Starting phenix.real_space_refine
on Wed Feb  4 01:56:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qic_53184/02_2026/9qic_53184_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qic_53184/02_2026/9qic_53184.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qic_53184/02_2026/9qic_53184_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qic_53184/02_2026/9qic_53184_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qic_53184/02_2026/9qic_53184.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qic_53184/02_2026/9qic_53184.map"
  }
  resolution = 3.29
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     S      37      5.16       5
     C    5139      2.51       5
     N    1348      2.21       5
     O    1544      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8077
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 8010
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1011, 8010
          Classifications: {'peptide': 1011}
          Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 50, 'TRANS': 955}
    Chain: "B"
      Number of atoms: 67
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 67
          Unusual residues: {'ATP': 1, 'IHP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.64, per 1000 atoms: 0.20
  Number of scatterers: 8077
  At special positions: 0
  Unit cell: (80.85, 102.3, 122.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      37     16.00
     P       9     15.00
     O    1544      8.00
     N    1348      7.00
     C    5139      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 332.9 milliseconds
  

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1922

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 7 sheets defined
      49.3% alpha, 13.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'B' and resid 40 through 52
      removed outlier: 6.895A  pdb=" N   ARG B  46 " --> pdb=" O   ALA B  42 " (cutoff:3.500A)
      removed outlier: 5.873A  pdb=" N   GLN B  47 " --> pdb=" O   LEU B  43 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   TYR B  49 " --> pdb=" O   SER B  45 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   VAL B  50 " --> pdb=" O   ARG B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 60
    Processing helix  chain 'B' and resid 70 through 84
      removed outlier: 3.577A  pdb=" N   GLU B  75 " --> pdb=" O   GLY B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 103
      removed outlier: 3.524A  pdb=" N   GLY B 102 " --> pdb=" O   TRP B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 115
    Processing helix  chain 'B' and resid 117 through 128
      removed outlier: 4.381A  pdb=" N   LYS B 124 " --> pdb=" O   GLU B 120 " (cutoff:3.500A)
      removed outlier: 4.816A  pdb=" N   HIS B 125 " --> pdb=" O   ALA B 121 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLU B 128 " --> pdb=" O   LYS B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 154
      removed outlier: 3.949A  pdb=" N   LYS B 153 " --> pdb=" O   PHE B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 163 through 176
      removed outlier: 3.513A  pdb=" N   SER B 176 " --> pdb=" O   ASP B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 257
    Processing helix  chain 'B' and resid 301 through 306
    Processing helix  chain 'B' and resid 320 through 340
    Processing helix  chain 'B' and resid 347 through 365
      removed outlier: 3.533A  pdb=" N   GLU B 363 " --> pdb=" O   THR B 359 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   THR B 364 " --> pdb=" O   SER B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 382
    Processing helix  chain 'B' and resid 387 through 408
    Processing helix  chain 'B' and resid 421 through 427
      removed outlier: 4.242A  pdb=" N   VAL B 425 " --> pdb=" O   ALA B 421 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   SER B 427 " --> pdb=" O   ASP B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 437
      removed outlier: 3.509A  pdb=" N   GLU B 435 " --> pdb=" O   GLU B 432 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU B 437 " --> pdb=" O   GLU B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 460
      removed outlier: 3.626A  pdb=" N   CYS B 449 " --> pdb=" O   ALA B 445 " (cutoff:3.500A)
      removed outlier: 8.165A  pdb=" N   ASP B 452 " --> pdb=" O   ALA B 448 " (cutoff:3.500A)
      removed outlier: 9.501A  pdb=" N   THR B 453 " --> pdb=" O   CYS B 449 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   LEU B 454 " --> pdb=" O   ILE B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 483
      removed outlier: 3.537A  pdb=" N   GLU B 474 " --> pdb=" O   ALA B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 508
      removed outlier: 3.653A  pdb=" N   ASN B 507 " --> pdb=" O   SER B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 517
    Processing helix  chain 'B' and resid 520 through 533
    Processing helix  chain 'B' and resid 546 through 550
    Processing helix  chain 'B' and resid 554 through 561
    Processing helix  chain 'B' and resid 571 through 585
    Processing helix  chain 'B' and resid 623 through 629
    Processing helix  chain 'B' and resid 633 through 650
      removed outlier: 3.503A  pdb=" N   THR B 637 " --> pdb=" O   ALA B 633 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 650 through 663
    Processing helix  chain 'B' and resid 665 through 675
    Processing helix  chain 'B' and resid 681 through 691
    Processing helix  chain 'B' and resid 695 through 712
    Processing helix  chain 'B' and resid 712 through 722
    Processing helix  chain 'B' and resid 751 through 770
    Processing helix  chain 'B' and resid 774 through 778
    Processing helix  chain 'B' and resid 779 through 789
      removed outlier: 4.198A  pdb=" N   GLU B 789 " --> pdb=" O   ASN B 785 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 817 through 834
    Processing helix  chain 'B' and resid 839 through 843
      removed outlier: 3.782A  pdb=" N   GLN B 843 " --> pdb=" O   SER B 840 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 857 through 873
    Processing helix  chain 'B' and resid 879 through 889
    Processing helix  chain 'B' and resid 894 through 915
      removed outlier: 3.572A  pdb=" N   THR B 898 " --> pdb=" O   ILE B 894 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 917 through 920
    Processing helix  chain 'B' and resid 967 through 979
    Processing helix  chain 'B' and resid 1001 through 1007
      removed outlier: 3.877A  pdb=" N   LEU B1005 " --> pdb=" O   ALA B1002 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1008 through 1013
    Processing sheet with id=AA1, first strand: chain 'B' and resid 134 through 138
      removed outlier: 6.364A  pdb=" N   VAL B  88 " --> pdb=" O   THR B 136 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   SER B 138 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ILE B  90 " --> pdb=" O   SER B 138 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   VAL B  64 " --> pdb=" O   THR B  89 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   HIS B  91 " --> pdb=" O   VAL B  64 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   LEU B  66 " --> pdb=" O   HIS B  91 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   HIS B  63 " --> pdb=" O   CYS B 156 " (cutoff:3.500A)
      removed outlier: 8.405A  pdb=" N   VAL B 158 " --> pdb=" O   HIS B  63 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   PHE B  65 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 205
    Processing sheet with id=AA3, first strand: chain 'B' and resid 260 through 262
      removed outlier: 4.544A  pdb=" N   PHE B 244 " --> pdb=" O   VAL B 291 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   GLY B 227 " --> pdb=" O   ILE B 273 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   SER B 270 " --> pdb=" O   ILE B 266 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 541
      removed outlier: 6.588A  pdb=" N   ILE B 493 " --> pdb=" O   ASP B 539 " (cutoff:3.500A)
      removed outlier: 7.535A  pdb=" N   HIS B 541 " --> pdb=" O   ILE B 493 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   VAL B 495 " --> pdb=" O   HIS B 541 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   VAL B 563 " --> pdb=" O   ASN B 462 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ILE B 564 " --> pdb=" O   LEU B 589 " (cutoff:3.500A)
      removed outlier: 8.382A  pdb=" N   SER B 591 " --> pdb=" O   ILE B 564 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   THR B 566 " --> pdb=" O   SER B 591 " (cutoff:3.500A)
      removed outlier: 8.815A  pdb=" N   THR B 593 " --> pdb=" O   THR B 566 " (cutoff:3.500A)
      removed outlier: 5.801A  pdb=" N   VAL B 602 " --> pdb=" O   LYS B 922 " (cutoff:3.500A)
      removed outlier: 7.344A  pdb=" N   LYS B 922 " --> pdb=" O   VAL B 602 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 944 through 945
    Processing sheet with id=AA6, first strand: chain 'B' and resid 958 through 961
      removed outlier: 6.394A  pdb=" N   TRP B 958 " --> pdb=" O   ARG B1044 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   TYR B1046 " --> pdb=" O   TRP B 958 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   VAL B 960 " --> pdb=" O   TYR B1046 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   VAL B 986 " --> pdb=" O   LEU B 993 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLN B 988 " --> pdb=" O   LYS B 991 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 958 through 961
      removed outlier: 6.394A  pdb=" N   TRP B 958 " --> pdb=" O   ARG B1044 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   TYR B1046 " --> pdb=" O   TRP B 958 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   VAL B 960 " --> pdb=" O   TYR B1046 " (cutoff:3.500A)

    388 hydrogen bonds defined for protein.
    1056 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.49

  Time building geometry restraints manager: 1.04 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2611
        1.34 -     1.46: 1545
        1.46 -     1.57: 4043
        1.57 -     1.69: 10
        1.69 -     1.81: 53
  Bond restraints: 8262
  Sorted by residual:
  bond pdb=" C1' ATP B1102 "
       pdb=" O4' ATP B1102 "
    ideal  model  delta    sigma   weight residual
    1.416  1.403  0.013 1.30e-02 5.92e+03 9.50e-01
  bond pdb=" CA  VAL B 140 "
       pdb=" CB  VAL B 140 "
    ideal  model  delta    sigma   weight residual
    1.537  1.526  0.012 1.29e-02 6.01e+03 7.97e-01
  bond pdb=" CA  ASN B 234 "
       pdb=" CB  ASN B 234 "
    ideal  model  delta    sigma   weight residual
    1.530  1.543 -0.013 1.69e-02 3.50e+03 6.16e-01
  bond pdb=" N   ASN B 130 "
       pdb=" CA  ASN B 130 "
    ideal  model  delta    sigma   weight residual
    1.463  1.456  0.006 8.80e-03 1.29e+04 5.10e-01
  bond pdb=" CA  VAL B 545 "
       pdb=" C   VAL B 545 "
    ideal  model  delta    sigma   weight residual
    1.527  1.520  0.007 9.70e-03 1.06e+04 5.04e-01
  ... (remaining 8257 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.97: 10791
        0.97 -     1.94: 323
        1.94 -     2.91: 74
        2.91 -     3.88: 25
        3.88 -     4.85: 9
  Bond angle restraints: 11222
  Sorted by residual:
  angle pdb=" C   GLU B 233 "
        pdb=" N   ASN B 234 "
        pdb=" CA  ASN B 234 "
      ideal   model   delta    sigma   weight residual
     121.54  126.17   -4.63 1.91e+00 2.74e-01 5.88e+00
  angle pdb=" C2' ATP B1102 "
        pdb=" C3' ATP B1102 "
        pdb=" C4' ATP B1102 "
      ideal   model   delta    sigma   weight residual
     102.49  104.46   -1.97 1.00e+00 1.00e+00 3.88e+00
  angle pdb=" N   THR B 209 "
        pdb=" CA  THR B 209 "
        pdb=" C   THR B 209 "
      ideal   model   delta    sigma   weight residual
     110.80  114.70   -3.90 2.13e+00 2.20e-01 3.36e+00
  angle pdb=" N   SER B 629 "
        pdb=" CA  SER B 629 "
        pdb=" C   SER B 629 "
      ideal   model   delta    sigma   weight residual
     110.80  114.45   -3.65 2.13e+00 2.20e-01 2.94e+00
  angle pdb=" C   ILE B 930 "
        pdb=" N   PRO B 931 "
        pdb=" CA  PRO B 931 "
      ideal   model   delta    sigma   weight residual
     127.00  131.04   -4.04 2.40e+00 1.74e-01 2.83e+00
  ... (remaining 11217 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.57: 4717
       15.57 -    31.15: 252
       31.15 -    46.72: 59
       46.72 -    62.29: 13
       62.29 -    77.87: 3
  Dihedral angle restraints: 5044
    sinusoidal: 2087
      harmonic: 2957
  Sorted by residual:
  dihedral pdb=" N   LYS B 163 "
           pdb=" CA  LYS B 163 "
           pdb=" CB  LYS B 163 "
           pdb=" CG  LYS B 163 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -120.66  -59.34     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CB  MET B 992 "
           pdb=" CG  MET B 992 "
           pdb=" SD  MET B 992 "
           pdb=" CE  MET B 992 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -124.85  -55.15     3      1.50e+01 4.44e-03 9.33e+00
  dihedral pdb=" CA  TYR B 994 "
           pdb=" C   TYR B 994 "
           pdb=" N   VAL B 995 "
           pdb=" CA  VAL B 995 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.86   15.14     0      5.00e+00 4.00e-02 9.17e+00
  ... (remaining 5041 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 711
       0.025 -    0.050: 334
       0.050 -    0.075: 120
       0.075 -    0.099: 49
       0.099 -    0.124: 54
  Chirality restraints: 1268
  Sorted by residual:
  chirality pdb=" CA  ILE B 493 "
            pdb=" N   ILE B 493 "
            pdb=" C   ILE B 493 "
            pdb=" CB  ILE B 493 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.86e-01
  chirality pdb=" CA  ILE B 891 "
            pdb=" N   ILE B 891 "
            pdb=" C   ILE B 891 "
            pdb=" CB  ILE B 891 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.85e-01
  chirality pdb=" CA  VAL B 987 "
            pdb=" N   VAL B 987 "
            pdb=" C   VAL B 987 "
            pdb=" CB  VAL B 987 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.84e-01
  ... (remaining 1265 not shown)

  Planarity restraints: 1430
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 497 "   -0.020 5.00e-02 4.00e+02   2.98e-02 1.42e+00
        pdb=" N   PRO B 498 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO B 498 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 498 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 546 "    0.018 5.00e-02 4.00e+02   2.80e-02 1.25e+00
        pdb=" N   PRO B 547 "   -0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO B 547 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B 547 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 513 "   -0.018 5.00e-02 4.00e+02   2.71e-02 1.18e+00
        pdb=" N   PRO B 514 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO B 514 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B 514 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 1427 not shown)

  Histogram of nonbonded interaction distances:
        2.53 -     3.00: 4525
        3.00 -     3.48: 8165
        3.48 -     3.95: 13235
        3.95 -     4.43: 15324
        4.43 -     4.90: 24008
  Nonbonded interactions: 65257
  Sorted by model distance:
  nonbonded pdb=" O   GLU B 233 "
            pdb=" OD1 ASN B 234 "
     model   vdw
     2.527 3.040
  nonbonded pdb=" O2' ATP B1102 "
            pdb=" O3' ATP B1102 "
     model   vdw
     2.589 2.432
  nonbonded pdb=" N   SER B 267 "
            pdb=" O   SER B 267 "
     model   vdw
     2.621 2.496
  nonbonded pdb=" N   CYS B 546 "
            pdb=" O   CYS B 546 "
     model   vdw
     2.627 2.496
  nonbonded pdb=" N   ASN B 143 "
            pdb=" O   ASN B 143 "
     model   vdw
     2.644 2.496
  ... (remaining 65252 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.390
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.550
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8918
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8262  Z= 0.155
  Angle     :  0.455   4.850  11222  Z= 0.235
  Chirality :  0.040   0.124   1268
  Planarity :  0.003   0.030   1430
  Dihedral  : 10.520  77.866   3122
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  2.91 %
    Favored  : 96.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.44 (0.28), residues: 1009
  helix:  2.71 (0.26), residues: 421
  sheet:  0.64 (0.42), residues: 160
  loop :  1.03 (0.33), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 508 
 TYR   0.007   0.001   TYR B  49 
 PHE   0.011   0.001   PHE B 656 
 TRP   0.009   0.001   TRP B 660 
 HIS   0.004   0.001   HIS B 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 8262)
  covalent geometry    : angle       0.45477 (11222)
  hydrogen bonds       : bond        0.15414 (  384)
  hydrogen bonds       : angle       6.22477 ( 1056)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 20
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 2
  residues processed: 23
  average time/residue: 0.0873
  time to fit residues: 3.0967
Evaluate side-chains
  20 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 18
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   63 HIS
Chi-restraints excluded: chain B residue  997 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
B 262 GLN
B 415 GLN
B 505 ASN
B 760 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.045276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2589 r_free = 0.2589 target = 0.029893 restraints weight = 40910.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.2567 rms_B_bonded: 4.38
r_work: 0.2397 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.2397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8920
moved from start:          0.0651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   8262  Z= 0.174
  Angle     :  0.487   5.244  11222  Z= 0.253
  Chirality :  0.040   0.133   1268
  Planarity :  0.003   0.031   1430
  Dihedral  :  5.716  75.775   1150
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  3.47 %
    Favored  : 96.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.51 (0.28), residues: 1009
  helix:  2.71 (0.26), residues: 428
  sheet:  0.83 (0.42), residues: 159
  loop :  1.05 (0.33), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 513 
 TYR   0.008   0.001   TYR B  49 
 PHE   0.010   0.001   PHE B 656 
 TRP   0.006   0.001   TRP B 378 
 HIS   0.003   0.001   HIS B1010 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 8262)
  covalent geometry    : angle       0.48725 (11222)
  hydrogen bonds       : bond        0.03996 (  384)
  hydrogen bonds       : angle       4.91206 ( 1056)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 18
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: B  844 MET cc_start: 0.8691 (ptt) cc_final: 0.8107 (ptt)
  outliers start: 4
  outliers final: 2
  residues processed: 22
  average time/residue: 0.0843
  time to fit residues: 2.8889
Evaluate side-chains
  20 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 18
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  997 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0770
   chunk 86 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9990
   chunk 100 optimal weight:    9.9990
   chunk 29 optimal weight:    4.9990
   chunk 70 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 64 optimal weight:    8.9990
   overall best weight:    0.7140

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

Flipped N/Q/H residues before XYZ refinement:
B  47 GLN
B  63 HIS
B 234 ASN
B 507 ASN
** B1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.046135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.030906 restraints weight = 40303.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.2580 rms_B_bonded: 4.37
r_work: 0.2413 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.2413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8867
moved from start:          0.0902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8262  Z= 0.094
  Angle     :  0.436   8.427  11222  Z= 0.226
  Chirality :  0.039   0.137   1268
  Planarity :  0.003   0.032   1430
  Dihedral  :  5.458  73.958   1148
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  3.81 %
    Favored  : 95.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.48 (0.28), residues: 1009
  helix:  2.65 (0.26), residues: 430
  sheet:  0.84 (0.42), residues: 159
  loop :  1.04 (0.33), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 704 
 TYR   0.008   0.001   TYR B 663 
 PHE   0.009   0.001   PHE B 656 
 TRP   0.006   0.001   TRP B 660 
 HIS   0.002   0.000   HIS B1010 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 8262)
  covalent geometry    : angle       0.43604 (11222)
  hydrogen bonds       : bond        0.03255 (  384)
  hydrogen bonds       : angle       4.45529 ( 1056)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 20
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
REVERT: B  475 MET cc_start: 0.9080 (mmm) cc_final: 0.8720 (mmm)
REVERT: B  594 MET cc_start: 0.8608 (tmm) cc_final: 0.8241 (tmm)
REVERT: B  844 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8258 (ptt)
  outliers start: 7
  outliers final: 4
  residues processed: 24
  average time/residue: 0.0623
  time to fit residues: 2.3798
Evaluate side-chains
  23 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 18
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   63 HIS
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  844 MET
Chi-restraints excluded: chain B residue  992 MET
Chi-restraints excluded: chain B residue  997 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 21 optimal weight:    0.0980
   chunk 81 optimal weight:    6.9990
   chunk 65 optimal weight:    0.7980
   chunk 27 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 95 optimal weight:    8.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B  47 GLN
B  63 HIS
B 234 ASN
B 507 ASN
B 599 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.045954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.030715 restraints weight = 40608.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.2574 rms_B_bonded: 4.38
r_work: 0.2401 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.2401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8879
moved from start:          0.0977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   8262  Z= 0.116
  Angle     :  0.434   5.574  11222  Z= 0.225
  Chirality :  0.039   0.133   1268
  Planarity :  0.003   0.031   1430
  Dihedral  :  5.441  74.178   1148
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  4.37 %
    Favored  : 94.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.48 (0.28), residues: 1009
  helix:  2.68 (0.26), residues: 431
  sheet:  0.78 (0.41), residues: 159
  loop :  1.04 (0.33), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 704 
 TYR   0.008   0.001   TYR B 663 
 PHE   0.010   0.001   PHE B 656 
 TRP   0.006   0.001   TRP B 660 
 HIS   0.004   0.000   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8262)
  covalent geometry    : angle       0.43442 (11222)
  hydrogen bonds       : bond        0.03092 (  384)
  hydrogen bonds       : angle       4.34569 ( 1056)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 19
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: B  475 MET cc_start: 0.9136 (mmm) cc_final: 0.8648 (mmm)
REVERT: B  594 MET cc_start: 0.8587 (tmm) cc_final: 0.8001 (tmm)
REVERT: B  844 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8233 (ptt)
  outliers start: 7
  outliers final: 5
  residues processed: 23
  average time/residue: 0.0630
  time to fit residues: 2.3498
Evaluate side-chains
  25 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 19
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   63 HIS
Chi-restraints excluded: chain B residue  234 ASN
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  844 MET
Chi-restraints excluded: chain B residue  992 MET
Chi-restraints excluded: chain B residue  997 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 70 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 2 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 100 optimal weight:    0.0770
   chunk 7 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.6542

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

Flipped N/Q/H residues before XYZ refinement:
B  63 HIS
B 234 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.046261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.030942 restraints weight = 40610.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.2582 rms_B_bonded: 4.42
r_work: 0.2413 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.2413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8867
moved from start:          0.1082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   8262  Z= 0.087
  Angle     :  0.416   5.416  11222  Z= 0.217
  Chirality :  0.039   0.134   1268
  Planarity :  0.003   0.030   1430
  Dihedral  :  5.362  73.026   1148
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  4.82 %
    Favored  : 94.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.46 (0.28), residues: 1009
  helix:  2.67 (0.26), residues: 431
  sheet:  0.77 (0.41), residues: 159
  loop :  1.01 (0.33), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 704 
 TYR   0.008   0.001   TYR B 663 
 PHE   0.010   0.001   PHE B 656 
 TRP   0.006   0.001   TRP B 660 
 HIS   0.002   0.000   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00183 ( 8262)
  covalent geometry    : angle       0.41644 (11222)
  hydrogen bonds       : bond        0.02905 (  384)
  hydrogen bonds       : angle       4.21816 ( 1056)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 19
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: B   63 HIS cc_start: 0.8102 (OUTLIER) cc_final: 0.7784 (m90)
REVERT: B  475 MET cc_start: 0.9106 (mmm) cc_final: 0.8661 (mmm)
REVERT: B  594 MET cc_start: 0.8630 (tmm) cc_final: 0.8039 (tmm)
REVERT: B  844 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8242 (ptt)
  outliers start: 9
  outliers final: 3
  residues processed: 26
  average time/residue: 0.0806
  time to fit residues: 3.2128
Evaluate side-chains
  23 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 18
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   63 HIS
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  844 MET
Chi-restraints excluded: chain B residue  992 MET
Chi-restraints excluded: chain B residue  997 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 99 optimal weight:    7.9990
   chunk 95 optimal weight:    6.9990
   chunk 89 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 70 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
B  63 HIS
B 234 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.045935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.030729 restraints weight = 40305.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.2573 rms_B_bonded: 4.37
r_work: 0.2405 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.2405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8878
moved from start:          0.1122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8262  Z= 0.122
  Angle     :  0.431   5.952  11222  Z= 0.223
  Chirality :  0.039   0.137   1268
  Planarity :  0.003   0.029   1430
  Dihedral  :  5.360  73.501   1148
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  5.26 %
    Favored  : 94.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.46 (0.28), residues: 1009
  helix:  2.72 (0.26), residues: 431
  sheet:  0.75 (0.40), residues: 166
  loop :  0.95 (0.34), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 704 
 TYR   0.008   0.001   TYR B 663 
 PHE   0.011   0.001   PHE B 656 
 TRP   0.005   0.001   TRP B 660 
 HIS   0.002   0.000   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 8262)
  covalent geometry    : angle       0.43055 (11222)
  hydrogen bonds       : bond        0.02919 (  384)
  hydrogen bonds       : angle       4.19386 ( 1056)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 19
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: B  594 MET cc_start: 0.8664 (tmm) cc_final: 0.8001 (tmm)
REVERT: B  844 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8229 (ptt)
  outliers start: 6
  outliers final: 5
  residues processed: 22
  average time/residue: 0.0709
  time to fit residues: 2.3587
Evaluate side-chains
  25 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 19
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   63 HIS
Chi-restraints excluded: chain B residue  234 ASN
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  844 MET
Chi-restraints excluded: chain B residue  992 MET
Chi-restraints excluded: chain B residue  997 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 28 optimal weight:    0.5980
   chunk 80 optimal weight:    0.2980
   chunk 16 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 71 optimal weight:    6.9990
   chunk 32 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.046292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2633 r_free = 0.2633 target = 0.031055 restraints weight = 40380.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.2587 rms_B_bonded: 4.39
r_work: 0.2420 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.2420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8864
moved from start:          0.1206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8262  Z= 0.087
  Angle     :  0.422   6.570  11222  Z= 0.219
  Chirality :  0.039   0.139   1268
  Planarity :  0.003   0.029   1430
  Dihedral  :  5.299  72.452   1148
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  5.38 %
    Favored  : 93.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.45 (0.28), residues: 1009
  helix:  2.73 (0.26), residues: 431
  sheet:  0.80 (0.41), residues: 166
  loop :  0.91 (0.34), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 574 
 TYR   0.007   0.001   TYR B 663 
 PHE   0.010   0.001   PHE B 656 
 TRP   0.005   0.001   TRP B 660 
 HIS   0.006   0.000   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00183 ( 8262)
  covalent geometry    : angle       0.42192 (11222)
  hydrogen bonds       : bond        0.02776 (  384)
  hydrogen bonds       : angle       4.10135 ( 1056)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 20
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: B  594 MET cc_start: 0.8674 (tmm) cc_final: 0.7988 (tmm)
REVERT: B  844 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8248 (ptt)
  outliers start: 6
  outliers final: 3
  residues processed: 24
  average time/residue: 0.0725
  time to fit residues: 2.7633
Evaluate side-chains
  23 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  844 MET
Chi-restraints excluded: chain B residue  992 MET
Chi-restraints excluded: chain B residue  997 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 10 optimal weight:    0.1980
   chunk 95 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 25 optimal weight:    9.9990
   chunk 62 optimal weight:    6.9990
   chunk 61 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0970
   chunk 75 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    1.2584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.047147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.032699 restraints weight = 38630.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.2706 rms_B_bonded: 4.23
r_work: 0.2546 rms_B_bonded: 4.65 restraints_weight: 0.5000
r_work (final): 0.2546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8866
moved from start:          0.1271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8262  Z= 0.122
  Angle     :  0.441   6.928  11222  Z= 0.226
  Chirality :  0.039   0.144   1268
  Planarity :  0.003   0.029   1430
  Dihedral  :  5.282  73.083   1148
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  5.71 %
    Favored  : 93.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.47 (0.28), residues: 1009
  helix:  2.76 (0.26), residues: 431
  sheet:  0.78 (0.40), residues: 166
  loop :  0.91 (0.34), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 704 
 TYR   0.008   0.001   TYR B 663 
 PHE   0.011   0.001   PHE B 656 
 TRP   0.005   0.001   TRP B 696 
 HIS   0.001   0.000   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8262)
  covalent geometry    : angle       0.44149 (11222)
  hydrogen bonds       : bond        0.02881 (  384)
  hydrogen bonds       : angle       4.11592 ( 1056)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: B  401 GLU cc_start: 0.9289 (mm-30) cc_final: 0.8879 (tp30)
REVERT: B  594 MET cc_start: 0.8728 (tmm) cc_final: 0.8022 (tmm)
REVERT: B  844 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8272 (ptt)
  outliers start: 4
  outliers final: 3
  residues processed: 21
  average time/residue: 0.0813
  time to fit residues: 2.6914
Evaluate side-chains
  23 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  816 ILE
Chi-restraints excluded: chain B residue  844 MET
Chi-restraints excluded: chain B residue  992 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 44 optimal weight:    0.4980
   chunk 8 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 5 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 94 optimal weight:    5.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B 234 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.046316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.031121 restraints weight = 40209.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.2590 rms_B_bonded: 4.37
r_work: 0.2424 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.2424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8867
moved from start:          0.1364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8262  Z= 0.093
  Angle     :  0.425   7.624  11222  Z= 0.219
  Chirality :  0.039   0.143   1268
  Planarity :  0.003   0.029   1430
  Dihedral  :  5.225  72.254   1147
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  5.82 %
    Favored  : 93.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.43 (0.28), residues: 1009
  helix:  2.72 (0.26), residues: 431
  sheet:  0.78 (0.40), residues: 168
  loop :  0.89 (0.34), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 574 
 TYR   0.010   0.001   TYR B 873 
 PHE   0.010   0.001   PHE B 656 
 TRP   0.005   0.001   TRP B 660 
 HIS   0.002   0.000   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 8262)
  covalent geometry    : angle       0.42543 (11222)
  hydrogen bonds       : bond        0.02738 (  384)
  hydrogen bonds       : angle       3.99835 ( 1056)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: B   53 ASP cc_start: 0.9012 (p0) cc_final: 0.8705 (p0)
REVERT: B  475 MET cc_start: 0.9083 (mmm) cc_final: 0.8750 (mmm)
REVERT: B  594 MET cc_start: 0.8738 (tmm) cc_final: 0.8013 (tmm)
REVERT: B  844 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8259 (ptt)
  outliers start: 4
  outliers final: 2
  residues processed: 22
  average time/residue: 0.0824
  time to fit residues: 2.9171
Evaluate side-chains
  23 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  844 MET
Chi-restraints excluded: chain B residue  992 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 70 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 76 optimal weight:    0.4980
   chunk 4 optimal weight:    0.8980
   chunk 87 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.046376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.031193 restraints weight = 40410.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.2593 rms_B_bonded: 4.38
r_work: 0.2427 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.2427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8866
moved from start:          0.1428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8262  Z= 0.095
  Angle     :  0.429   8.156  11222  Z= 0.221
  Chirality :  0.039   0.174   1268
  Planarity :  0.003   0.035   1430
  Dihedral  :  5.233  72.309   1147
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  5.94 %
    Favored  : 93.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.44 (0.28), residues: 1009
  helix:  2.73 (0.26), residues: 431
  sheet:  0.78 (0.39), residues: 168
  loop :  0.90 (0.34), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 574 
 TYR   0.009   0.001   TYR B 873 
 PHE   0.010   0.001   PHE B 656 
 TRP   0.005   0.001   TRP B 660 
 HIS   0.001   0.000   HIS B 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 8262)
  covalent geometry    : angle       0.42893 (11222)
  hydrogen bonds       : bond        0.02745 (  384)
  hydrogen bonds       : angle       3.96296 ( 1056)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: B   53 ASP cc_start: 0.9010 (p0) cc_final: 0.8714 (p0)
REVERT: B  594 MET cc_start: 0.8763 (tmm) cc_final: 0.8045 (tmm)
REVERT: B  844 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8305 (ptt)
  outliers start: 3
  outliers final: 2
  residues processed: 22
  average time/residue: 0.0797
  time to fit residues: 2.7771
Evaluate side-chains
  23 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  614 HIS
Chi-restraints excluded: chain B residue  844 MET
Chi-restraints excluded: chain B residue  992 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 68 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 18 optimal weight:    8.9990
   chunk 25 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 27 optimal weight:    6.9990
   chunk 87 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0000
   overall best weight:    0.6984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.046433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2643 r_free = 0.2643 target = 0.031308 restraints weight = 40430.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.2597 rms_B_bonded: 4.38
r_work: 0.2431 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.2431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8863
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   8262  Z= 0.087
  Angle     :  0.438  11.991  11222  Z= 0.221
  Chirality :  0.039   0.140   1268
  Planarity :  0.003   0.040   1430
  Dihedral  :  5.137  72.106   1147
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  6.27 %
    Favored  : 93.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.45 (0.28), residues: 1009
  helix:  2.75 (0.26), residues: 431
  sheet:  0.77 (0.39), residues: 168
  loop :  0.90 (0.34), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 869 
 TYR   0.008   0.001   TYR B 663 
 PHE   0.010   0.001   PHE B 656 
 TRP   0.005   0.001   TRP B 660 
 HIS   0.001   0.000   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00191 ( 8262)
  covalent geometry    : angle       0.43821 (11222)
  hydrogen bonds       : bond        0.02640 (  384)
  hydrogen bonds       : angle       3.89380 ( 1056)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1565.34 seconds
wall clock time: 27 minutes 33.55 seconds (1653.55 seconds total)