 ASN cc_start: 0.7992 (OUTLIER) cc_final: 0.7770 (t0)
REVERT: A 1018 SER cc_start: 0.7957 (m) cc_final: 0.7730 (t)
REVERT: A 1029 PHE cc_start: 0.6708 (OUTLIER) cc_final: 0.5552 (m-80)
REVERT: A 1169 ASP cc_start: 0.7326 (t0) cc_final: 0.7101 (t0)
  outliers start: 32
  outliers final: 20
  residues processed: 220
  average time/residue: 0.6640
  time to fit residues: 155.2219
Evaluate side-chains
  224 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 200
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  395 GLU
Chi-restraints excluded: chain A residue  399 ARG
Chi-restraints excluded: chain A residue  442 GLU
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  649 ILE
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  735 THR
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  759 LEU
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  989 ASN
Chi-restraints excluded: chain A residue 1029 PHE
Chi-restraints excluded: chain A residue 1038 VAL
Chi-restraints excluded: chain A residue 1121 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 94 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9990
   chunk 64 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 108 optimal weight:    4.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 136 ASN
A 400 GLN
A 772 ASN
A1125 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.157143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.140713 restraints weight = 12429.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3810 rms_B_bonded: 1.63
r_work: 0.3706 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3565 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9663  Z= 0.204
  Angle     :  0.574   9.768  13219  Z= 0.307
  Chirality :  0.042   0.178   1501
  Planarity :  0.005   0.049   1638
  Dihedral  : 15.069 134.986   1522
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 18.67 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.67 (0.25), residues: 1135
  helix:  1.24 (0.20), residues: 646
  sheet: -0.30 (0.57), residues: 87
  loop : -0.58 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 758 
 TYR   0.013   0.002   TYR A 842 
 PHE   0.015   0.002   PHE A 966 
 TRP   0.022   0.002   TRP A 266 
 HIS   0.007   0.001   HIS A1125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 ( 9663)
  covalent geometry    : angle       0.57372 (13219)
  hydrogen bonds       : bond        0.03935 (  499)
  hydrogen bonds       : angle       4.52022 ( 1452)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 209
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 ILE cc_start: 0.7796 (pt) cc_final: 0.7506 (pp)
REVERT: A  210 TYR cc_start: 0.8043 (t80) cc_final: 0.7631 (t80)
REVERT: A  211 MET cc_start: 0.6063 (OUTLIER) cc_final: 0.5351 (mmm)
REVERT: A  264 ASP cc_start: 0.7378 (p0) cc_final: 0.7086 (p0)
REVERT: A  266 TRP cc_start: 0.7154 (t-100) cc_final: 0.6745 (t-100)
REVERT: A  312 ARG cc_start: 0.7941 (mpp80) cc_final: 0.7717 (mtm-85)
REVERT: A  322 ASN cc_start: 0.7643 (t0) cc_final: 0.7399 (t0)
REVERT: A  328 SER cc_start: 0.8382 (t) cc_final: 0.8024 (p)
REVERT: A  432 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7117 (mm-30)
REVERT: A  649 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7716 (pt)
REVERT: A  671 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8347 (tt)
REVERT: A  740 MET cc_start: 0.8443 (mmm) cc_final: 0.7930 (mmm)
REVERT: A  758 ARG cc_start: 0.6917 (mtp-110) cc_final: 0.6616 (mtm110)
REVERT: A  779 PHE cc_start: 0.8303 (t80) cc_final: 0.7941 (t80)
REVERT: A  802 SER cc_start: 0.8245 (t) cc_final: 0.7860 (p)
REVERT: A  814 GLU cc_start: 0.6785 (tp30) cc_final: 0.6581 (tp30)
REVERT: A  831 GLN cc_start: 0.7834 (tp-100) cc_final: 0.7620 (mm-40)
REVERT: A  989 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7753 (t0)
REVERT: A 1018 SER cc_start: 0.8008 (m) cc_final: 0.7733 (t)
REVERT: A 1029 PHE cc_start: 0.6748 (OUTLIER) cc_final: 0.5547 (m-80)
REVERT: A 1099 TYR cc_start: 0.8001 (m-10) cc_final: 0.7661 (m-80)
REVERT: A 1162 MET cc_start: 0.7263 (tmm) cc_final: 0.6902 (tpt)
REVERT: A 1169 ASP cc_start: 0.7386 (t0) cc_final: 0.7097 (t0)
  outliers start: 32
  outliers final: 18
  residues processed: 224
  average time/residue: 0.6364
  time to fit residues: 151.3417
Evaluate side-chains
  230 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 207
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  395 GLU
Chi-restraints excluded: chain A residue  399 ARG
Chi-restraints excluded: chain A residue  442 GLU
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  649 ILE
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  731 LEU
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  926 THR
Chi-restraints excluded: chain A residue  950 GLU
Chi-restraints excluded: chain A residue  989 ASN
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1029 PHE
Chi-restraints excluded: chain A residue 1121 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9980
   chunk 99 optimal weight:    0.7980
   chunk 4 optimal weight:    0.3980
   chunk 20 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0470
   chunk 75 optimal weight:    0.5980
   chunk 29 optimal weight:    0.5980
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN
A 815 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.157480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.140658 restraints weight = 12494.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3813 rms_B_bonded: 1.71
r_work: 0.3706 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3564 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9663  Z= 0.154
  Angle     :  0.557   9.302  13219  Z= 0.299
  Chirality :  0.041   0.188   1501
  Planarity :  0.005   0.057   1638
  Dihedral  : 15.017 135.019   1522
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 18.78 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.80 (0.25), residues: 1135
  helix:  1.36 (0.20), residues: 645
  sheet: -0.61 (0.55), residues: 97
  loop : -0.45 (0.32), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 758 
 TYR   0.012   0.002   TYR A 445 
 PHE   0.016   0.001   PHE A 966 
 TRP   0.016   0.002   TRP A  35 
 HIS   0.003   0.001   HIS A 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 9663)
  covalent geometry    : angle       0.55696 (13219)
  hydrogen bonds       : bond        0.03604 (  499)
  hydrogen bonds       : angle       4.43174 ( 1452)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 202
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 ILE cc_start: 0.7729 (pt) cc_final: 0.7443 (pp)
REVERT: A  210 TYR cc_start: 0.8015 (t80) cc_final: 0.7601 (t80)
REVERT: A  211 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.5318 (mmm)
REVERT: A  264 ASP cc_start: 0.7325 (p0) cc_final: 0.7047 (p0)
REVERT: A  322 ASN cc_start: 0.7646 (t0) cc_final: 0.7345 (t0)
REVERT: A  328 SER cc_start: 0.8495 (t) cc_final: 0.8130 (p)
REVERT: A  432 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7103 (mm-30)
REVERT: A  445 TYR cc_start: 0.8449 (t80) cc_final: 0.8109 (t80)
REVERT: A  497 ARG cc_start: 0.7484 (ttm110) cc_final: 0.7283 (ttp80)
REVERT: A  649 ILE cc_start: 0.8171 (tt) cc_final: 0.7881 (mp)
REVERT: A  671 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8262 (tt)
REVERT: A  690 ILE cc_start: 0.7822 (pt) cc_final: 0.7601 (pt)
REVERT: A  695 PHE cc_start: 0.8106 (t80) cc_final: 0.7763 (t80)
REVERT: A  740 MET cc_start: 0.8468 (mmm) cc_final: 0.7940 (mmm)
REVERT: A  779 PHE cc_start: 0.8251 (t80) cc_final: 0.7848 (t80)
REVERT: A  802 SER cc_start: 0.8238 (t) cc_final: 0.7824 (p)
REVERT: A  814 GLU cc_start: 0.6786 (tp30) cc_final: 0.6533 (tp30)
REVERT: A  831 GLN cc_start: 0.7841 (tp-100) cc_final: 0.7603 (mm-40)
REVERT: A  989 ASN cc_start: 0.7991 (OUTLIER) cc_final: 0.7729 (t0)
REVERT: A 1018 SER cc_start: 0.8025 (m) cc_final: 0.7705 (t)
REVERT: A 1029 PHE cc_start: 0.6508 (OUTLIER) cc_final: 0.5407 (m-80)
REVERT: A 1099 TYR cc_start: 0.7993 (m-10) cc_final: 0.7742 (m-10)
REVERT: A 1162 MET cc_start: 0.7325 (tmm) cc_final: 0.6952 (tpt)
REVERT: A 1169 ASP cc_start: 0.7360 (t0) cc_final: 0.7147 (t0)
  outliers start: 31
  outliers final: 21
  residues processed: 217
  average time/residue: 0.6514
  time to fit residues: 150.3487
Evaluate side-chains
  230 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 205
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  395 GLU
Chi-restraints excluded: chain A residue  399 ARG
Chi-restraints excluded: chain A residue  442 GLU
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  608 ILE
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  731 LEU
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  759 LEU
Chi-restraints excluded: chain A residue  781 GLU
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  926 THR
Chi-restraints excluded: chain A residue  989 ASN
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1029 PHE
Chi-restraints excluded: chain A residue 1121 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9990
   chunk 101 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 6 optimal weight:    0.4980
   chunk 100 optimal weight:    0.8980
   chunk 112 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 136 ASN
A 400 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.156506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.140154 restraints weight = 12457.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3793 rms_B_bonded: 1.69
r_work: 0.3690 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3549 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9663  Z= 0.187
  Angle     :  0.574   9.508  13219  Z= 0.309
  Chirality :  0.042   0.199   1501
  Planarity :  0.005   0.063   1638
  Dihedral  : 15.050 135.907   1522
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 19.30 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.75 (0.25), residues: 1135
  helix:  1.32 (0.20), residues: 645
  sheet: -0.67 (0.54), residues: 97
  loop : -0.46 (0.32), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 758 
 TYR   0.011   0.002   TYR A 217 
 PHE   0.013   0.002   PHE A 966 
 TRP   0.018   0.002   TRP A  35 
 HIS   0.003   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 9663)
  covalent geometry    : angle       0.57415 (13219)
  hydrogen bonds       : bond        0.03834 (  499)
  hydrogen bonds       : angle       4.46776 ( 1452)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 209
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 ILE cc_start: 0.7774 (pt) cc_final: 0.7494 (pp)
REVERT: A  210 TYR cc_start: 0.8027 (t80) cc_final: 0.7611 (t80)
REVERT: A  211 MET cc_start: 0.6086 (OUTLIER) cc_final: 0.5389 (mmm)
REVERT: A  266 TRP cc_start: 0.7099 (t-100) cc_final: 0.6741 (t-100)
REVERT: A  312 ARG cc_start: 0.7903 (mpp80) cc_final: 0.7670 (mtm-85)
REVERT: A  322 ASN cc_start: 0.7649 (t0) cc_final: 0.7359 (t0)
REVERT: A  432 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7118 (mm-30)
REVERT: A  445 TYR cc_start: 0.8461 (t80) cc_final: 0.8148 (t80)
REVERT: A  483 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8657 (mt)
REVERT: A  497 ARG cc_start: 0.7551 (ttm110) cc_final: 0.7351 (ttp80)
REVERT: A  649 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7759 (pt)
REVERT: A  690 ILE cc_start: 0.7855 (pt) cc_final: 0.7609 (pt)
REVERT: A  740 MET cc_start: 0.8438 (mmm) cc_final: 0.7938 (mmm)
REVERT: A  802 SER cc_start: 0.8229 (t) cc_final: 0.7835 (p)
REVERT: A  814 GLU cc_start: 0.6817 (tp30) cc_final: 0.6612 (tp30)
REVERT: A  831 GLN cc_start: 0.7849 (tp-100) cc_final: 0.7639 (mm-40)
REVERT: A  989 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7701 (t0)
REVERT: A 1018 SER cc_start: 0.7940 (m) cc_final: 0.7678 (t)
REVERT: A 1029 PHE cc_start: 0.6708 (OUTLIER) cc_final: 0.5533 (m-80)
REVERT: A 1099 TYR cc_start: 0.7996 (m-10) cc_final: 0.7754 (m-10)
REVERT: A 1160 ARG cc_start: 0.7104 (mtm180) cc_final: 0.6723 (mtm180)
REVERT: A 1162 MET cc_start: 0.7313 (tmm) cc_final: 0.6989 (tpt)
  outliers start: 32
  outliers final: 22
  residues processed: 223
  average time/residue: 0.6473
  time to fit residues: 153.4054
Evaluate side-chains
  231 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 204
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue   96 LYS
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  395 GLU
Chi-restraints excluded: chain A residue  399 ARG
Chi-restraints excluded: chain A residue  442 GLU
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  608 ILE
Chi-restraints excluded: chain A residue  649 ILE
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  731 LEU
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  781 GLU
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue  926 THR
Chi-restraints excluded: chain A residue  989 ASN
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1029 PHE
Chi-restraints excluded: chain A residue 1121 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 69 optimal weight:    0.2980
   chunk 92 optimal weight:    0.5980
   chunk 39 optimal weight:    0.2980
   chunk 101 optimal weight:    0.8980
   chunk 112 optimal weight:    0.9990
   chunk 90 optimal weight:    0.6980
   chunk 83 optimal weight:    0.8980
   chunk 114 optimal weight:    0.4980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN
A 959 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.158144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.141768 restraints weight = 12415.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3822 rms_B_bonded: 1.64
r_work: 0.3718 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3579 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9663  Z= 0.153
  Angle     :  0.559   9.587  13219  Z= 0.299
  Chirality :  0.041   0.203   1501
  Planarity :  0.005   0.065   1638
  Dihedral  : 14.987 136.756   1522
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 20.68 %
    Favored  : 76.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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:  0.88 (0.25), residues: 1135
  helix:  1.43 (0.20), residues: 645
  sheet: -0.61 (0.55), residues: 96
  loop : -0.41 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 758 
 TYR   0.016   0.002   TYR A 874 
 PHE   0.014   0.001   PHE A 966 
 TRP   0.017   0.002   TRP A  35 
 HIS   0.003   0.001   HIS A 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 9663)
  covalent geometry    : angle       0.55921 (13219)
  hydrogen bonds       : bond        0.03608 (  499)
  hydrogen bonds       : angle       4.38353 ( 1452)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 199
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 ILE cc_start: 0.7748 (pt) cc_final: 0.7469 (pp)
REVERT: A  211 MET cc_start: 0.6133 (OUTLIER) cc_final: 0.5355 (mmm)
REVERT: A  312 ARG cc_start: 0.7924 (mpp80) cc_final: 0.7687 (mtm-85)
REVERT: A  322 ASN cc_start: 0.7611 (t0) cc_final: 0.7339 (t0)
REVERT: A  432 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7100 (mm-30)
REVERT: A  445 TYR cc_start: 0.8458 (t80) cc_final: 0.8125 (t80)
REVERT: A  483 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8624 (mt)
REVERT: A  497 ARG cc_start: 0.7463 (ttm110) cc_final: 0.7251 (ttp80)
REVERT: A  649 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7916 (mp)
REVERT: A  690 ILE cc_start: 0.7805 (pt) cc_final: 0.7592 (pt)
REVERT: A  695 PHE cc_start: 0.8045 (t80) cc_final: 0.7739 (t80)
REVERT: A  740 MET cc_start: 0.8431 (mmm) cc_final: 0.7938 (mmm)
REVERT: A  802 SER cc_start: 0.8233 (t) cc_final: 0.7844 (p)
REVERT: A  831 GLN cc_start: 0.7834 (tp-100) cc_final: 0.7627 (mm-40)
REVERT: A  989 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7699 (t0)
REVERT: A 1029 PHE cc_start: 0.6408 (OUTLIER) cc_final: 0.5340 (m-80)
REVERT: A 1104 ASP cc_start: 0.7405 (t0) cc_final: 0.7056 (t0)
REVERT: A 1160 ARG cc_start: 0.7129 (mtm180) cc_final: 0.6761 (mtm180)
  outliers start: 30
  outliers final: 18
  residues processed: 214
  average time/residue: 0.6761
  time to fit residues: 153.8305
Evaluate side-chains
  220 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 197
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  395 GLU
Chi-restraints excluded: chain A residue  399 ARG
Chi-restraints excluded: chain A residue  442 GLU
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  608 ILE
Chi-restraints excluded: chain A residue  649 ILE
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue  959 GLN
Chi-restraints excluded: chain A residue  989 ASN
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1029 PHE
Chi-restraints excluded: chain A residue 1121 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 86 optimal weight:    0.3980
   chunk 38 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN
A 959 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.156462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.140143 restraints weight = 12456.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3802 rms_B_bonded: 1.63
r_work: 0.3698 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3560 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   9663  Z= 0.209
  Angle     :  0.609   9.673  13219  Z= 0.325
  Chirality :  0.043   0.253   1501
  Planarity :  0.005   0.066   1638
  Dihedral  : 15.033 138.038   1522
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 21.20 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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 (0.25), residues: 1135
  helix:  1.29 (0.20), residues: 644
  sheet: -0.36 (0.55), residues: 89
  loop : -0.56 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 758 
 TYR   0.011   0.002   TYR A 874 
 PHE   0.014   0.002   PHE A1029 
 TRP   0.020   0.002   TRP A  35 
 HIS   0.004   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 9663)
  covalent geometry    : angle       0.60926 (13219)
  hydrogen bonds       : bond        0.03907 (  499)
  hydrogen bonds       : angle       4.49074 ( 1452)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 199
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 ILE cc_start: 0.7775 (pt) cc_final: 0.7505 (pp)
REVERT: A  211 MET cc_start: 0.6061 (OUTLIER) cc_final: 0.5349 (mmm)
REVERT: A  266 TRP cc_start: 0.7031 (t-100) cc_final: 0.6684 (t-100)
REVERT: A  312 ARG cc_start: 0.7945 (mpp80) cc_final: 0.7719 (mtm-85)
REVERT: A  322 ASN cc_start: 0.7633 (t0) cc_final: 0.7358 (t0)
REVERT: A  328 SER cc_start: 0.8509 (t) cc_final: 0.8285 (p)
REVERT: A  432 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7144 (mm-30)
REVERT: A  445 TYR cc_start: 0.8457 (t80) cc_final: 0.8167 (t80)
REVERT: A  483 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8658 (mt)
REVERT: A  497 ARG cc_start: 0.7511 (ttm110) cc_final: 0.7285 (ttp80)
REVERT: A  548 LYS cc_start: 0.8375 (mtpt) cc_final: 0.8052 (mtmm)
REVERT: A  649 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7709 (pt)
REVERT: A  671 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8327 (tt)
REVERT: A  690 ILE cc_start: 0.7829 (pt) cc_final: 0.7592 (pt)
REVERT: A  740 MET cc_start: 0.8458 (mmm) cc_final: 0.7978 (mmm)
REVERT: A  802 SER cc_start: 0.8266 (t) cc_final: 0.7879 (p)
REVERT: A  831 GLN cc_start: 0.7831 (tp-100) cc_final: 0.7616 (mm-40)
REVERT: A  989 ASN cc_start: 0.7933 (OUTLIER) cc_final: 0.7703 (t0)
REVERT: A 1018 SER cc_start: 0.8017 (m) cc_final: 0.7733 (t)
REVERT: A 1029 PHE cc_start: 0.6724 (OUTLIER) cc_final: 0.5462 (m-80)
REVERT: A 1099 TYR cc_start: 0.7971 (m-10) cc_final: 0.7666 (m-80)
REVERT: A 1104 ASP cc_start: 0.7307 (t0) cc_final: 0.6966 (t0)
REVERT: A 1162 MET cc_start: 0.7290 (tmm) cc_final: 0.6875 (tpt)
  outliers start: 28
  outliers final: 19
  residues processed: 213
  average time/residue: 0.6552
  time to fit residues: 148.4099
Evaluate side-chains
  222 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 197
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 SER
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  380 THR
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  395 GLU
Chi-restraints excluded: chain A residue  399 ARG
Chi-restraints excluded: chain A residue  442 GLU
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  519 VAL
Chi-restraints excluded: chain A residue  608 ILE
Chi-restraints excluded: chain A residue  649 ILE
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue  959 GLN
Chi-restraints excluded: chain A residue  989 ASN
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1029 PHE
Chi-restraints excluded: chain A residue 1121 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 76 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 78 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 104 optimal weight:    0.9990
   chunk 106 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 102 optimal weight:    0.8980
   chunk 64 optimal weight:    0.1980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 400 GLN
A 959 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.157282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.140891 restraints weight = 12356.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3819 rms_B_bonded: 1.64
r_work: 0.3720 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3583 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.2964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9663  Z= 0.175
  Angle     :  0.590   9.629  13219  Z= 0.315
  Chirality :  0.042   0.272   1501
  Planarity :  0.005   0.061   1638
  Dihedral  : 14.998 138.728   1522
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 21.10 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.16 %
    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 (0.25), residues: 1135
  helix:  1.32 (0.20), residues: 644
  sheet: -0.37 (0.55), residues: 87
  loop : -0.58 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 758 
 TYR   0.022   0.002   TYR A 874 
 PHE   0.013   0.001   PHE A 966 
 TRP   0.019   0.002   TRP A  35 
 HIS   0.003   0.001   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 9663)
  covalent geometry    : angle       0.59048 (13219)
  hydrogen bonds       : bond        0.03719 (  499)
  hydrogen bonds       : angle       4.46821 ( 1452)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3813.14 seconds
wall clock time: 65 minutes 37.04 seconds (3937.04 seconds total)