Starting phenix.real_space_refine
on Wed Sep 17 09:56:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jbz_61331/09_2025/9jbz_61331.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jbz_61331/09_2025/9jbz_61331.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jbz_61331/09_2025/9jbz_61331.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jbz_61331/09_2025/9jbz_61331.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jbz_61331/09_2025/9jbz_61331.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jbz_61331/09_2025/9jbz_61331.cif"
  }
  resolution = 3.67
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.039
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      47      5.16       5
     C    5131      2.51       5
     N    1334      2.21       5
     O    1436      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7948
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1016, 7948
          Classifications: {'peptide': 1016}
          Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 962}
          Chain breaks: 1
  Time building chain proxies: 2.03, per 1000 atoms: 0.26
  Number of scatterers: 7948
  At special positions: 0
  Unit cell: (83.2, 95.68, 145.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      47     16.00
     O    1436      8.00
     N    1334      7.00
     C    5131      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.54
  Conformation dependent library (CDL) restraints added in 385.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 8 sheets defined
      51.1% alpha, 13.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 118 through 130
      removed outlier: 3.589A  pdb=" N   HIS A 123 " --> pdb=" O   HIS A 119 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ALA A 124 " --> pdb=" O   TRP A 120 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   HIS A 125 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   CYS A 126 " --> pdb=" O   VAL A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 198
      removed outlier: 3.806A  pdb=" N   GLY A 197 " --> pdb=" O   PHE A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 206
      removed outlier: 3.991A  pdb=" N   SER A 205 " --> pdb=" O   SER A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 223
    Processing helix  chain 'A' and resid 233 through 243
    Processing helix  chain 'A' and resid 244 through 260
    Processing helix  chain 'A' and resid 262 through 295
      removed outlier: 3.566A  pdb=" N   GLU A 290 " --> pdb=" O   ARG A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 382
      removed outlier: 3.777A  pdb=" N   HIS A 382 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 378 through 382'
    Processing helix  chain 'A' and resid 417 through 420
    Processing helix  chain 'A' and resid 421 through 432
    Processing helix  chain 'A' and resid 441 through 468
    Processing helix  chain 'A' and resid 473 through 489
      removed outlier: 3.630A  pdb=" N   LEU A 477 " --> pdb=" O   ASN A 473 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   VAL A 489 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 510
      removed outlier: 3.990A  pdb=" N   LEU A 497 " --> pdb=" O   LEU A 493 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LYS A 510 " --> pdb=" O   ILE A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 525
      Proline residue:  A 522  - end of helix
    Processing helix  chain 'A' and resid 533 through 538
      removed outlier: 3.760A  pdb=" N   THR A 537 " --> pdb=" O   ASP A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 574
      removed outlier: 3.543A  pdb=" N   CYS A 574 " --> pdb=" O   ALA A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'A' and resid 656 through 663
      removed outlier: 4.510A  pdb=" N   SER A 662 " --> pdb=" O   GLU A 658 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   MET A 663 " --> pdb=" O   THR A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 681
    Processing helix  chain 'A' and resid 697 through 704
      removed outlier: 3.674A  pdb=" N   ARG A 702 " --> pdb=" O   HIS A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 711
      removed outlier: 4.055A  pdb=" N   LEU A 709 " --> pdb=" O   ARG A 706 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   GLU A 710 " --> pdb=" O   GLU A 707 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   CYS A 711 " --> pdb=" O   ALA A 708 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 738
    Processing helix  chain 'A' and resid 750 through 761
    Processing helix  chain 'A' and resid 800 through 807
    Processing helix  chain 'A' and resid 813 through 823
    Processing helix  chain 'A' and resid 823 through 831
      removed outlier: 3.747A  pdb=" N   LEU A 827 " --> pdb=" O   ASP A 823 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 832 through 834
      No H-bonds generated for 'chain 'A' and resid 832 through 834'
    Processing helix  chain 'A' and resid 841 through 855
      removed outlier: 3.523A  pdb=" N   GLU A 846 " --> pdb=" O   PRO A 842 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 867
      No H-bonds generated for 'chain 'A' and resid 865 through 867'
    Processing helix  chain 'A' and resid 868 through 875
      removed outlier: 3.931A  pdb=" N   HIS A 874 " --> pdb=" O   GLY A 870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 952 through 956
    Processing helix  chain 'A' and resid 967 through 1009
      removed outlier: 3.953A  pdb=" N   CYS A 971 " --> pdb=" O   ILE A 967 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU A1007 " --> pdb=" O   SER A1003 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1033
      removed outlier: 3.556A  pdb=" N   ARG A1033 " --> pdb=" O   LEU A1029 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1051 through 1078
      removed outlier: 3.513A  pdb=" N   ILE A1055 " --> pdb=" O   ASN A1051 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   SER A1068 " --> pdb=" O   VAL A1064 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1097 through 1118
      removed outlier: 3.648A  pdb=" N   SER A1101 " --> pdb=" O   SER A1097 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1127 through 1130
    Processing helix  chain 'A' and resid 1131 through 1151
    Processing helix  chain 'A' and resid 1153 through 1160
    Processing helix  chain 'A' and resid 1166 through 1195
      removed outlier: 3.944A  pdb=" N   VAL A1172 " --> pdb=" O   GLU A1168 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143
      removed outlier: 3.586A  pdb=" N   VAL A 156 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 174
      removed outlier: 3.668A  pdb=" N   PHE A 172 " --> pdb=" O   TYR A 179 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 308 through 313
      removed outlier: 5.248A  pdb=" N   GLN A 302 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   SER A 324 " --> pdb=" O   GLN A 302 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ILE A 322 " --> pdb=" O   TYR A 304 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 359 through 361
      removed outlier: 3.525A  pdb=" N   GLN A 359 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL A 347 " --> pdb=" O   GLN A 359 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LYS A 361 " --> pdb=" O   CYS A 345 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   CYS A 345 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLN A 392 " --> pdb=" O   ILE A 346 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ASP A 348 " --> pdb=" O   VAL A 390 " (cutoff:3.500A)
      removed outlier: 5.911A  pdb=" N   VAL A 390 " --> pdb=" O   ASP A 348 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 513 through 515
      removed outlier: 6.494A  pdb=" N   GLY A 878 " --> pdb=" O   PHE A 960 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   SER A 962 " --> pdb=" O   GLY A 878 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ALA A 880 " --> pdb=" O   SER A 962 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   THR A 859 " --> pdb=" O   VAL A 877 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   VAL A 879 " --> pdb=" O   THR A 859 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   MET A 861 " --> pdb=" O   VAL A 879 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   VAL A 858 " --> pdb=" O   VAL A 527 " (cutoff:3.500A)
      removed outlier: 8.570A  pdb=" N   PHE A 837 " --> pdb=" O   VAL A 743 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   MET A 745 " --> pdb=" O   PHE A 837 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   LEU A 809 " --> pdb=" O   VAL A 836 " (cutoff:3.500A)
      removed outlier: 8.672A  pdb=" N   ALA A 838 " --> pdb=" O   LEU A 809 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   LEU A 811 " --> pdb=" O   ALA A 838 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU A 770 " --> pdb=" O   ALA A 808 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   CYS A 810 " --> pdb=" O   LEU A 770 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU A 772 " --> pdb=" O   CYS A 810 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   THR A 812 " --> pdb=" O   LEU A 772 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 544 through 547
      removed outlier: 5.655A  pdb=" N   VAL A 545 " --> pdb=" O   SER A 722 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   SER A 722 " --> pdb=" O   VAL A 545 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   GLY A 547 " --> pdb=" O   VAL A 720 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   PHE A 715 " --> pdb=" O   TYR A 690 " (cutoff:3.500A)
      removed outlier: 6.031A  pdb=" N   TYR A 690 " --> pdb=" O   PHE A 715 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLY A 717 " --> pdb=" O   LEU A 688 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA A 687 " --> pdb=" O   GLY A 655 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLY A 655 " --> pdb=" O   ALA A 687 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   VAL A 653 " --> pdb=" O   GLY A 689 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   VAL A 635 " --> pdb=" O   ALA A 652 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ARG A 632 " --> pdb=" O   PHE A 626 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   PHE A 626 " --> pdb=" O   ARG A 632 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   SER A 638 " --> pdb=" O   ILE A 620 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   ILE A 620 " --> pdb=" O   SER A 638 " (cutoff:3.500A)
      removed outlier: 8.736A  pdb=" N   GLU A 640 " --> pdb=" O   LEU A 618 " (cutoff:3.500A)
      removed outlier: 8.437A  pdb=" N   LEU A 618 " --> pdb=" O   GLU A 640 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 544 through 547
      removed outlier: 5.655A  pdb=" N   VAL A 545 " --> pdb=" O   SER A 722 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   SER A 722 " --> pdb=" O   VAL A 545 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   GLY A 547 " --> pdb=" O   VAL A 720 " (cutoff:3.500A)
      removed outlier: 7.511A  pdb=" N   PHE A 715 " --> pdb=" O   SER A 665 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 578 through 579
      removed outlier: 3.910A  pdb=" N   MET A 578 " --> pdb=" O   VAL A 586 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   VAL A 586 " --> pdb=" O   MET A 578 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    401 hydrogen bonds defined for protein.
    1146 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.54

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2552
        1.34 -     1.46: 1739
        1.46 -     1.58: 3765
        1.58 -     1.69: 0
        1.69 -     1.81: 69
  Bond restraints: 8125
  Sorted by residual:
  bond pdb=" CG1 ILE A 430 "
       pdb=" CD1 ILE A 430 "
    ideal  model  delta    sigma   weight residual
    1.513  1.445  0.068 3.90e-02 6.57e+02 3.07e+00
  bond pdb=" CB  MET A 229 "
       pdb=" CG  MET A 229 "
    ideal  model  delta    sigma   weight residual
    1.520  1.481  0.039 3.00e-02 1.11e+03 1.68e+00
  bond pdb=" CG  ARG A1079 "
       pdb=" CD  ARG A1079 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.47e-01
  bond pdb=" CB  MET A1110 "
       pdb=" CG  MET A1110 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.46e-01
  bond pdb=" CB  THR A 482 "
       pdb=" CG2 THR A 482 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.01e-01
  ... (remaining 8120 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 10855
        2.03 -     4.05: 144
        4.05 -     6.08: 22
        6.08 -     8.11: 1
        8.11 -    10.13: 2
  Bond angle restraints: 11024
  Sorted by residual:
  angle pdb=" CB  MET A 229 "
        pdb=" CG  MET A 229 "
        pdb=" SD  MET A 229 "
      ideal   model   delta    sigma   weight residual
     112.70  102.57   10.13 3.00e+00 1.11e-01 1.14e+01
  angle pdb=" CB  MET A 288 "
        pdb=" CG  MET A 288 "
        pdb=" SD  MET A 288 "
      ideal   model   delta    sigma   weight residual
     112.70  121.30   -8.60 3.00e+00 1.11e-01 8.21e+00
  angle pdb=" N   TRP A 257 "
        pdb=" CA  TRP A 257 "
        pdb=" CB  TRP A 257 "
      ideal   model   delta    sigma   weight residual
     110.28  114.63   -4.35 1.55e+00 4.16e-01 7.88e+00
  angle pdb=" CA  TRP A 257 "
        pdb=" CB  TRP A 257 "
        pdb=" CG  TRP A 257 "
      ideal   model   delta    sigma   weight residual
     113.60  118.67   -5.07 1.90e+00 2.77e-01 7.12e+00
  angle pdb=" CA  ARG A 436 "
        pdb=" CB  ARG A 436 "
        pdb=" CG  ARG A 436 "
      ideal   model   delta    sigma   weight residual
     114.10  118.63   -4.53 2.00e+00 2.50e-01 5.14e+00
  ... (remaining 11019 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.05: 4506
       17.05 -    34.09: 336
       34.09 -    51.14: 58
       51.14 -    68.19: 4
       68.19 -    85.23: 4
  Dihedral angle restraints: 4908
    sinusoidal: 1946
      harmonic: 2962
  Sorted by residual:
  dihedral pdb=" CA  MET A 229 "
           pdb=" C   MET A 229 "
           pdb=" N   VAL A 230 "
           pdb=" CA  VAL A 230 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.44   27.56     0      5.00e+00 4.00e-02 3.04e+01
  dihedral pdb=" CG  ARG A 520 "
           pdb=" CD  ARG A 520 "
           pdb=" NE  ARG A 520 "
           pdb=" CZ  ARG A 520 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.23  -44.23     2      1.50e+01 4.44e-03 1.04e+01
  dihedral pdb=" CA  ASN A 884 "
           pdb=" CB  ASN A 884 "
           pdb=" CG  ASN A 884 "
           pdb=" OD1 ASN A 884 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -173.75  -66.25     2      2.00e+01 2.50e-03 1.01e+01
  ... (remaining 4905 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1063
       0.054 -    0.108: 190
       0.108 -    0.162: 25
       0.162 -    0.217: 1
       0.217 -    0.271: 1
  Chirality restraints: 1280
  Sorted by residual:
  chirality pdb=" CG  LEU A 431 "
            pdb=" CB  LEU A 431 "
            pdb=" CD1 LEU A 431 "
            pdb=" CD2 LEU A 431 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.32   -0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" CA  ILE A 771 "
            pdb=" N   ILE A 771 "
            pdb=" C   ILE A 771 "
            pdb=" CB  ILE A 771 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.82e-01
  chirality pdb=" CB  VAL A 338 "
            pdb=" CA  VAL A 338 "
            pdb=" CG1 VAL A 338 "
            pdb=" CG2 VAL A 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 5.06e-01
  ... (remaining 1277 not shown)

  Planarity restraints: 1398
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 257 "   -0.025 2.00e-02 2.50e+03   2.55e-02 1.63e+01
        pdb=" CG  TRP A 257 "    0.069 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 257 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 257 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 257 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 257 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 257 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 257 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 257 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 257 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 558 "    0.046 5.00e-02 4.00e+02   7.04e-02 7.93e+00
        pdb=" N   PRO A 559 "   -0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO A 559 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 559 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A1165 "   -0.034 5.00e-02 4.00e+02   5.26e-02 4.43e+00
        pdb=" N   PRO A1166 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A1166 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A1166 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1395 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 349
        2.72 -     3.27: 8189
        3.27 -     3.81: 12789
        3.81 -     4.36: 14440
        4.36 -     4.90: 24710
  Nonbonded interactions: 60477
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 558 "
            pdb=" OG  SER A 562 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" O   LEU A 352 "
            pdb=" ND2 ASN A 867 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" OG  SER A 328 "
            pdb=" OD1 ASN A 332 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" NZ  LYS A 853 "
            pdb=" OD1 ASP A 876 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" OE2 GLU A1008 "
            pdb=" NZ  LYS A1083 "
     model   vdw
     2.247 3.120
  ... (remaining 60472 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.240
  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:             0.020
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.900
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
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   0.068   8125  Z= 0.133
  Angle     :  0.578  10.135  11024  Z= 0.297
  Chirality :  0.041   0.271   1280
  Planarity :  0.005   0.070   1398
  Dihedral  : 11.945  85.232   2988
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.27 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.26), residues: 1012
  helix:  1.79 (0.24), residues: 441
  sheet:  0.18 (0.57), residues: 97
  loop :  0.47 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 829 
 TYR   0.017   0.001   TYR A1091 
 PHE   0.029   0.001   PHE A1169 
 TRP   0.069   0.003   TRP A 257 
 HIS   0.004   0.001   HIS A 675 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8125)
  covalent geometry    : angle       0.57762 (11024)
  hydrogen bonds       : bond        0.16921 (  400)
  hydrogen bonds       : angle       6.07223 ( 1146)

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 MET cc_start: 0.7974 (tpt) cc_final: 0.7625 (tpt)
REVERT: A  276 PHE cc_start: 0.7617 (t80) cc_final: 0.6989 (t80)
REVERT: A  347 VAL cc_start: 0.8607 (p) cc_final: 0.8293 (t)
REVERT: A  351 MET cc_start: 0.6600 (ttt) cc_final: 0.6301 (ttt)
REVERT: A  374 ASP cc_start: 0.7911 (t70) cc_final: 0.7695 (t70)
REVERT: A  476 LYS cc_start: 0.8117 (ttpp) cc_final: 0.7487 (ttpp)
REVERT: A  479 LEU cc_start: 0.8209 (tp) cc_final: 0.7988 (tp)
REVERT: A  492 GLU cc_start: 0.6593 (mp0) cc_final: 0.6186 (mp0)
REVERT: A  626 PHE cc_start: 0.8169 (m-80) cc_final: 0.7951 (m-80)
REVERT: A  631 LYS cc_start: 0.7884 (mmpt) cc_final: 0.7581 (mmpt)
REVERT: A  675 HIS cc_start: 0.8211 (t-90) cc_final: 0.7570 (t-90)
REVERT: A  677 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7267 (mt-10)
REVERT: A  827 LEU cc_start: 0.8578 (tp) cc_final: 0.8340 (tp)
REVERT: A  839 ARG cc_start: 0.7484 (ttm-80) cc_final: 0.7039 (ttm-80)
REVERT: A 1027 CYS cc_start: 0.6969 (t) cc_final: 0.6451 (t)
REVERT: A 1065 HIS cc_start: 0.6515 (m-70) cc_final: 0.6302 (m-70)
REVERT: A 1117 ILE cc_start: 0.8592 (tt) cc_final: 0.8366 (tt)
REVERT: A 1132 LYS cc_start: 0.8353 (mttt) cc_final: 0.8046 (mttt)
REVERT: A 1138 LEU cc_start: 0.8330 (mm) cc_final: 0.7964 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.0944
  time to fit residues: 30.0413
Evaluate side-chains
  215 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    0.0770
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0770
   overall best weight:    0.5496

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 625 HIS
A 741 HIS
** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.157657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.131714 restraints weight = 13863.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.136230 restraints weight = 6536.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.139264 restraints weight = 3890.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.141124 restraints weight = 2725.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.142200 restraints weight = 2173.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.1238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   8125  Z= 0.134
  Angle     :  0.594   8.765  11024  Z= 0.299
  Chirality :  0.042   0.174   1280
  Planarity :  0.005   0.055   1398
  Dihedral  :  3.910  20.908   1086
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.88 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 10.02 %
    Favored  : 88.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.26), residues: 1012
  helix:  1.77 (0.24), residues: 443
  sheet:  0.14 (0.58), residues: 92
  loop :  0.44 (0.27), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 829 
 TYR   0.015   0.001   TYR A1119 
 PHE   0.025   0.001   PHE A1066 
 TRP   0.065   0.003   TRP A 257 
 HIS   0.007   0.001   HIS A 575 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8125)
  covalent geometry    : angle       0.59356 (11024)
  hydrogen bonds       : bond        0.04740 (  400)
  hydrogen bonds       : angle       4.66154 ( 1146)

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 222
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 MET cc_start: 0.5207 (mmm) cc_final: 0.4519 (mmm)
REVERT: A  272 MET cc_start: 0.7824 (tpt) cc_final: 0.7520 (tpt)
REVERT: A  276 PHE cc_start: 0.7587 (t80) cc_final: 0.6981 (t80)
REVERT: A  349 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6851 (mt-10)
REVERT: A  362 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7462 (mp0)
REVERT: A  428 ARG cc_start: 0.7799 (tmm160) cc_final: 0.7516 (tmm160)
REVERT: A  479 LEU cc_start: 0.8238 (tp) cc_final: 0.8011 (tp)
REVERT: A  492 GLU cc_start: 0.6649 (mp0) cc_final: 0.6301 (mp0)
REVERT: A  626 PHE cc_start: 0.8196 (m-80) cc_final: 0.7978 (m-10)
REVERT: A  677 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7089 (mt-10)
REVERT: A  726 LYS cc_start: 0.6723 (mtmm) cc_final: 0.6474 (mtmm)
REVERT: A  827 LEU cc_start: 0.8581 (tp) cc_final: 0.8362 (tp)
REVERT: A  845 LYS cc_start: 0.8508 (mttm) cc_final: 0.8035 (mttm)
REVERT: A  994 ASN cc_start: 0.7351 (t0) cc_final: 0.7148 (t0)
REVERT: A 1108 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7506 (mmt)
REVERT: A 1117 ILE cc_start: 0.8581 (tt) cc_final: 0.8349 (tt)
REVERT: A 1118 ASN cc_start: 0.8146 (m110) cc_final: 0.7809 (m-40)
REVERT: A 1138 LEU cc_start: 0.8257 (mm) cc_final: 0.7983 (mt)
  outliers start: 9
  outliers final: 4
  residues processed: 223
  average time/residue: 0.0946
  time to fit residues: 27.6411
Evaluate side-chains
  223 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 217
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue 1108 MET
Chi-restraints excluded: chain A residue 1191 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0570
   chunk 76 optimal weight:    1.9990
   chunk 3 optimal weight:    7.9990
   chunk 59 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0010
   overall best weight:    1.2110

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

Flipped N/Q/H residues before XYZ refinement:
A 359 GLN
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 575 HIS
A 741 HIS
** A1118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.155294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.128944 restraints weight = 13685.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.133442 restraints weight = 6421.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.136358 restraints weight = 3846.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.138060 restraints weight = 2742.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.138791 restraints weight = 2227.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7022
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   8125  Z= 0.162
  Angle     :  0.587   7.591  11024  Z= 0.295
  Chirality :  0.043   0.169   1280
  Planarity :  0.005   0.058   1398
  Dihedral  :  3.952  16.285   1086
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.08 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 12.64 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.26), residues: 1012
  helix:  1.67 (0.24), residues: 448
  sheet:  0.04 (0.57), residues: 89
  loop :  0.30 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 307 
 TYR   0.020   0.001   TYR A 671 
 PHE   0.020   0.002   PHE A1066 
 TRP   0.035   0.002   TRP A 257 
 HIS   0.006   0.001   HIS A 575 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 8125)
  covalent geometry    : angle       0.58680 (11024)
  hydrogen bonds       : bond        0.04577 (  400)
  hydrogen bonds       : angle       4.40316 ( 1146)

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 224
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 VAL cc_start: 0.8634 (t) cc_final: 0.8405 (m)
REVERT: A  229 MET cc_start: 0.5380 (mmm) cc_final: 0.4930 (mmm)
REVERT: A  272 MET cc_start: 0.7849 (tpt) cc_final: 0.7548 (tpt)
REVERT: A  276 PHE cc_start: 0.7588 (t80) cc_final: 0.6986 (t80)
REVERT: A  362 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7348 (mp0)
REVERT: A  479 LEU cc_start: 0.8275 (tp) cc_final: 0.8027 (tp)
REVERT: A  492 GLU cc_start: 0.6762 (mp0) cc_final: 0.6400 (mp0)
REVERT: A  631 LYS cc_start: 0.8132 (mmpt) cc_final: 0.7792 (mmpt)
REVERT: A  671 TYR cc_start: 0.8379 (t80) cc_final: 0.8148 (t80)
REVERT: A  677 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7108 (mt-10)
REVERT: A  734 ARG cc_start: 0.7625 (tpp80) cc_final: 0.7285 (tpp80)
REVERT: A  827 LEU cc_start: 0.8563 (tp) cc_final: 0.8359 (tp)
REVERT: A  845 LYS cc_start: 0.8530 (mttm) cc_final: 0.8104 (mtpp)
REVERT: A  853 LYS cc_start: 0.8068 (tttp) cc_final: 0.7693 (tptm)
REVERT: A  963 LYS cc_start: 0.8702 (mttt) cc_final: 0.8360 (mttt)
REVERT: A  994 ASN cc_start: 0.7538 (t0) cc_final: 0.7301 (t0)
REVERT: A 1008 GLU cc_start: 0.7922 (tp30) cc_final: 0.7682 (tp30)
REVERT: A 1061 GLN cc_start: 0.6980 (mt0) cc_final: 0.6687 (mt0)
REVERT: A 1118 ASN cc_start: 0.8220 (m110) cc_final: 0.7873 (m-40)
REVERT: A 1138 LEU cc_start: 0.8232 (mm) cc_final: 0.7984 (mt)
  outliers start: 21
  outliers final: 11
  residues processed: 229
  average time/residue: 0.0934
  time to fit residues: 28.4398
Evaluate side-chains
  230 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 218
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  359 GLN
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  755 CYS
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  996 LEU
Chi-restraints excluded: chain A residue 1052 LEU
Chi-restraints excluded: chain A residue 1064 VAL
Chi-restraints excluded: chain A residue 1191 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 17 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 66 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   chunk 7 optimal weight:    3.9990
   chunk 93 optimal weight:    0.8980
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 741 HIS
** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.154944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.128728 restraints weight = 14020.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.133219 restraints weight = 6510.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.136144 restraints weight = 3868.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.138075 restraints weight = 2722.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.138474 restraints weight = 2162.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7051
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   8125  Z= 0.179
  Angle     :  0.596   8.663  11024  Z= 0.300
  Chirality :  0.044   0.267   1280
  Planarity :  0.005   0.059   1398
  Dihedral  :  3.963  14.395   1086
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.47 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.06 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.26), residues: 1012
  helix:  1.58 (0.24), residues: 450
  sheet: -0.19 (0.52), residues: 101
  loop :  0.28 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 829 
 TYR   0.016   0.001   TYR A1119 
 PHE   0.019   0.002   PHE A1066 
 TRP   0.050   0.003   TRP A 257 
 HIS   0.005   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 8125)
  covalent geometry    : angle       0.59557 (11024)
  hydrogen bonds       : bond        0.04532 (  400)
  hydrogen bonds       : angle       4.37803 ( 1146)

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 221
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 LYS cc_start: 0.8054 (mmtm) cc_final: 0.7654 (mtmm)
REVERT: A  196 VAL cc_start: 0.8633 (t) cc_final: 0.8425 (m)
REVERT: A  229 MET cc_start: 0.5592 (mmm) cc_final: 0.5186 (mmm)
REVERT: A  272 MET cc_start: 0.7860 (tpt) cc_final: 0.7562 (tpt)
REVERT: A  276 PHE cc_start: 0.7575 (t80) cc_final: 0.6961 (t80)
REVERT: A  291 ILE cc_start: 0.5578 (OUTLIER) cc_final: 0.5143 (mt)
REVERT: A  349 GLU cc_start: 0.7312 (mt-10) cc_final: 0.6836 (mt-10)
REVERT: A  360 MET cc_start: 0.6894 (tmm) cc_final: 0.6428 (tmm)
REVERT: A  362 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7221 (mp0)
REVERT: A  425 LYS cc_start: 0.7612 (mmtt) cc_final: 0.7383 (mttm)
REVERT: A  479 LEU cc_start: 0.8286 (tp) cc_final: 0.8019 (tp)
REVERT: A  492 GLU cc_start: 0.6776 (mp0) cc_final: 0.6432 (mp0)
REVERT: A  631 LYS cc_start: 0.8103 (mmpt) cc_final: 0.7882 (mmpt)
REVERT: A  675 HIS cc_start: 0.8129 (t-90) cc_final: 0.7733 (t-90)
REVERT: A  677 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7052 (mt-10)
REVERT: A  726 LYS cc_start: 0.6994 (mtmm) cc_final: 0.6772 (mtmm)
REVERT: A  734 ARG cc_start: 0.7647 (tpp80) cc_final: 0.7300 (tpp80)
REVERT: A  827 LEU cc_start: 0.8590 (tp) cc_final: 0.8387 (tp)
REVERT: A  845 LYS cc_start: 0.8528 (mttm) cc_final: 0.8158 (mtpp)
REVERT: A  853 LYS cc_start: 0.8130 (tttp) cc_final: 0.7600 (tptm)
REVERT: A  987 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7687 (mtm)
REVERT: A 1008 GLU cc_start: 0.7927 (tp30) cc_final: 0.7694 (tp30)
REVERT: A 1056 LEU cc_start: 0.8276 (tp) cc_final: 0.7997 (tt)
REVERT: A 1061 GLN cc_start: 0.7070 (mt0) cc_final: 0.6799 (mt0)
REVERT: A 1108 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7479 (mmm)
REVERT: A 1118 ASN cc_start: 0.8345 (m110) cc_final: 0.7994 (m110)
REVERT: A 1138 LEU cc_start: 0.8213 (mm) cc_final: 0.8000 (mt)
  outliers start: 23
  outliers final: 13
  residues processed: 229
  average time/residue: 0.0977
  time to fit residues: 29.2847
Evaluate side-chains
  230 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 213
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  516 THR
Chi-restraints excluded: chain A residue  755 CYS
Chi-restraints excluded: chain A residue  785 ARG
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue  987 MET
Chi-restraints excluded: chain A residue  996 LEU
Chi-restraints excluded: chain A residue 1040 LEU
Chi-restraints excluded: chain A residue 1064 VAL
Chi-restraints excluded: chain A residue 1108 MET
Chi-restraints excluded: chain A residue 1191 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 66 optimal weight:    0.0770
   chunk 38 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 43 optimal weight:    7.9990
   chunk 45 optimal weight:    7.9990
   overall best weight:    0.7140

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

Flipped N/Q/H residues before XYZ refinement:
A 359 GLN
A 741 HIS
** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.156288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.129579 restraints weight = 13907.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.134103 restraints weight = 6508.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.137112 restraints weight = 3889.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.138939 restraints weight = 2759.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.139940 restraints weight = 2221.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   8125  Z= 0.125
  Angle     :  0.560   8.276  11024  Z= 0.279
  Chirality :  0.042   0.202   1280
  Planarity :  0.004   0.059   1398
  Dihedral  :  3.846  13.674   1086
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.17 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 16.74 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.26), residues: 1012
  helix:  1.66 (0.24), residues: 450
  sheet: -0.32 (0.51), residues: 108
  loop :  0.34 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 829 
 TYR   0.020   0.001   TYR A 671 
 PHE   0.013   0.001   PHE A1115 
 TRP   0.069   0.003   TRP A 257 
 HIS   0.004   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 8125)
  covalent geometry    : angle       0.55987 (11024)
  hydrogen bonds       : bond        0.04078 (  400)
  hydrogen bonds       : angle       4.24094 ( 1146)

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 221
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 LYS cc_start: 0.8052 (mmtm) cc_final: 0.7640 (mtmm)
REVERT: A  196 VAL cc_start: 0.8599 (t) cc_final: 0.8361 (m)
REVERT: A  229 MET cc_start: 0.5707 (mmm) cc_final: 0.5228 (mmm)
REVERT: A  272 MET cc_start: 0.7826 (tpt) cc_final: 0.7622 (tpt)
REVERT: A  276 PHE cc_start: 0.7565 (t80) cc_final: 0.6975 (t80)
REVERT: A  339 LEU cc_start: 0.7998 (tp) cc_final: 0.7785 (tt)
REVERT: A  349 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6790 (mt-10)
REVERT: A  362 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7493 (mp0)
REVERT: A  444 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8336 (t)
REVERT: A  479 LEU cc_start: 0.8272 (tp) cc_final: 0.8033 (tp)
REVERT: A  492 GLU cc_start: 0.6735 (mp0) cc_final: 0.6422 (mp0)
REVERT: A  631 LYS cc_start: 0.8142 (mmpt) cc_final: 0.7877 (mmpt)
REVERT: A  675 HIS cc_start: 0.8117 (t-90) cc_final: 0.7776 (t-90)
REVERT: A  734 ARG cc_start: 0.7644 (tpp80) cc_final: 0.7307 (tpp80)
REVERT: A  845 LYS cc_start: 0.8514 (mttm) cc_final: 0.8129 (mtpp)
REVERT: A  853 LYS cc_start: 0.8120 (tttp) cc_final: 0.7497 (tppp)
REVERT: A 1008 GLU cc_start: 0.7862 (tp30) cc_final: 0.7657 (tp30)
REVERT: A 1049 ILE cc_start: 0.8396 (tp) cc_final: 0.8062 (tt)
REVERT: A 1056 LEU cc_start: 0.8237 (tp) cc_final: 0.7990 (tt)
REVERT: A 1061 GLN cc_start: 0.6935 (mt0) cc_final: 0.6659 (mt0)
REVERT: A 1108 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7377 (mmm)
REVERT: A 1118 ASN cc_start: 0.8277 (m110) cc_final: 0.7933 (m-40)
REVERT: A 1138 LEU cc_start: 0.8199 (mm) cc_final: 0.7926 (mt)
  outliers start: 21
  outliers final: 13
  residues processed: 228
  average time/residue: 0.0970
  time to fit residues: 29.3506
Evaluate side-chains
  234 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 218
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  359 GLN
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  771 ILE
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue  996 LEU
Chi-restraints excluded: chain A residue 1040 LEU
Chi-restraints excluded: chain A residue 1108 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0470
   chunk 21 optimal weight:    0.9990
   chunk 35 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 94 optimal weight:    0.6980
   chunk 71 optimal weight:    0.8980
   chunk 60 optimal weight:    0.3980
   chunk 37 optimal weight:    0.0030
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.4088

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

Flipped N/Q/H residues before XYZ refinement:
A 359 GLN
A 741 HIS
** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.156784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.130178 restraints weight = 13849.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.134750 restraints weight = 6560.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.137762 restraints weight = 3926.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.139306 restraints weight = 2774.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.140801 restraints weight = 2269.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6979
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.058   8125  Z= 0.110
  Angle     :  0.569   9.172  11024  Z= 0.278
  Chirality :  0.042   0.173   1280
  Planarity :  0.004   0.059   1398
  Dihedral  :  3.787  12.781   1086
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.37 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 18.11 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.26), residues: 1012
  helix:  1.67 (0.24), residues: 450
  sheet: -0.17 (0.53), residues: 98
  loop :  0.32 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 829 
 TYR   0.018   0.001   TYR A 671 
 PHE   0.014   0.001   PHE A 174 
 TRP   0.063   0.002   TRP A 257 
 HIS   0.004   0.001   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 8125)
  covalent geometry    : angle       0.56884 (11024)
  hydrogen bonds       : bond        0.03813 (  400)
  hydrogen bonds       : angle       4.13908 ( 1146)

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 221
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 VAL cc_start: 0.8560 (t) cc_final: 0.8335 (m)
REVERT: A  207 ARG cc_start: 0.7627 (mmp80) cc_final: 0.7368 (mmp80)
REVERT: A  225 ASN cc_start: 0.7863 (t0) cc_final: 0.7651 (p0)
REVERT: A  272 MET cc_start: 0.7806 (tpt) cc_final: 0.7584 (tpt)
REVERT: A  276 PHE cc_start: 0.7563 (t80) cc_final: 0.7037 (t80)
REVERT: A  362 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7474 (mp0)
REVERT: A  444 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8336 (t)
REVERT: A  479 LEU cc_start: 0.8267 (tp) cc_final: 0.7995 (tp)
REVERT: A  492 GLU cc_start: 0.6701 (mp0) cc_final: 0.6411 (mp0)
REVERT: A  592 LYS cc_start: 0.8442 (mmmm) cc_final: 0.8063 (mmmm)
REVERT: A  631 LYS cc_start: 0.8150 (mmpt) cc_final: 0.7873 (mmpt)
REVERT: A  675 HIS cc_start: 0.8080 (t-90) cc_final: 0.7759 (t-90)
REVERT: A  734 ARG cc_start: 0.7628 (tpp80) cc_final: 0.7302 (tpp80)
REVERT: A  773 GLN cc_start: 0.8176 (pm20) cc_final: 0.7608 (pm20)
REVERT: A  785 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6807 (ptp-110)
REVERT: A  845 LYS cc_start: 0.8503 (mttm) cc_final: 0.8129 (mtpp)
REVERT: A  853 LYS cc_start: 0.8100 (tttp) cc_final: 0.7554 (tptm)
REVERT: A  987 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7629 (mtm)
REVERT: A 1049 ILE cc_start: 0.8401 (tp) cc_final: 0.8048 (tt)
REVERT: A 1056 LEU cc_start: 0.8174 (tp) cc_final: 0.7922 (tt)
REVERT: A 1061 GLN cc_start: 0.6834 (mt0) cc_final: 0.6548 (mt0)
REVERT: A 1118 ASN cc_start: 0.8172 (m110) cc_final: 0.7796 (m-40)
REVERT: A 1138 LEU cc_start: 0.8203 (mm) cc_final: 0.7913 (mt)
  outliers start: 23
  outliers final: 15
  residues processed: 227
  average time/residue: 0.0935
  time to fit residues: 28.1878
Evaluate side-chains
  233 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 214
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  345 CYS
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  755 CYS
Chi-restraints excluded: chain A residue  771 ILE
Chi-restraints excluded: chain A residue  785 ARG
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue  987 MET
Chi-restraints excluded: chain A residue 1040 LEU
Chi-restraints excluded: chain A residue 1108 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 43 optimal weight:    9.9990
   chunk 98 optimal weight:    4.9990
   chunk 48 optimal weight:    0.2980
   chunk 38 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 440 ASN
A 741 HIS
** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.154503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.128128 restraints weight = 13914.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.132640 restraints weight = 6548.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.135595 restraints weight = 3904.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.137362 restraints weight = 2752.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.138133 restraints weight = 2225.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8125  Z= 0.141
  Angle     :  0.583   8.534  11024  Z= 0.285
  Chirality :  0.042   0.150   1280
  Planarity :  0.004   0.058   1398
  Dihedral  :  3.816  13.335   1086
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.27 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 18.56 %
    Favored  : 78.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.26), residues: 1012
  helix:  1.62 (0.24), residues: 450
  sheet: -0.24 (0.53), residues: 101
  loop :  0.24 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 829 
 TYR   0.017   0.001   TYR A 671 
 PHE   0.013   0.001   PHE A1124 
 TRP   0.055   0.002   TRP A 257 
 HIS   0.004   0.001   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8125)
  covalent geometry    : angle       0.58262 (11024)
  hydrogen bonds       : bond        0.04055 (  400)
  hydrogen bonds       : angle       4.16436 ( 1146)

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 220
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 VAL cc_start: 0.8555 (t) cc_final: 0.8343 (m)
REVERT: A  225 ASN cc_start: 0.7893 (t0) cc_final: 0.7626 (p0)
REVERT: A  272 MET cc_start: 0.7839 (tpt) cc_final: 0.7627 (tpt)
REVERT: A  276 PHE cc_start: 0.7586 (t80) cc_final: 0.7054 (t80)
REVERT: A  291 ILE cc_start: 0.5698 (OUTLIER) cc_final: 0.5312 (mt)
REVERT: A  349 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6908 (mt-10)
REVERT: A  362 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7490 (mp0)
REVERT: A  469 ASP cc_start: 0.6666 (t70) cc_final: 0.6149 (t70)
REVERT: A  479 LEU cc_start: 0.8301 (tp) cc_final: 0.8025 (tp)
REVERT: A  492 GLU cc_start: 0.6749 (mp0) cc_final: 0.6500 (mp0)
REVERT: A  592 LYS cc_start: 0.8436 (mmmm) cc_final: 0.8054 (mmmm)
REVERT: A  631 LYS cc_start: 0.8167 (mmpt) cc_final: 0.7932 (mmpt)
REVERT: A  675 HIS cc_start: 0.8102 (t-90) cc_final: 0.7777 (t-90)
REVERT: A  734 ARG cc_start: 0.7653 (tpp80) cc_final: 0.7316 (tpp80)
REVERT: A  773 GLN cc_start: 0.8252 (pm20) cc_final: 0.7639 (pm20)
REVERT: A  785 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6858 (ptp-110)
REVERT: A  829 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.7666 (mtm-85)
REVERT: A  845 LYS cc_start: 0.8549 (mttm) cc_final: 0.8189 (mttm)
REVERT: A  853 LYS cc_start: 0.8139 (tttp) cc_final: 0.7587 (tptm)
REVERT: A  963 LYS cc_start: 0.8522 (mttt) cc_final: 0.8254 (mttt)
REVERT: A  987 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7629 (mtm)
REVERT: A 1049 ILE cc_start: 0.8417 (tp) cc_final: 0.8077 (tt)
REVERT: A 1056 LEU cc_start: 0.8231 (tp) cc_final: 0.7964 (tt)
REVERT: A 1061 GLN cc_start: 0.6923 (mt0) cc_final: 0.6661 (mt0)
REVERT: A 1118 ASN cc_start: 0.8231 (m110) cc_final: 0.7854 (m-40)
REVERT: A 1138 LEU cc_start: 0.8211 (mm) cc_final: 0.7975 (mt)
  outliers start: 29
  outliers final: 21
  residues processed: 229
  average time/residue: 0.0976
  time to fit residues: 29.7720
Evaluate side-chains
  246 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 221
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 TRP
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  345 CYS
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  516 THR
Chi-restraints excluded: chain A residue  626 PHE
Chi-restraints excluded: chain A residue  658 GLU
Chi-restraints excluded: chain A residue  755 CYS
Chi-restraints excluded: chain A residue  785 ARG
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  859 THR
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue  987 MET
Chi-restraints excluded: chain A residue  994 ASN
Chi-restraints excluded: chain A residue 1011 LYS
Chi-restraints excluded: chain A residue 1040 LEU
Chi-restraints excluded: chain A residue 1059 MET
Chi-restraints excluded: chain A residue 1108 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 49 optimal weight:   10.0000
   chunk 88 optimal weight:    4.9990
   chunk 73 optimal weight:    0.5980
   chunk 25 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 43 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 55 optimal weight:    0.0570
   chunk 39 optimal weight:    4.9990
   overall best weight:    1.1100

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

Flipped N/Q/H residues before XYZ refinement:
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.154725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.128382 restraints weight = 13939.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.132870 restraints weight = 6566.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.135818 restraints weight = 3922.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.137725 restraints weight = 2770.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.138442 restraints weight = 2216.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7035
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   8125  Z= 0.149
  Angle     :  0.589   8.188  11024  Z= 0.291
  Chirality :  0.043   0.202   1280
  Planarity :  0.004   0.058   1398
  Dihedral  :  3.905  13.778   1086
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.37 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 18.68 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.26), residues: 1012
  helix:  1.54 (0.24), residues: 450
  sheet: -0.25 (0.53), residues: 101
  loop :  0.23 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 829 
 TYR   0.017   0.001   TYR A 671 
 PHE   0.013   0.001   PHE A1087 
 TRP   0.053   0.002   TRP A 257 
 HIS   0.006   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8125)
  covalent geometry    : angle       0.58851 (11024)
  hydrogen bonds       : bond        0.04106 (  400)
  hydrogen bonds       : angle       4.16815 ( 1146)

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 220
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 LYS cc_start: 0.8051 (mmtm) cc_final: 0.7687 (mtmm)
REVERT: A  196 VAL cc_start: 0.8536 (t) cc_final: 0.8317 (m)
REVERT: A  225 ASN cc_start: 0.7906 (t0) cc_final: 0.7622 (p0)
REVERT: A  272 MET cc_start: 0.7837 (tpt) cc_final: 0.7610 (tpt)
REVERT: A  276 PHE cc_start: 0.7580 (t80) cc_final: 0.7042 (t80)
REVERT: A  291 ILE cc_start: 0.5672 (OUTLIER) cc_final: 0.5307 (mt)
REVERT: A  349 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6956 (mt-10)
REVERT: A  362 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7499 (mp0)
REVERT: A  425 LYS cc_start: 0.7533 (mmtt) cc_final: 0.7270 (mttm)
REVERT: A  432 PHE cc_start: 0.6458 (m-10) cc_final: 0.5418 (m-10)
REVERT: A  444 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8388 (t)
REVERT: A  479 LEU cc_start: 0.8284 (tp) cc_final: 0.8008 (tp)
REVERT: A  492 GLU cc_start: 0.6730 (mp0) cc_final: 0.6477 (mp0)
REVERT: A  592 LYS cc_start: 0.8429 (mmmm) cc_final: 0.8037 (mmmm)
REVERT: A  631 LYS cc_start: 0.8187 (mmpt) cc_final: 0.7962 (mmpt)
REVERT: A  675 HIS cc_start: 0.8081 (t-90) cc_final: 0.7785 (t-90)
REVERT: A  734 ARG cc_start: 0.7665 (tpp80) cc_final: 0.7310 (tpp80)
REVERT: A  773 GLN cc_start: 0.8241 (pm20) cc_final: 0.7741 (pm20)
REVERT: A  785 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6896 (ptp-110)
REVERT: A  845 LYS cc_start: 0.8519 (mttm) cc_final: 0.8170 (mtpp)
REVERT: A  846 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7317 (mt-10)
REVERT: A  853 LYS cc_start: 0.8138 (tttp) cc_final: 0.7474 (tptm)
REVERT: A  987 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7662 (mtm)
REVERT: A 1049 ILE cc_start: 0.8431 (tp) cc_final: 0.8056 (tt)
REVERT: A 1061 GLN cc_start: 0.6920 (mt0) cc_final: 0.6663 (mt0)
REVERT: A 1118 ASN cc_start: 0.8267 (m110) cc_final: 0.7951 (m-40)
REVERT: A 1138 LEU cc_start: 0.8183 (mm) cc_final: 0.7963 (mt)
  outliers start: 25
  outliers final: 16
  residues processed: 228
  average time/residue: 0.0941
  time to fit residues: 28.5385
Evaluate side-chains
  237 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 216
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 TRP
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  516 THR
Chi-restraints excluded: chain A residue  755 CYS
Chi-restraints excluded: chain A residue  785 ARG
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue  987 MET
Chi-restraints excluded: chain A residue  994 ASN
Chi-restraints excluded: chain A residue 1040 LEU
Chi-restraints excluded: chain A residue 1059 MET
Chi-restraints excluded: chain A residue 1108 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 84 optimal weight:    1.9990
   chunk 90 optimal weight:    8.9990
   chunk 39 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0770
   overall best weight:    1.5744

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

Flipped N/Q/H residues before XYZ refinement:
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1061 GLN
A1118 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.152466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.126086 restraints weight = 13939.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.130541 restraints weight = 6543.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.133465 restraints weight = 3904.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.135288 restraints weight = 2764.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.136552 restraints weight = 2225.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7054
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8125  Z= 0.190
  Angle     :  0.624   8.610  11024  Z= 0.312
  Chirality :  0.044   0.211   1280
  Planarity :  0.005   0.057   1398
  Dihedral  :  4.103  17.039   1086
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.57 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.68 %
    Favored  : 78.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.26), residues: 1012
  helix:  1.34 (0.24), residues: 452
  sheet: -0.25 (0.53), residues: 101
  loop :  0.14 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 829 
 TYR   0.016   0.001   TYR A 671 
 PHE   0.014   0.001   PHE A1087 
 TRP   0.053   0.002   TRP A 257 
 HIS   0.007   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 8125)
  covalent geometry    : angle       0.62443 (11024)
  hydrogen bonds       : bond        0.04522 (  400)
  hydrogen bonds       : angle       4.26654 ( 1146)

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 222
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 LYS cc_start: 0.8044 (mmtm) cc_final: 0.7625 (mttp)
REVERT: A  196 VAL cc_start: 0.8617 (t) cc_final: 0.8387 (m)
REVERT: A  272 MET cc_start: 0.7804 (tpt) cc_final: 0.7558 (tpt)
REVERT: A  276 PHE cc_start: 0.7574 (t80) cc_final: 0.6967 (t80)
REVERT: A  291 ILE cc_start: 0.5720 (OUTLIER) cc_final: 0.5344 (mt)
REVERT: A  349 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6823 (mt-10)
REVERT: A  362 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7489 (mp0)
REVERT: A  380 ARG cc_start: 0.7602 (mtp180) cc_final: 0.7063 (ttm-80)
REVERT: A  425 LYS cc_start: 0.7685 (mmtt) cc_final: 0.7328 (mttm)
REVERT: A  432 PHE cc_start: 0.6502 (m-10) cc_final: 0.6009 (m-10)
REVERT: A  444 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8436 (t)
REVERT: A  479 LEU cc_start: 0.8286 (tp) cc_final: 0.7999 (tp)
REVERT: A  592 LYS cc_start: 0.8454 (mmmm) cc_final: 0.8035 (mmmm)
REVERT: A  631 LYS cc_start: 0.8220 (mmpt) cc_final: 0.7931 (mmpt)
REVERT: A  633 MET cc_start: 0.6857 (tmm) cc_final: 0.6562 (tmm)
REVERT: A  675 HIS cc_start: 0.8080 (t-90) cc_final: 0.7804 (t-90)
REVERT: A  734 ARG cc_start: 0.7707 (tpp80) cc_final: 0.7336 (tpp80)
REVERT: A  773 GLN cc_start: 0.8270 (pm20) cc_final: 0.7557 (pm20)
REVERT: A  785 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6839 (ptp-110)
REVERT: A  816 LEU cc_start: 0.8398 (tt) cc_final: 0.8147 (tp)
REVERT: A  845 LYS cc_start: 0.8543 (mttm) cc_final: 0.8260 (mttm)
REVERT: A  853 LYS cc_start: 0.8164 (tttp) cc_final: 0.7333 (tppp)
REVERT: A  987 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7646 (mtm)
REVERT: A 1049 ILE cc_start: 0.8431 (tp) cc_final: 0.8060 (tt)
REVERT: A 1056 LEU cc_start: 0.8262 (tp) cc_final: 0.8012 (tt)
REVERT: A 1061 GLN cc_start: 0.6988 (mt0) cc_final: 0.6663 (mt0)
REVERT: A 1064 VAL cc_start: 0.8174 (OUTLIER) cc_final: 0.7941 (p)
REVERT: A 1108 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7350 (mmm)
REVERT: A 1115 PHE cc_start: 0.7265 (m-80) cc_final: 0.6954 (m-80)
REVERT: A 1118 ASN cc_start: 0.8485 (m-40) cc_final: 0.8108 (m-40)
REVERT: A 1138 LEU cc_start: 0.8223 (mm) cc_final: 0.7940 (mt)
  outliers start: 28
  outliers final: 16
  residues processed: 235
  average time/residue: 0.1038
  time to fit residues: 31.7987
Evaluate side-chains
  242 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 219
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 TRP
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  345 CYS
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  516 THR
Chi-restraints excluded: chain A residue  755 CYS
Chi-restraints excluded: chain A residue  785 ARG
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  987 MET
Chi-restraints excluded: chain A residue  994 ASN
Chi-restraints excluded: chain A residue  996 LEU
Chi-restraints excluded: chain A residue 1040 LEU
Chi-restraints excluded: chain A residue 1059 MET
Chi-restraints excluded: chain A residue 1064 VAL
Chi-restraints excluded: chain A residue 1108 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 58 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0980
   chunk 83 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.6188

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

Flipped N/Q/H residues before XYZ refinement:
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.151950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.125748 restraints weight = 13819.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.130112 restraints weight = 6506.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.132958 restraints weight = 3890.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.134574 restraints weight = 2756.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.135906 restraints weight = 2249.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   8125  Z= 0.196
  Angle     :  0.653  11.601  11024  Z= 0.325
  Chirality :  0.045   0.206   1280
  Planarity :  0.005   0.057   1398
  Dihedral  :  4.245  19.599   1086
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.77 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 19.59 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.26), residues: 1012
  helix:  1.31 (0.24), residues: 449
  sheet: -0.25 (0.53), residues: 101
  loop :  0.11 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 829 
 TYR   0.017   0.001   TYR A 671 
 PHE   0.021   0.001   PHE A1115 
 TRP   0.052   0.002   TRP A 257 
 HIS   0.007   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 8125)
  covalent geometry    : angle       0.65340 (11024)
  hydrogen bonds       : bond        0.04511 (  400)
  hydrogen bonds       : angle       4.29461 ( 1146)

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 221
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 VAL cc_start: 0.8614 (t) cc_final: 0.8389 (m)
REVERT: A  272 MET cc_start: 0.7811 (tpt) cc_final: 0.7561 (tpt)
REVERT: A  276 PHE cc_start: 0.7530 (t80) cc_final: 0.6935 (t80)
REVERT: A  291 ILE cc_start: 0.5654 (OUTLIER) cc_final: 0.5261 (mt)
REVERT: A  297 LYS cc_start: 0.8175 (tmtt) cc_final: 0.7682 (ttpp)
REVERT: A  349 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6763 (mt-10)
REVERT: A  362 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7490 (mp0)
REVERT: A  380 ARG cc_start: 0.7614 (mtp180) cc_final: 0.7074 (ttm-80)
REVERT: A  425 LYS cc_start: 0.7670 (mmtt) cc_final: 0.7342 (mttm)
REVERT: A  444 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8422 (t)
REVERT: A  479 LEU cc_start: 0.8309 (tp) cc_final: 0.8032 (tp)
REVERT: A  541 ASP cc_start: 0.7687 (t0) cc_final: 0.7446 (t0)
REVERT: A  592 LYS cc_start: 0.8443 (mmmm) cc_final: 0.8034 (mmmm)
REVERT: A  631 LYS cc_start: 0.8208 (mmpt) cc_final: 0.7873 (mmpt)
REVERT: A  633 MET cc_start: 0.6793 (tmm) cc_final: 0.6492 (tmm)
REVERT: A  675 HIS cc_start: 0.8072 (t-90) cc_final: 0.7786 (t-90)
REVERT: A  734 ARG cc_start: 0.7711 (tpp80) cc_final: 0.7347 (tpp80)
REVERT: A  785 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6735 (ptp-110)
REVERT: A  816 LEU cc_start: 0.8408 (tt) cc_final: 0.8177 (tp)
REVERT: A  845 LYS cc_start: 0.8554 (mttm) cc_final: 0.8287 (mtpp)
REVERT: A  853 LYS cc_start: 0.8200 (tttp) cc_final: 0.7532 (tptm)
REVERT: A  987 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7639 (mtm)
REVERT: A 1049 ILE cc_start: 0.8416 (tp) cc_final: 0.8061 (tt)
REVERT: A 1056 LEU cc_start: 0.8263 (tp) cc_final: 0.8006 (tt)
REVERT: A 1064 VAL cc_start: 0.8181 (OUTLIER) cc_final: 0.7951 (p)
REVERT: A 1108 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7444 (mmm)
REVERT: A 1138 LEU cc_start: 0.8073 (mm) cc_final: 0.7826 (mt)
REVERT: A 1192 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7660 (tm-30)
  outliers start: 25
  outliers final: 16
  residues processed: 231
  average time/residue: 0.1064
  time to fit residues: 32.3777
Evaluate side-chains
  242 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 219
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 TRP
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  345 CYS
Chi-restraints excluded: chain A residue  362 GLU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  516 THR
Chi-restraints excluded: chain A residue  755 CYS
Chi-restraints excluded: chain A residue  785 ARG
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  987 MET
Chi-restraints excluded: chain A residue  994 ASN
Chi-restraints excluded: chain A residue  996 LEU
Chi-restraints excluded: chain A residue 1040 LEU
Chi-restraints excluded: chain A residue 1059 MET
Chi-restraints excluded: chain A residue 1064 VAL
Chi-restraints excluded: chain A residue 1108 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 31 optimal weight:    0.0030
   chunk 74 optimal weight:    0.5980
   chunk 11 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0970
   chunk 3 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 741 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.155551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.129208 restraints weight = 13828.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.133673 restraints weight = 6573.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.136643 restraints weight = 3955.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.138304 restraints weight = 2803.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.139552 restraints weight = 2278.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
moved from start:          0.2882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8125  Z= 0.118
  Angle     :  0.635  11.327  11024  Z= 0.306
  Chirality :  0.042   0.183   1280
  Planarity :  0.004   0.057   1398
  Dihedral  :  4.041  19.262   1086
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.78 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 20.96 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.26), residues: 1012
  helix:  1.56 (0.24), residues: 447
  sheet: -0.27 (0.53), residues: 101
  loop :  0.19 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 310 
 TYR   0.017   0.001   TYR A 671 
 PHE   0.014   0.001   PHE A1087 
 TRP   0.060   0.002   TRP A 257 
 HIS   0.005   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8125)
  covalent geometry    : angle       0.63541 (11024)
  hydrogen bonds       : bond        0.03796 (  400)
  hydrogen bonds       : angle       4.13057 ( 1146)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1481.83 seconds
wall clock time: 26 minutes 19.61 seconds (1579.61 seconds total)