Starting phenix.real_space_refine
on Thu May  1 00:15:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8syn_40885/05_2025/8syn_40885.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8syn_40885/05_2025/8syn_40885.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8syn_40885/05_2025/8syn_40885.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8syn_40885/05_2025/8syn_40885.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8syn_40885/05_2025/8syn_40885.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8syn_40885/05_2025/8syn_40885.cif"
  }
  resolution = 2.94
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.018
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      62      5.16       5
     C    6487      2.51       5
     N    1695      2.21       5
     O    1825      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 10069
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6474
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 802, 6474
          Classifications: {'peptide': 802}
          Link IDs: {'PTRANS': 31, 'TRANS': 770}
          Chain breaks: 3
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 1463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1463
          Classifications: {'peptide': 184}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 175}
    Chain: "C"
      Number of atoms: 2132
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2132
          Classifications: {'peptide': 273}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 15, 'TRANS': 257}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 5.92, per 1000 atoms: 0.59
  Number of scatterers: 10069
  At special positions: 0
  Unit cell: (78.6176, 108.365, 172.109, 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      62     16.00
     O    1825      8.00
     N    1695      7.00
     C    6487      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: 2.33
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2410

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 10 sheets defined
      53.5% alpha, 20.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 21
    Processing helix  chain 'A' and resid 116 through 128
      removed outlier: 3.805A  pdb=" N   LYS A 120 " --> pdb=" O   PRO A 116 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   GLY A 122 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLU A 123 " --> pdb=" O   ASN A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 201
    Processing helix  chain 'A' and resid 203 through 218
      removed outlier: 3.731A  pdb=" N   LEU A 218 " --> pdb=" O   CYS A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 225
      No H-bonds generated for 'chain 'A' and resid 223 through 225'
    Processing helix  chain 'A' and resid 226 through 254
      removed outlier: 3.628A  pdb=" N   ASP A 236 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ILE A 237 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ARG A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 286
    Processing helix  chain 'A' and resid 289 through 300
      removed outlier: 3.647A  pdb=" N   ILE A 300 " --> pdb=" O   VAL A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 307
    Processing helix  chain 'A' and resid 310 through 323
      Proline residue:  A 317  - end of helix
    Processing helix  chain 'A' and resid 324 through 326
      No H-bonds generated for 'chain 'A' and resid 324 through 326'
    Processing helix  chain 'A' and resid 328 through 347
    Processing helix  chain 'A' and resid 350 through 365
      removed outlier: 4.224A  pdb=" N   LYS A 356 " --> pdb=" O   GLU A 352 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ASN A 357 " --> pdb=" O   THR A 353 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   PHE A 358 " --> pdb=" O   LEU A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 368
      No H-bonds generated for 'chain 'A' and resid 366 through 368'
    Processing helix  chain 'A' and resid 370 through 381
    Processing helix  chain 'A' and resid 383 through 388
    Processing helix  chain 'A' and resid 391 through 403
      removed outlier: 4.004A  pdb=" N   TRP A 397 " --> pdb=" O   PRO A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 420
    Processing helix  chain 'A' and resid 424 through 435
      removed outlier: 3.666A  pdb=" N   ASN A 429 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   SER A 430 " --> pdb=" O   LEU A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 443
    Processing helix  chain 'A' and resid 443 through 453
      removed outlier: 3.666A  pdb=" N   GLU A 453 " --> pdb=" O   GLY A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 473
      removed outlier: 3.885A  pdb=" N   LEU A 464 " --> pdb=" O   PRO A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 480
      No H-bonds generated for 'chain 'A' and resid 478 through 480'
    Processing helix  chain 'A' and resid 481 through 494
      removed outlier: 3.569A  pdb=" N   VAL A 492 " --> pdb=" O   GLU A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 517
      removed outlier: 3.879A  pdb=" N   VAL A 508 " --> pdb=" O   ASN A 504 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   GLU A 511 " --> pdb=" O   GLU A 507 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   TYR A 512 " --> pdb=" O   VAL A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 534
    Processing helix  chain 'A' and resid 537 through 541
      removed outlier: 3.805A  pdb=" N   GLU A 540 " --> pdb=" O   ARG A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 556
    Processing helix  chain 'A' and resid 559 through 564
      removed outlier: 3.689A  pdb=" N   PHE A 564 " --> pdb=" O   PHE A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 576
      removed outlier: 4.008A  pdb=" N   PHE A 576 " --> pdb=" O   PHE A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 596
      removed outlier: 3.607A  pdb=" N   GLU A 584 " --> pdb=" O   SER A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 619
    Processing helix  chain 'A' and resid 626 through 643
      removed outlier: 3.773A  pdb=" N   MET A 643 " --> pdb=" O   GLY A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 649 through 664
    Processing helix  chain 'A' and resid 667 through 689
    Processing helix  chain 'A' and resid 694 through 712
      removed outlier: 3.736A  pdb=" N   ALA A 699 " --> pdb=" O   ARG A 695 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   PHE A 700 " --> pdb=" O   LYS A 696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 715
      No H-bonds generated for 'chain 'A' and resid 713 through 715'
    Processing helix  chain 'A' and resid 717 through 734
    Processing helix  chain 'A' and resid 738 through 752
    Processing helix  chain 'A' and resid 753 through 755
      No H-bonds generated for 'chain 'A' and resid 753 through 755'
    Processing helix  chain 'A' and resid 768 through 784
    Processing helix  chain 'A' and resid 795 through 808
    Processing helix  chain 'A' and resid 815 through 832
      removed outlier: 3.587A  pdb=" N   ARG A 819 " --> pdb=" O   ASP A 815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 850
    Processing helix  chain 'A' and resid 853 through 881
    Processing helix  chain 'A' and resid 883 through 901
    Processing helix  chain 'A' and resid 906 through 923
      removed outlier: 3.633A  pdb=" N   HIS A 923 " --> pdb=" O   LEU A 919 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 30
      removed outlier: 3.602A  pdb=" N   LYS B  27 " --> pdb=" O   PRO B  23 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LYS B  28 " --> pdb=" O   ALA B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 55
      removed outlier: 3.784A  pdb=" N   TYR B  50 " --> pdb=" O   THR B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 111
    Processing helix  chain 'C' and resid 166 through 171
      removed outlier: 3.862A  pdb=" N   ALA C 171 " --> pdb=" O   VAL C 167 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26
      removed outlier: 3.589A  pdb=" N   ARG B 180 " --> pdb=" O   VAL A  25 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 758 through 761
    Processing sheet with id=AA3, first strand: chain 'B' and resid 76 through 81
      removed outlier: 6.530A  pdb=" N   LYS B  85 " --> pdb=" O   ILE B 114 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   ILE B 116 " --> pdb=" O   LYS B  85 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   GLY B  87 " --> pdb=" O   ILE B 116 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE B 134 " --> pdb=" O   LEU B 115 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SER B 117 " --> pdb=" O   ILE B 134 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 9
    Processing sheet with id=AA5, first strand: chain 'C' and resid 15 through 16
    Processing sheet with id=AA6, first strand: chain 'C' and resid 69 through 79
      removed outlier: 5.878A  pdb=" N   GLN C  70 " --> pdb=" O   VAL C  47 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   VAL C  47 " --> pdb=" O   GLN C  70 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE C  72 " --> pdb=" O   GLY C  45 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   VAL C  39 " --> pdb=" O   MET C  78 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 69 through 79
      removed outlier: 5.878A  pdb=" N   GLN C  70 " --> pdb=" O   VAL C  47 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   VAL C  47 " --> pdb=" O   GLN C  70 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE C  72 " --> pdb=" O   GLY C  45 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   VAL C  39 " --> pdb=" O   MET C  78 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 155 through 159
      removed outlier: 6.726A  pdb=" N   LEU C 177 " --> pdb=" O   GLU C 200 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 226 through 239
      removed outlier: 6.962A  pdb=" N   LEU C 213 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   ASN C 234 " --> pdb=" O   LEU C 211 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   LEU C 211 " --> pdb=" O   ASN C 234 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   GLN C 236 " --> pdb=" O   VAL C 209 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   VAL C 209 " --> pdb=" O   GLN C 236 " (cutoff:3.500A)
      removed outlier: 7.159A  pdb=" N   ALA C 238 " --> pdb=" O   ARG C 207 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ARG C 207 " --> pdb=" O   ALA C 238 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 226 through 239
      removed outlier: 6.962A  pdb=" N   LEU C 213 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   ASN C 234 " --> pdb=" O   LEU C 211 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   LEU C 211 " --> pdb=" O   ASN C 234 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   GLN C 236 " --> pdb=" O   VAL C 209 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   VAL C 209 " --> pdb=" O   GLN C 236 " (cutoff:3.500A)
      removed outlier: 7.159A  pdb=" N   ALA C 238 " --> pdb=" O   ARG C 207 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ARG C 207 " --> pdb=" O   ALA C 238 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   PHE C 272 " --> pdb=" O   LEU C 292 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   HIS C 284 " --> pdb=" O   LEU C 280 " (cutoff:3.500A)

    610 hydrogen bonds defined for protein.
    1761 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: 3.75

  Time building geometry restraints manager: 2.84 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: 3228
        1.34 -     1.46: 1988
        1.46 -     1.58: 4977
        1.58 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 10283
  Sorted by residual:
  bond pdb=" CG1 ILE A 712 "
       pdb=" CD1 ILE A 712 "
    ideal  model  delta    sigma   weight residual
    1.513  1.444  0.069 3.90e-02 6.57e+02 3.11e+00
  bond pdb=" CA  ILE A 712 "
       pdb=" CB  ILE A 712 "
    ideal  model  delta    sigma   weight residual
    1.539  1.547 -0.008 5.40e-03 3.43e+04 2.09e+00
  bond pdb=" N   ILE A 712 "
       pdb=" CA  ILE A 712 "
    ideal  model  delta    sigma   weight residual
    1.463  1.478 -0.015 1.20e-02 6.94e+03 1.55e+00
  bond pdb=" C   THR A 534 "
       pdb=" N   PRO A 535 "
    ideal  model  delta    sigma   weight residual
    1.334  1.361 -0.027 2.34e-02 1.83e+03 1.36e+00
  bond pdb=" SD  MET A 395 "
       pdb=" CE  MET A 395 "
    ideal  model  delta    sigma   weight residual
    1.791  1.762  0.029 2.50e-02 1.60e+03 1.34e+00
  ... (remaining 10278 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 13658
        1.95 -     3.90: 222
        3.90 -     5.85: 34
        5.85 -     7.80: 4
        7.80 -     9.75: 2
  Bond angle restraints: 13920
  Sorted by residual:
  angle pdb=" N   ILE A 712 "
        pdb=" CA  ILE A 712 "
        pdb=" CB  ILE A 712 "
      ideal   model   delta    sigma   weight residual
     110.45  115.92   -5.47 7.80e-01 1.64e+00 4.91e+01
  angle pdb=" C   ILE A 712 "
        pdb=" CA  ILE A 712 "
        pdb=" CB  ILE A 712 "
      ideal   model   delta    sigma   weight residual
     114.00  106.87    7.13 1.31e+00 5.83e-01 2.96e+01
  angle pdb=" C   LEU B  44 "
        pdb=" N   CYS B  45 "
        pdb=" CA  CYS B  45 "
      ideal   model   delta    sigma   weight residual
     121.54  129.09   -7.55 1.91e+00 2.74e-01 1.56e+01
  angle pdb=" CB  LYS A 602 "
        pdb=" CG  LYS A 602 "
        pdb=" CD  LYS A 602 "
      ideal   model   delta    sigma   weight residual
     111.30  103.21    8.09 2.30e+00 1.89e-01 1.24e+01
  angle pdb=" CB  MET A 533 "
        pdb=" CG  MET A 533 "
        pdb=" SD  MET A 533 "
      ideal   model   delta    sigma   weight residual
     112.70  102.95    9.75 3.00e+00 1.11e-01 1.06e+01
  ... (remaining 13915 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 5653
       17.65 -    35.31: 473
       35.31 -    52.96: 67
       52.96 -    70.61: 8
       70.61 -    88.27: 9
  Dihedral angle restraints: 6210
    sinusoidal: 2513
      harmonic: 3697
  Sorted by residual:
  dihedral pdb=" CA  CYS A 737 "
           pdb=" C   CYS A 737 "
           pdb=" N   LEU A 738 "
           pdb=" CA  LEU A 738 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.24  -18.76     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  GLY C 148 "
           pdb=" C   GLY C 148 "
           pdb=" N   LYS C 149 "
           pdb=" CA  LYS C 149 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.28   18.72     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  PRO A 535 "
           pdb=" C   PRO A 535 "
           pdb=" N   ASP A 536 "
           pdb=" CA  ASP A 536 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.34  -17.66     0      5.00e+00 4.00e-02 1.25e+01
  ... (remaining 6207 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1131
       0.040 -    0.080: 318
       0.080 -    0.120: 130
       0.120 -    0.160: 23
       0.160 -    0.199: 1
  Chirality restraints: 1603
  Sorted by residual:
  chirality pdb=" CB  ILE A 718 "
            pdb=" CA  ILE A 718 "
            pdb=" CG1 ILE A 718 "
            pdb=" CG2 ILE A 718 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.95e-01
  chirality pdb=" CA  MET A 533 "
            pdb=" N   MET A 533 "
            pdb=" C   MET A 533 "
            pdb=" CB  MET A 533 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.82e-01
  chirality pdb=" CA  PRO A 535 "
            pdb=" N   PRO A 535 "
            pdb=" C   PRO A 535 "
            pdb=" CB  PRO A 535 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.75e-01
  ... (remaining 1600 not shown)

  Planarity restraints: 1761
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 384 "   -0.055 5.00e-02 4.00e+02   8.35e-02 1.11e+01
        pdb=" N   PRO A 385 "    0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO A 385 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 385 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 821 "   -0.019 2.00e-02 2.50e+03   1.65e-02 5.45e+00
        pdb=" CG  TYR A 821 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 821 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 821 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 821 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 821 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 821 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 821 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 534 "   -0.032 5.00e-02 4.00e+02   4.83e-02 3.74e+00
        pdb=" N   PRO A 535 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 535 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 535 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1758 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 453
        2.73 -     3.27: 10483
        3.27 -     3.81: 16677
        3.81 -     4.36: 19664
        4.36 -     4.90: 33992
  Nonbonded interactions: 81269
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B  25 "
            pdb=" O   ASP B 174 "
     model   vdw
     2.182 3.120
  nonbonded pdb=" OH  TYR A 387 "
            pdb=" OH  TYR A 391 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OE2 GLU A 297 "
            pdb=" NH2 ARG A 318 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" O   PRO A  34 "
            pdb=" NZ  LYS B  34 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" O   PHE A 656 "
            pdb=" OG  SER A 660 "
     model   vdw
     2.232 3.040
  ... (remaining 81264 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     25.840
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:15.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6791
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  10283  Z= 0.167
  Angle     :  0.625   9.753  13920  Z= 0.341
  Chirality :  0.044   0.199   1603
  Planarity :  0.005   0.083   1761
  Dihedral  : 13.189  88.268   3800
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.25), residues: 1237
  helix:  1.23 (0.21), residues: 597
  sheet:  0.19 (0.38), residues: 197
  loop :  0.04 (0.32), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 490 
 HIS   0.014   0.001   HIS A 596 
 PHE   0.024   0.002   PHE C  93 
 TYR   0.041   0.002   TYR A 821 
 ARG   0.003   0.000   ARG A 318 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13598 (  575)
  hydrogen bonds       : angle       6.51715 ( 1761)
  covalent geometry    : bond        0.00387 (10283)
  covalent geometry    : angle       0.62483 (13920)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 264
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  206 LYS cc_start: 0.7396 (tttt) cc_final: 0.7129 (tttp)
REVERT: A  344 MET cc_start: 0.8505 (mmt) cc_final: 0.8076 (mpp)
REVERT: A  366 LYS cc_start: 0.7729 (tptp) cc_final: 0.7400 (tppt)
REVERT: A  488 GLU cc_start: 0.7811 (tp30) cc_final: 0.7489 (mm-30)
REVERT: A  514 CYS cc_start: 0.7977 (m) cc_final: 0.7600 (m)
REVERT: A  584 GLU cc_start: 0.6888 (tm-30) cc_final: 0.6471 (tm-30)
REVERT: A  595 LYS cc_start: 0.8420 (tmmt) cc_final: 0.8215 (tmmm)
REVERT: A  599 GLU cc_start: 0.7619 (pm20) cc_final: 0.7386 (mp0)
REVERT: A  630 LYS cc_start: 0.7670 (mttp) cc_final: 0.7330 (mtmm)
REVERT: A  659 GLU cc_start: 0.6575 (pp20) cc_final: 0.6102 (tm-30)
REVERT: A  868 MET cc_start: 0.5468 (mtm) cc_final: 0.4972 (mtm)
REVERT: B   43 ASN cc_start: 0.7578 (m110) cc_final: 0.7253 (m110)
REVERT: C   14 LYS cc_start: 0.8518 (mtmt) cc_final: 0.8299 (mtmt)
REVERT: C   44 GLU cc_start: 0.8046 (tt0) cc_final: 0.7820 (tt0)
REVERT: C  175 LYS cc_start: 0.8205 (mppt) cc_final: 0.7831 (mppt)
REVERT: C  176 PHE cc_start: 0.7972 (p90) cc_final: 0.7755 (p90)
REVERT: C  231 GLU cc_start: 0.7546 (pt0) cc_final: 0.7304 (pt0)
REVERT: C  269 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7895 (mtmm)
  outliers start: 0
  outliers final: 0
  residues processed: 264
  average time/residue: 1.1509
  time to fit residues: 327.4449
Evaluate side-chains
  238 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 105 optimal weight:    0.5980
   chunk 94 optimal weight:    0.4980
   chunk 52 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0770
   chunk 50 optimal weight:    5.9990
   chunk 97 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0670
   chunk 59 optimal weight:    0.0570
   chunk 72 optimal weight:   30.0000
   chunk 113 optimal weight:    0.6980
   overall best weight:    0.2594

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

Flipped N/Q/H residues before XYZ refinement:
A 727 HIS
A 778 ASN
C 115 ASN
C 117 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.176487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.149125 restraints weight = 15634.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3896 rms_B_bonded: 2.42
r_work: 0.3751 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start:          0.1264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  10283  Z= 0.134
  Angle     :  0.604   8.179  13920  Z= 0.309
  Chirality :  0.044   0.144   1603
  Planarity :  0.004   0.061   1761
  Dihedral  :  4.269  19.212   1338
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 10.18 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.25), residues: 1237
  helix:  1.60 (0.21), residues: 624
  sheet:  0.48 (0.39), residues: 197
  loop :  0.05 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 810 
 HIS   0.009   0.001   HIS B  90 
 PHE   0.025   0.002   PHE A 796 
 TYR   0.028   0.002   TYR B  73 
 ARG   0.006   0.000   ARG A 819 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04171 (  575)
  hydrogen bonds       : angle       4.85701 ( 1761)
  covalent geometry    : bond        0.00311 (10283)
  covalent geometry    : angle       0.60449 (13920)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 250
  time to evaluate  : 1.017 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 ASP cc_start: 0.7684 (t0) cc_final: 0.7421 (t0)
REVERT: A  344 MET cc_start: 0.8693 (mmt) cc_final: 0.8330 (tpp)
REVERT: A  366 LYS cc_start: 0.7833 (tptp) cc_final: 0.7546 (tppt)
REVERT: A  395 MET cc_start: 0.8089 (mtt) cc_final: 0.7888 (mtp)
REVERT: A  419 LYS cc_start: 0.8126 (ttpt) cc_final: 0.7874 (ttmt)
REVERT: A  488 GLU cc_start: 0.7653 (tp30) cc_final: 0.7380 (mm-30)
REVERT: A  514 CYS cc_start: 0.7845 (m) cc_final: 0.7485 (m)
REVERT: A  584 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6701 (tm-30)
REVERT: A  595 LYS cc_start: 0.8739 (tmmt) cc_final: 0.8305 (tmmm)
REVERT: A  596 HIS cc_start: 0.8302 (m170) cc_final: 0.8080 (m-70)
REVERT: A  630 LYS cc_start: 0.7886 (mttp) cc_final: 0.7678 (mtmm)
REVERT: A  652 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6746 (tp-100)
REVERT: A  659 GLU cc_start: 0.6660 (pp20) cc_final: 0.6187 (tm-30)
REVERT: A  661 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7869 (ttm110)
REVERT: A  684 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6921 (mm-30)
REVERT: A  868 MET cc_start: 0.7413 (mtm) cc_final: 0.6284 (mtm)
REVERT: B   12 ASP cc_start: 0.8331 (m-30) cc_final: 0.8122 (m-30)
REVERT: B  176 VAL cc_start: 0.8077 (OUTLIER) cc_final: 0.7819 (m)
REVERT: C   14 LYS cc_start: 0.8600 (mtmt) cc_final: 0.8356 (mtmt)
REVERT: C   43 MET cc_start: 0.7995 (tmm) cc_final: 0.7706 (ttm)
REVERT: C  175 LYS cc_start: 0.8115 (mppt) cc_final: 0.7726 (mppt)
REVERT: C  269 LYS cc_start: 0.8216 (mtmm) cc_final: 0.7928 (mtmm)
  outliers start: 19
  outliers final: 8
  residues processed: 258
  average time/residue: 1.2016
  time to fit residues: 336.3315
Evaluate side-chains
  240 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 229
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  561 SER
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  652 GLN
Chi-restraints excluded: chain A residue  661 ARG
Chi-restraints excluded: chain A residue  822 THR
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain C residue  277 VAL
Chi-restraints excluded: chain C residue  289 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0870
   chunk 71 optimal weight:    4.9990
   chunk 94 optimal weight:    0.0170
   chunk 36 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 100 optimal weight:    0.8980
   chunk 64 optimal weight:    0.1980
   chunk 54 optimal weight:    0.9980
   chunk 110 optimal weight:    2.9990
   overall best weight:    0.3996

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

Flipped N/Q/H residues before XYZ refinement:
A 516 HIS
A 727 HIS
** B  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 115 ASN
C 186 ASN
C 234 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.176254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.148428 restraints weight = 15884.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3889 rms_B_bonded: 2.47
r_work: 0.3741 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10283  Z= 0.141
  Angle     :  0.587   8.672  13920  Z= 0.300
  Chirality :  0.043   0.154   1603
  Planarity :  0.004   0.052   1761
  Dihedral  :  4.208  18.575   1338
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 13.72 %
    Favored  : 84.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.25), residues: 1237
  helix:  1.75 (0.21), residues: 626
  sheet:  0.45 (0.39), residues: 197
  loop :  0.07 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 490 
 HIS   0.006   0.001   HIS B  90 
 PHE   0.037   0.002   PHE A 796 
 TYR   0.027   0.002   TYR B  73 
 ARG   0.008   0.000   ARG A 819 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03932 (  575)
  hydrogen bonds       : angle       4.64810 ( 1761)
  covalent geometry    : bond        0.00334 (10283)
  covalent geometry    : angle       0.58683 (13920)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 244
  time to evaluate  : 1.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  366 LYS cc_start: 0.7840 (tptp) cc_final: 0.7556 (tppt)
REVERT: A  375 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7634 (m-40)
REVERT: A  419 LYS cc_start: 0.8137 (ttpt) cc_final: 0.7843 (ttmp)
REVERT: A  488 GLU cc_start: 0.7747 (tp30) cc_final: 0.7473 (mm-30)
REVERT: A  574 ASP cc_start: 0.7533 (t70) cc_final: 0.7306 (t0)
REVERT: A  584 GLU cc_start: 0.7058 (tm-30) cc_final: 0.6629 (tm-30)
REVERT: A  595 LYS cc_start: 0.8765 (tmmt) cc_final: 0.8394 (tmmm)
REVERT: A  596 HIS cc_start: 0.8278 (m170) cc_final: 0.7949 (m-70)
REVERT: A  630 LYS cc_start: 0.7931 (mttp) cc_final: 0.7689 (mtmm)
REVERT: A  659 GLU cc_start: 0.6708 (pp20) cc_final: 0.6320 (tm-30)
REVERT: A  683 MET cc_start: 0.7892 (mmm) cc_final: 0.7627 (mmp)
REVERT: A  684 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6946 (mm-30)
REVERT: A  686 ARG cc_start: 0.7226 (tmm160) cc_final: 0.6984 (tmm160)
REVERT: A  819 ARG cc_start: 0.7604 (mpp80) cc_final: 0.7399 (mpp80)
REVERT: A  868 MET cc_start: 0.7451 (mtm) cc_final: 0.6328 (mtm)
REVERT: B  105 LEU cc_start: 0.8520 (mp) cc_final: 0.8307 (tp)
REVERT: B  122 LYS cc_start: 0.8098 (tmmt) cc_final: 0.7752 (tmmt)
REVERT: B  131 LYS cc_start: 0.7684 (mmmt) cc_final: 0.7330 (mmmm)
REVERT: B  133 TYR cc_start: 0.7711 (m-80) cc_final: 0.7456 (m-80)
REVERT: C   14 LYS cc_start: 0.8607 (mtmt) cc_final: 0.8379 (mtmt)
REVERT: C   43 MET cc_start: 0.7996 (tmm) cc_final: 0.7724 (ttm)
REVERT: C  175 LYS cc_start: 0.8089 (mppt) cc_final: 0.7689 (mppt)
REVERT: C  269 LYS cc_start: 0.8211 (mtmm) cc_final: 0.7909 (mtmm)
  outliers start: 23
  outliers final: 12
  residues processed: 254
  average time/residue: 1.1311
  time to fit residues: 310.5738
Evaluate side-chains
  247 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 234
  time to evaluate  : 1.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  356 LYS
Chi-restraints excluded: chain A residue  375 ASN
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  765 MET
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  822 THR
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain C residue   91 ILE
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain C residue  277 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 60 optimal weight:    0.4980
   chunk 0 optimal weight:   80.0000
   chunk 78 optimal weight:   10.0000
   chunk 68 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 81 optimal weight:    0.0000
   chunk 117 optimal weight:    1.9990
   chunk 99 optimal weight:    0.8980
   overall best weight:    0.5984

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

Flipped N/Q/H residues before XYZ refinement:
A 608 ASN
A 727 HIS
A 911 GLN
C 115 ASN
C 186 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.175226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.147470 restraints weight = 15843.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3884 rms_B_bonded: 2.45
r_work: 0.3733 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  10283  Z= 0.169
  Angle     :  0.596  12.313  13920  Z= 0.303
  Chirality :  0.044   0.175   1603
  Planarity :  0.004   0.050   1761
  Dihedral  :  4.220  19.372   1338
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.84 %
    Favored  : 81.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.25), residues: 1237
  helix:  1.78 (0.21), residues: 628
  sheet:  0.41 (0.39), residues: 199
  loop :  0.10 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 490 
 HIS   0.006   0.001   HIS B  90 
 PHE   0.044   0.002   PHE A 796 
 TYR   0.025   0.002   TYR B 143 
 ARG   0.003   0.000   ARG C  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03976 (  575)
  hydrogen bonds       : angle       4.62472 ( 1761)
  covalent geometry    : bond        0.00400 (10283)
  covalent geometry    : angle       0.59640 (13920)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 239
  time to evaluate  : 1.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 SER cc_start: 0.8082 (t) cc_final: 0.7788 (t)
REVERT: A  202 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7389 (t0)
REVERT: A  249 ILE cc_start: 0.8428 (mp) cc_final: 0.8227 (mt)
REVERT: A  366 LYS cc_start: 0.7867 (tptp) cc_final: 0.7579 (tppt)
REVERT: A  416 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7195 (mm-30)
REVERT: A  419 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7955 (ttmt)
REVERT: A  488 GLU cc_start: 0.7775 (tp30) cc_final: 0.7506 (mm-30)
REVERT: A  567 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7435 (mp0)
REVERT: A  574 ASP cc_start: 0.7570 (t70) cc_final: 0.7319 (t0)
REVERT: A  584 GLU cc_start: 0.7098 (tm-30) cc_final: 0.6635 (tm-30)
REVERT: A  590 MET cc_start: 0.8428 (mmm) cc_final: 0.8046 (tpt)
REVERT: A  595 LYS cc_start: 0.8789 (tmmt) cc_final: 0.8162 (tppp)
REVERT: A  630 LYS cc_start: 0.7948 (mttp) cc_final: 0.7700 (mtmm)
REVERT: A  659 GLU cc_start: 0.6874 (pp20) cc_final: 0.6413 (tm-30)
REVERT: A  661 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7728 (ttm110)
REVERT: A  771 PHE cc_start: 0.8769 (m-80) cc_final: 0.8492 (m-80)
REVERT: A  800 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7551 (mp0)
REVERT: A  819 ARG cc_start: 0.7575 (mpp80) cc_final: 0.7157 (mpp80)
REVERT: A  868 MET cc_start: 0.7354 (mtm) cc_final: 0.6242 (mtm)
REVERT: B  105 LEU cc_start: 0.8559 (mp) cc_final: 0.8344 (tp)
REVERT: B  122 LYS cc_start: 0.8124 (tmmt) cc_final: 0.7692 (tmmt)
REVERT: B  133 TYR cc_start: 0.7736 (m-80) cc_final: 0.7505 (m-80)
REVERT: C   95 PHE cc_start: 0.8262 (m-80) cc_final: 0.7975 (m-80)
REVERT: C  175 LYS cc_start: 0.8077 (mppt) cc_final: 0.7684 (mppt)
REVERT: C  176 PHE cc_start: 0.8361 (p90) cc_final: 0.8112 (p90)
REVERT: C  269 LYS cc_start: 0.8193 (mtmm) cc_final: 0.7923 (mtmm)
  outliers start: 25
  outliers final: 12
  residues processed: 246
  average time/residue: 1.1345
  time to fit residues: 300.8212
Evaluate side-chains
  252 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 237
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  202 ASP
Chi-restraints excluded: chain A residue  356 LYS
Chi-restraints excluded: chain A residue  534 THR
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  661 ARG
Chi-restraints excluded: chain A residue  765 MET
Chi-restraints excluded: chain A residue  800 GLU
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain C residue   91 ILE
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  217 GLU
Chi-restraints excluded: chain C residue  277 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 101 optimal weight:    0.6980
   chunk 86 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   chunk 76 optimal weight:   40.0000
   chunk 59 optimal weight:    0.0980
   chunk 115 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 727 HIS
B 170 GLN
C 115 ASN
C 186 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.174420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.146734 restraints weight = 15711.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3868 rms_B_bonded: 2.45
r_work: 0.3718 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  10283  Z= 0.179
  Angle     :  0.606  10.034  13920  Z= 0.307
  Chirality :  0.044   0.154   1603
  Planarity :  0.004   0.047   1761
  Dihedral  :  4.247  18.499   1338
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 16.99 %
    Favored  : 80.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.25), residues: 1237
  helix:  1.80 (0.21), residues: 625
  sheet:  0.36 (0.39), residues: 199
  loop :  0.18 (0.33), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 490 
 HIS   0.006   0.001   HIS A 596 
 PHE   0.031   0.002   PHE A 796 
 TYR   0.026   0.002   TYR B 143 
 ARG   0.004   0.000   ARG A 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03977 (  575)
  hydrogen bonds       : angle       4.58545 ( 1761)
  covalent geometry    : bond        0.00426 (10283)
  covalent geometry    : angle       0.60631 (13920)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 243
  time to evaluate  : 1.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 SER cc_start: 0.8065 (t) cc_final: 0.7763 (t)
REVERT: A  202 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7374 (t0)
REVERT: A  366 LYS cc_start: 0.7851 (tptp) cc_final: 0.7575 (tppt)
REVERT: A  416 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7220 (mp0)
REVERT: A  419 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7937 (ttmt)
REVERT: A  488 GLU cc_start: 0.7848 (tp30) cc_final: 0.7594 (mm-30)
REVERT: A  574 ASP cc_start: 0.7581 (t70) cc_final: 0.7332 (t0)
REVERT: A  584 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6597 (tm-30)
REVERT: A  590 MET cc_start: 0.8429 (mmm) cc_final: 0.8017 (tpt)
REVERT: A  595 LYS cc_start: 0.8784 (tmmt) cc_final: 0.8199 (tppp)
REVERT: A  630 LYS cc_start: 0.8010 (mttp) cc_final: 0.7742 (mtmm)
REVERT: A  659 GLU cc_start: 0.6972 (pp20) cc_final: 0.6532 (tm-30)
REVERT: A  661 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7778 (ttm110)
REVERT: A  666 ASN cc_start: 0.7513 (t0) cc_final: 0.7235 (t0)
REVERT: A  684 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7066 (mt-10)
REVERT: A  868 MET cc_start: 0.7343 (mtm) cc_final: 0.6236 (mtm)
REVERT: B  122 LYS cc_start: 0.8120 (tmmt) cc_final: 0.7647 (tmmt)
REVERT: C   95 PHE cc_start: 0.8280 (m-80) cc_final: 0.8028 (m-80)
REVERT: C  175 LYS cc_start: 0.8088 (mppt) cc_final: 0.7796 (mppt)
REVERT: C  176 PHE cc_start: 0.8374 (p90) cc_final: 0.8046 (p90)
REVERT: C  203 GLU cc_start: 0.7828 (tt0) cc_final: 0.7159 (tt0)
REVERT: C  269 LYS cc_start: 0.8195 (mtmm) cc_final: 0.7924 (mtmm)
  outliers start: 29
  outliers final: 17
  residues processed: 250
  average time/residue: 1.1754
  time to fit residues: 316.0562
Evaluate side-chains
  256 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 237
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  202 ASP
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  534 THR
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  652 GLN
Chi-restraints excluded: chain A residue  661 ARG
Chi-restraints excluded: chain A residue  765 MET
Chi-restraints excluded: chain A residue  822 THR
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   91 ILE
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain C residue  217 GLU
Chi-restraints excluded: chain C residue  277 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 62 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0050
   chunk 122 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0980
   chunk 80 optimal weight:    0.9980
   chunk 94 optimal weight:    0.0670
   chunk 112 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.3532

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

Flipped N/Q/H residues before XYZ refinement:
A 471 ASN
A 516 HIS
A 727 HIS
C 115 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.176123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.148435 restraints weight = 15817.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3888 rms_B_bonded: 2.47
r_work: 0.3739 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10283  Z= 0.134
  Angle     :  0.594  10.047  13920  Z= 0.300
  Chirality :  0.043   0.155   1603
  Planarity :  0.004   0.046   1761
  Dihedral  :  4.199  20.575   1338
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 19.20 %
    Favored  : 78.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.25), residues: 1237
  helix:  1.88 (0.21), residues: 627
  sheet:  0.39 (0.38), residues: 199
  loop :  0.15 (0.33), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 490 
 HIS   0.005   0.001   HIS B  90 
 PHE   0.020   0.002   PHE A 745 
 TYR   0.022   0.002   TYR B 143 
 ARG   0.006   0.000   ARG A 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03709 (  575)
  hydrogen bonds       : angle       4.50064 ( 1761)
  covalent geometry    : bond        0.00315 (10283)
  covalent geometry    : angle       0.59417 (13920)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 241
  time to evaluate  : 1.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 SER cc_start: 0.7972 (t) cc_final: 0.7668 (t)
REVERT: A  366 LYS cc_start: 0.7879 (tptp) cc_final: 0.7594 (tppt)
REVERT: A  416 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7230 (mm-30)
REVERT: A  419 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7930 (ttmt)
REVERT: A  488 GLU cc_start: 0.7793 (tp30) cc_final: 0.7523 (mm-30)
REVERT: A  574 ASP cc_start: 0.7562 (t70) cc_final: 0.7321 (t0)
REVERT: A  584 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6573 (tm-30)
REVERT: A  595 LYS cc_start: 0.8742 (tmmt) cc_final: 0.8270 (tttm)
REVERT: A  630 LYS cc_start: 0.7995 (mttp) cc_final: 0.7644 (mtmm)
REVERT: A  659 GLU cc_start: 0.6988 (pp20) cc_final: 0.6566 (tm-30)
REVERT: A  666 ASN cc_start: 0.7338 (t0) cc_final: 0.7057 (t0)
REVERT: A  684 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7054 (mt-10)
REVERT: A  686 ARG cc_start: 0.7416 (tmm160) cc_final: 0.7187 (tmm160)
REVERT: A  771 PHE cc_start: 0.8775 (m-80) cc_final: 0.8495 (m-80)
REVERT: A  800 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8046 (mm-30)
REVERT: A  819 ARG cc_start: 0.7578 (mpp80) cc_final: 0.7214 (mpp80)
REVERT: A  868 MET cc_start: 0.7365 (mtm) cc_final: 0.6255 (mtm)
REVERT: C   95 PHE cc_start: 0.8176 (m-80) cc_final: 0.7943 (m-80)
REVERT: C  175 LYS cc_start: 0.8088 (mppt) cc_final: 0.7791 (mppt)
REVERT: C  176 PHE cc_start: 0.8360 (p90) cc_final: 0.8065 (p90)
REVERT: C  203 GLU cc_start: 0.7797 (tt0) cc_final: 0.7140 (tt0)
REVERT: C  269 LYS cc_start: 0.8162 (mtmm) cc_final: 0.7892 (mtmm)
REVERT: C  285 LEU cc_start: 0.8736 (tp) cc_final: 0.8502 (tt)
  outliers start: 26
  outliers final: 15
  residues processed: 251
  average time/residue: 1.1856
  time to fit residues: 321.1763
Evaluate side-chains
  252 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 237
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  632 MET
Chi-restraints excluded: chain A residue  652 GLN
Chi-restraints excluded: chain A residue  744 PHE
Chi-restraints excluded: chain A residue  822 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   91 ILE
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain C residue  277 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 41 optimal weight:    0.7980
   chunk 39 optimal weight:    0.2980
   chunk 57 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   chunk 75 optimal weight:    0.4980
   chunk 12 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 104 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0770
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
A 516 HIS
A 727 HIS
A 730 GLN
C 115 ASN
C 233 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.175456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.147701 restraints weight = 16001.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 2.49
r_work: 0.3731 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  10283  Z= 0.149
  Angle     :  0.626  15.000  13920  Z= 0.309
  Chirality :  0.043   0.148   1603
  Planarity :  0.004   0.047   1761
  Dihedral  :  4.192  23.530   1338
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 19.12 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.25), residues: 1237
  helix:  1.84 (0.21), residues: 629
  sheet:  0.40 (0.38), residues: 199
  loop :  0.08 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 490 
 HIS   0.006   0.001   HIS B  90 
 PHE   0.019   0.002   PHE B 132 
 TYR   0.022   0.001   TYR B 143 
 ARG   0.008   0.000   ARG A 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03753 (  575)
  hydrogen bonds       : angle       4.52379 ( 1761)
  covalent geometry    : bond        0.00357 (10283)
  covalent geometry    : angle       0.62636 (13920)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 243
  time to evaluate  : 1.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 SER cc_start: 0.7991 (t) cc_final: 0.7686 (t)
REVERT: A  248 ARG cc_start: 0.7332 (tpt90) cc_final: 0.6854 (tpt90)
REVERT: A  252 MET cc_start: 0.8165 (mtt) cc_final: 0.7191 (mtt)
REVERT: A  366 LYS cc_start: 0.7873 (tptp) cc_final: 0.7581 (tppt)
REVERT: A  417 ARG cc_start: 0.7974 (tpp80) cc_final: 0.7727 (ttm170)
REVERT: A  419 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7922 (ttmt)
REVERT: A  488 GLU cc_start: 0.7847 (tp30) cc_final: 0.7575 (mm-30)
REVERT: A  567 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7539 (mp0)
REVERT: A  574 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7368 (t0)
REVERT: A  584 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6559 (tm-30)
REVERT: A  595 LYS cc_start: 0.8704 (tmmt) cc_final: 0.8265 (tttm)
REVERT: A  630 LYS cc_start: 0.8000 (mttp) cc_final: 0.7652 (mtmm)
REVERT: A  643 MET cc_start: 0.8345 (mmm) cc_final: 0.8111 (mmt)
REVERT: A  659 GLU cc_start: 0.7106 (pp20) cc_final: 0.6703 (tm-30)
REVERT: A  666 ASN cc_start: 0.7336 (t0) cc_final: 0.7041 (t0)
REVERT: A  684 GLU cc_start: 0.7239 (mt-10) cc_final: 0.7027 (mt-10)
REVERT: A  708 CYS cc_start: 0.7850 (p) cc_final: 0.7476 (t)
REVERT: A  712 ILE cc_start: 0.8301 (mp) cc_final: 0.8070 (mp)
REVERT: A  771 PHE cc_start: 0.8795 (m-80) cc_final: 0.8348 (m-80)
REVERT: A  800 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7991 (mm-30)
REVERT: A  819 ARG cc_start: 0.7640 (mpp80) cc_final: 0.7250 (mpp80)
REVERT: A  868 MET cc_start: 0.7368 (mtm) cc_final: 0.6263 (mtm)
REVERT: B  133 TYR cc_start: 0.7612 (m-80) cc_final: 0.7405 (m-80)
REVERT: C   42 THR cc_start: 0.8339 (m) cc_final: 0.7985 (p)
REVERT: C   95 PHE cc_start: 0.8152 (m-80) cc_final: 0.7762 (m-80)
REVERT: C  176 PHE cc_start: 0.8364 (p90) cc_final: 0.8033 (p90)
REVERT: C  269 LYS cc_start: 0.8145 (mtmm) cc_final: 0.7885 (mtmm)
REVERT: C  285 LEU cc_start: 0.8739 (tp) cc_final: 0.8497 (tt)
  outliers start: 31
  outliers final: 20
  residues processed: 254
  average time/residue: 1.1442
  time to fit residues: 313.0994
Evaluate side-chains
  276 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 255
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  532 HIS
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  632 MET
Chi-restraints excluded: chain A residue  652 GLN
Chi-restraints excluded: chain A residue  683 MET
Chi-restraints excluded: chain A residue  744 PHE
Chi-restraints excluded: chain A residue  765 MET
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   91 ILE
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain C residue  217 GLU
Chi-restraints excluded: chain C residue  277 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 52 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9990
   chunk 63 optimal weight:    0.4980
   chunk 68 optimal weight:    4.9990
   chunk 78 optimal weight:    0.4980
   chunk 0 optimal weight:   20.0000
   chunk 59 optimal weight:    0.3980
   chunk 72 optimal weight:    5.9990
   chunk 92 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 516 HIS
A 727 HIS
A 730 GLN
C 115 ASN
C 233 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.174978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.147266 restraints weight = 15944.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3872 rms_B_bonded: 2.48
r_work: 0.3722 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10283  Z= 0.180
  Angle     :  0.655  13.377  13920  Z= 0.325
  Chirality :  0.045   0.199   1603
  Planarity :  0.004   0.048   1761
  Dihedral  :  4.254  20.749   1338
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 19.91 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.25), residues: 1237
  helix:  1.77 (0.21), residues: 625
  sheet:  0.34 (0.38), residues: 199
  loop :  0.12 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 199 
 HIS   0.005   0.001   HIS B  90 
 PHE   0.035   0.002   PHE A 640 
 TYR   0.034   0.002   TYR B  73 
 ARG   0.009   0.000   ARG A 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03977 (  575)
  hydrogen bonds       : angle       4.57198 ( 1761)
  covalent geometry    : bond        0.00431 (10283)
  covalent geometry    : angle       0.65454 (13920)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 235
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
REVERT: A  201 SER cc_start: 0.8058 (t) cc_final: 0.7748 (t)
REVERT: A  248 ARG cc_start: 0.7378 (tpt90) cc_final: 0.6994 (tpt90)
REVERT: A  366 LYS cc_start: 0.7863 (tptp) cc_final: 0.7575 (tppt)
REVERT: A  417 ARG cc_start: 0.7986 (tpp80) cc_final: 0.7745 (ttm170)
REVERT: A  419 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7886 (ttmp)
REVERT: A  488 GLU cc_start: 0.7902 (tp30) cc_final: 0.7615 (mm-30)
REVERT: A  567 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7534 (mp0)
REVERT: A  574 ASP cc_start: 0.7605 (t70) cc_final: 0.7384 (t0)
REVERT: A  584 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6610 (tm-30)
REVERT: A  595 LYS cc_start: 0.8730 (tmmt) cc_final: 0.8287 (tttm)
REVERT: A  630 LYS cc_start: 0.8074 (mttp) cc_final: 0.7720 (mtmm)
REVERT: A  637 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8732 (mp)
REVERT: A  643 MET cc_start: 0.8321 (mmm) cc_final: 0.8061 (mmt)
REVERT: A  659 GLU cc_start: 0.7144 (pp20) cc_final: 0.6526 (tm-30)
REVERT: A  666 ASN cc_start: 0.7338 (t0) cc_final: 0.7036 (t0)
REVERT: A  684 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6904 (mt-10)
REVERT: A  708 CYS cc_start: 0.7923 (p) cc_final: 0.7678 (t)
REVERT: A  800 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7983 (mm-30)
REVERT: A  819 ARG cc_start: 0.7593 (mpp80) cc_final: 0.7319 (mpp80)
REVERT: A  868 MET cc_start: 0.7365 (mtm) cc_final: 0.6272 (mtm)
REVERT: B  122 LYS cc_start: 0.8081 (tmmt) cc_final: 0.7664 (tmmt)
REVERT: B  133 TYR cc_start: 0.7661 (m-80) cc_final: 0.7426 (m-80)
REVERT: C   95 PHE cc_start: 0.8080 (m-80) cc_final: 0.7676 (m-80)
REVERT: C  176 PHE cc_start: 0.8390 (p90) cc_final: 0.8079 (p90)
REVERT: C  201 SER cc_start: 0.8536 (p) cc_final: 0.8270 (p)
REVERT: C  202 SER cc_start: 0.8789 (t) cc_final: 0.8586 (p)
REVERT: C  269 LYS cc_start: 0.8177 (mtmm) cc_final: 0.7913 (mtmm)
  outliers start: 30
  outliers final: 20
  residues processed: 247
  average time/residue: 1.1364
  time to fit residues: 302.3645
Evaluate side-chains
  255 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 234
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  532 HIS
Chi-restraints excluded: chain A residue  534 THR
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  632 MET
Chi-restraints excluded: chain A residue  637 ILE
Chi-restraints excluded: chain A residue  652 GLN
Chi-restraints excluded: chain A residue  744 PHE
Chi-restraints excluded: chain A residue  765 MET
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   91 ILE
Chi-restraints excluded: chain C residue  217 GLU
Chi-restraints excluded: chain C residue  277 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 36 optimal weight:    0.5980
   chunk 64 optimal weight:    0.0870
   chunk 98 optimal weight:    0.9980
   chunk 102 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 85 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0980
   chunk 9 optimal weight:    1.9990
   chunk 123 optimal weight:    0.8980
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
A 516 HIS
A 727 HIS
A 730 GLN
C 115 ASN
C 233 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.175869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.148384 restraints weight = 15887.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 2.48
r_work: 0.3734 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10283  Z= 0.148
  Angle     :  0.669  13.430  13920  Z= 0.327
  Chirality :  0.044   0.151   1603
  Planarity :  0.005   0.057   1761
  Dihedral  :  4.234  20.203   1338
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 20.62 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.25), residues: 1237
  helix:  1.76 (0.21), residues: 629
  sheet:  0.33 (0.38), residues: 199
  loop :  0.05 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 490 
 HIS   0.005   0.001   HIS B  90 
 PHE   0.027   0.002   PHE A 640 
 TYR   0.021   0.002   TYR B  73 
 ARG   0.009   0.000   ARG A 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03804 (  575)
  hydrogen bonds       : angle       4.51195 ( 1761)
  covalent geometry    : bond        0.00355 (10283)
  covalent geometry    : angle       0.66869 (13920)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 240
  time to evaluate  : 1.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 SER cc_start: 0.7965 (t) cc_final: 0.7659 (t)
REVERT: A  248 ARG cc_start: 0.7380 (tpt90) cc_final: 0.7032 (tpt90)
REVERT: A  366 LYS cc_start: 0.7861 (tptp) cc_final: 0.7576 (tppt)
REVERT: A  417 ARG cc_start: 0.7967 (tpp80) cc_final: 0.7731 (ttm170)
REVERT: A  419 LYS cc_start: 0.8160 (ttpt) cc_final: 0.7868 (ttmp)
REVERT: A  488 GLU cc_start: 0.7904 (tp30) cc_final: 0.7616 (mm-30)
REVERT: A  567 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7530 (mp0)
REVERT: A  574 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7358 (t0)
REVERT: A  584 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6612 (tm-30)
REVERT: A  591 ASP cc_start: 0.7599 (t70) cc_final: 0.7327 (t0)
REVERT: A  630 LYS cc_start: 0.7991 (mttp) cc_final: 0.7687 (mtmm)
REVERT: A  659 GLU cc_start: 0.7225 (pp20) cc_final: 0.6796 (tm-30)
REVERT: A  666 ASN cc_start: 0.7228 (t0) cc_final: 0.6940 (t0)
REVERT: A  684 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6859 (mt-10)
REVERT: A  708 CYS cc_start: 0.7839 (p) cc_final: 0.7539 (t)
REVERT: A  712 ILE cc_start: 0.8276 (mp) cc_final: 0.8066 (mp)
REVERT: A  771 PHE cc_start: 0.8787 (m-80) cc_final: 0.8406 (m-80)
REVERT: A  800 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8009 (mm-30)
REVERT: A  868 MET cc_start: 0.7370 (mtm) cc_final: 0.6273 (mtm)
REVERT: B  122 LYS cc_start: 0.8066 (tmmt) cc_final: 0.7642 (tmmt)
REVERT: B  133 TYR cc_start: 0.7750 (m-80) cc_final: 0.7506 (m-80)
REVERT: C   42 THR cc_start: 0.8315 (m) cc_final: 0.7989 (p)
REVERT: C   95 PHE cc_start: 0.8065 (m-80) cc_final: 0.7592 (m-80)
REVERT: C  176 PHE cc_start: 0.8382 (p90) cc_final: 0.8021 (p90)
REVERT: C  201 SER cc_start: 0.8456 (p) cc_final: 0.8184 (p)
REVERT: C  269 LYS cc_start: 0.8159 (mtmm) cc_final: 0.7894 (mtmm)
  outliers start: 26
  outliers final: 20
  residues processed: 249
  average time/residue: 1.1430
  time to fit residues: 306.5931
Evaluate side-chains
  257 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 236
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  532 HIS
Chi-restraints excluded: chain A residue  534 THR
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  632 MET
Chi-restraints excluded: chain A residue  652 GLN
Chi-restraints excluded: chain A residue  744 PHE
Chi-restraints excluded: chain A residue  765 MET
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   91 ILE
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  217 GLU
Chi-restraints excluded: chain C residue  277 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 113 optimal weight:    3.9990
   chunk 17 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   chunk 114 optimal weight:    0.9990
   chunk 29 optimal weight:    0.1980
   chunk 72 optimal weight:   40.0000
   chunk 124 optimal weight:    1.9990
   chunk 104 optimal weight:    0.4980
   chunk 28 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 727 HIS
C 115 ASN
C 233 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.174961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.147355 restraints weight = 15929.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3870 rms_B_bonded: 2.47
r_work: 0.3719 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7289
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  10283  Z= 0.181
  Angle     :  0.691  12.853  13920  Z= 0.339
  Chirality :  0.045   0.178   1603
  Planarity :  0.005   0.049   1761
  Dihedral  :  4.287  18.733   1338
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 21.59 %
    Favored  : 76.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.24), residues: 1237
  helix:  1.61 (0.21), residues: 628
  sheet:  0.30 (0.38), residues: 199
  loop :  0.08 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 199 
 HIS   0.006   0.001   HIS A 596 
 PHE   0.029   0.002   PHE C 113 
 TYR   0.024   0.002   TYR B  73 
 ARG   0.009   0.001   ARG A 121 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04026 (  575)
  hydrogen bonds       : angle       4.62739 ( 1761)
  covalent geometry    : bond        0.00438 (10283)
  covalent geometry    : angle       0.69077 (13920)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 235
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 SER cc_start: 0.8016 (t) cc_final: 0.7710 (t)
REVERT: A  248 ARG cc_start: 0.7398 (tpt90) cc_final: 0.7013 (tpt90)
REVERT: A  366 LYS cc_start: 0.7856 (tptp) cc_final: 0.7565 (tppt)
REVERT: A  416 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7121 (mp0)
REVERT: A  417 ARG cc_start: 0.7966 (tpp80) cc_final: 0.7724 (ttm170)
REVERT: A  419 LYS cc_start: 0.8166 (ttpt) cc_final: 0.7842 (ttmp)
REVERT: A  488 GLU cc_start: 0.7933 (tp30) cc_final: 0.7640 (mm-30)
REVERT: A  567 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7551 (mp0)
REVERT: A  574 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7308 (t0)
REVERT: A  584 GLU cc_start: 0.7205 (tm-30) cc_final: 0.6663 (tm-30)
REVERT: A  630 LYS cc_start: 0.8138 (mttp) cc_final: 0.7826 (mtmm)
REVERT: A  643 MET cc_start: 0.8451 (tpp) cc_final: 0.8057 (mmm)
REVERT: A  659 GLU cc_start: 0.7260 (pp20) cc_final: 0.6872 (tm-30)
REVERT: A  661 ARG cc_start: 0.8328 (tmm-80) cc_final: 0.7806 (ttt-90)
REVERT: A  666 ASN cc_start: 0.7260 (t0) cc_final: 0.6957 (t0)
REVERT: A  684 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6853 (mt-10)
REVERT: A  708 CYS cc_start: 0.7905 (p) cc_final: 0.7662 (t)
REVERT: A  771 PHE cc_start: 0.8837 (m-80) cc_final: 0.8381 (m-80)
REVERT: A  800 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8001 (mm-30)
REVERT: A  819 ARG cc_start: 0.7599 (mpp80) cc_final: 0.7229 (mpp80)
REVERT: A  868 MET cc_start: 0.7366 (mtm) cc_final: 0.6286 (mtm)
REVERT: B  122 LYS cc_start: 0.8070 (tmmt) cc_final: 0.7660 (tmmt)
REVERT: B  133 TYR cc_start: 0.7759 (m-80) cc_final: 0.7541 (m-80)
REVERT: C   95 PHE cc_start: 0.8032 (m-80) cc_final: 0.7578 (m-80)
REVERT: C  176 PHE cc_start: 0.8380 (p90) cc_final: 0.8077 (p90)
REVERT: C  201 SER cc_start: 0.8628 (p) cc_final: 0.8359 (p)
REVERT: C  269 LYS cc_start: 0.8176 (mtmm) cc_final: 0.7908 (mtmm)
  outliers start: 21
  outliers final: 18
  residues processed: 241
  average time/residue: 1.1659
  time to fit residues: 302.5269
Evaluate side-chains
  254 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 235
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  532 HIS
Chi-restraints excluded: chain A residue  534 THR
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  652 GLN
Chi-restraints excluded: chain A residue  744 PHE
Chi-restraints excluded: chain A residue  765 MET
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  172 ILE
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   91 ILE
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  217 GLU
Chi-restraints excluded: chain C residue  277 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 114 optimal weight:    0.9990
   chunk 109 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   chunk 26 optimal weight:    0.3980
   chunk 9 optimal weight:    0.9980
   chunk 121 optimal weight:    0.0980
   chunk 33 optimal weight:    0.5980
   chunk 81 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 112 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0570
   overall best weight:    0.3698

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

Flipped N/Q/H residues before XYZ refinement:
A 516 HIS
A 727 HIS
A 778 ASN
C 115 ASN
C 233 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.176323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.148356 restraints weight = 15891.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 2.50
r_work: 0.3731 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10283  Z= 0.144
  Angle     :  0.681  12.757  13920  Z= 0.332
  Chirality :  0.045   0.313   1603
  Planarity :  0.005   0.048   1761
  Dihedral  :  4.231  17.500   1338
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 21.50 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.25), residues: 1237
  helix:  1.64 (0.21), residues: 627
  sheet:  0.31 (0.38), residues: 201
  loop :  0.11 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 490 
 HIS   0.005   0.001   HIS B  90 
 PHE   0.025   0.002   PHE C 113 
 TYR   0.021   0.001   TYR B  73 
 ARG   0.008   0.001   ARG A 686 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03846 (  575)
  hydrogen bonds       : angle       4.59167 ( 1761)
  covalent geometry    : bond        0.00348 (10283)
  covalent geometry    : angle       0.68081 (13920)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8198.22 seconds
wall clock time: 143 minutes 27.11 seconds (8607.11 seconds total)