Starting phenix.real_space_refine
on Wed Feb  4 14:49:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9waw_65827/02_2026/9waw_65827.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9waw_65827/02_2026/9waw_65827.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9waw_65827/02_2026/9waw_65827.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9waw_65827/02_2026/9waw_65827.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9waw_65827/02_2026/9waw_65827.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9waw_65827/02_2026/9waw_65827.cif"
  }
  resolution = 3.95
  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=   0.005 sd=   0.037
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     135      5.49       5
     S      19      5.16       5
     C    6647      2.51       5
     N    1985      2.21       5
     O    2454      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 11240
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1025, 8391
          Classifications: {'peptide': 1025}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 27, 'TRANS': 997}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 582
          Classifications: {'DNA': 28}
          Link IDs: {'rna3p': 27}
    Chain: "C"
      Number of atoms: 308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 308
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
    Chain: "D"
      Number of atoms: 1959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 1959
          Classifications: {'RNA': 92}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 43, 'rna3p_pyr': 35}
          Link IDs: {'rna2p': 13, 'rna3p': 78}
  Time building chain proxies: 2.17, per 1000 atoms: 0.19
  Number of scatterers: 11240
  At special positions: 0
  Unit cell: (120.736, 101.332, 150.92, 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      19     16.00
     P     135     15.00
     O    2454      8.00
     N    1985      7.00
     C    6647      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: 0.96
  Conformation dependent library (CDL) restraints added in 407.7 milliseconds
  

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1950

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 6 sheets defined
      54.4% alpha, 9.3% beta
      49 base pairs and 80 stacking pairs defined.
    Time for finding SS restraints: 1.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 94
      removed outlier: 4.567A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.299A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LYS A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL A  93 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 104
    Processing helix  chain 'A' and resid 121 through 132
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 3.555A  pdb=" N   LEU A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
    Processing helix  chain 'A' and resid 293 through 306
      removed outlier: 3.581A  pdb=" N   ILE A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 343
      removed outlier: 3.704A  pdb=" N   ALA A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 352
    Processing helix  chain 'A' and resid 358 through 364
    Processing helix  chain 'A' and resid 368 through 383
      Proline residue:  A 378  - end of helix
    Processing helix  chain 'A' and resid 386 through 395
    Processing helix  chain 'A' and resid 404 through 410
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 4.122A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 446
      removed outlier: 3.824A  pdb=" N   LYS A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
      removed outlier: 4.968A  pdb=" N   GLU A 438 " --> pdb=" O   LYS A 434 " (cutoff:3.500A)
      removed outlier: 5.300A  pdb=" N   LYS A 439 " --> pdb=" O   ASP A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 476
      No H-bonds generated for 'chain 'A' and resid 474 through 476'
    Processing helix  chain 'A' and resid 477 through 482
    Processing helix  chain 'A' and resid 483 through 494
    Processing helix  chain 'A' and resid 512 through 526
      removed outlier: 3.999A  pdb=" N   LYS A 526 " --> pdb=" O   ASN A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 552
    Processing helix  chain 'A' and resid 560 through 568
    Processing helix  chain 'A' and resid 591 through 601
    Processing helix  chain 'A' and resid 603 through 609
    Processing helix  chain 'A' and resid 612 through 626
    Processing helix  chain 'A' and resid 628 through 637
    Processing helix  chain 'A' and resid 638 through 640
      No H-bonds generated for 'chain 'A' and resid 638 through 640'
    Processing helix  chain 'A' and resid 644 through 654
      removed outlier: 3.519A  pdb=" N   ARG A 653 " --> pdb=" O   LYS A 649 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ARG A 654 " --> pdb=" O   GLN A 650 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 664 through 668
    Processing helix  chain 'A' and resid 678 through 685
    Processing helix  chain 'A' and resid 692 through 699
    Processing helix  chain 'A' and resid 703 through 712
    Processing helix  chain 'A' and resid 721 through 727
    Processing helix  chain 'A' and resid 730 through 751
    Processing helix  chain 'A' and resid 925 through 940
      removed outlier: 3.685A  pdb=" N   LYS A 929 " --> pdb=" O   ARG A 925 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 959 through 970
      removed outlier: 3.838A  pdb=" N   VAL A 963 " --> pdb=" O   LYS A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 980 through 1000
      removed outlier: 4.457A  pdb=" N   ALA A 984 " --> pdb=" O   ASN A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1078 through 1088
      removed outlier: 3.579A  pdb=" N   SER A1088 " --> pdb=" O   ARG A1084 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1170 through 1177
      removed outlier: 3.735A  pdb=" N   ASN A1177 " --> pdb=" O   SER A1173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1185
    Processing helix  chain 'A' and resid 1191 through 1195
    Processing helix  chain 'A' and resid 1207 through 1209
      No H-bonds generated for 'chain 'A' and resid 1207 through 1209'
    Processing helix  chain 'A' and resid 1229 through 1241
    Processing helix  chain 'A' and resid 1248 through 1262
    Processing helix  chain 'A' and resid 1264 through 1281
      removed outlier: 3.662A  pdb=" N   GLU A1268 " --> pdb=" O   HIS A1264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1297
    Processing helix  chain 'A' and resid 1301 through 1313
      removed outlier: 3.718A  pdb=" N   PHE A1313 " --> pdb=" O   ILE A1309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1314 through 1316
      No H-bonds generated for 'chain 'A' and resid 1314 through 1316'
    Processing helix  chain 'A' and resid 1340 through 1344
    Processing helix  chain 'A' and resid 1363 through 1365
      No H-bonds generated for 'chain 'A' and resid 1363 through 1365'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957
      removed outlier: 6.610A  pdb=" N   ILE A 759 " --> pdb=" O   ILE A 956 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASN A1093 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   VAL A1095 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46
      removed outlier: 9.752A  pdb=" N   GLU A1357 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   LYS A  33 " --> pdb=" O   GLU A1357 " (cutoff:3.500A)
      removed outlier: 8.078A  pdb=" N   ARG A1359 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   SER A1202 " --> pdb=" O   LEU A1214 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 509
      removed outlier: 5.259A  pdb=" N   LEU A 508 " --> pdb=" O   GLY A 660 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539
      removed outlier: 3.612A  pdb=" N   ALA A 538 " --> pdb=" O   TYR A 529 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   LYS A 528 " --> pdb=" O   SER A 581 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.532A  pdb=" N   ALA A1147 " --> pdb=" O   VAL A1160 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1324 through 1326
      removed outlier: 3.560A  pdb=" N   PHE A1324 " --> pdb=" O   ILE A1331 " (cutoff:3.500A)

    400 hydrogen bonds defined for protein.
    1164 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      121 hydrogen bonds
      230 hydrogen bond angles
      0 basepair planarities
      49 basepair parallelities
      80 stacking parallelities
  Total time for adding SS restraints: 2.33

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2477
        1.33 -     1.45: 3068
        1.45 -     1.57: 5885
        1.57 -     1.69: 267
        1.69 -     1.81: 36
  Bond restraints: 11733
  Sorted by residual:
  bond pdb=" C3'  DG B   7 "
       pdb=" O3'  DG B   7 "
    ideal  model  delta    sigma   weight residual
    1.422  1.459 -0.037 3.00e-02 1.11e+03 1.51e+00
  bond pdb=" CA  ASP A  94 "
       pdb=" C   ASP A  94 "
    ideal  model  delta    sigma   weight residual
    1.522  1.534 -0.012 1.08e-02 8.57e+03 1.25e+00
  bond pdb=" C4'  DC B  14 "
       pdb=" O4'  DC B  14 "
    ideal  model  delta    sigma   weight residual
    1.450  1.433  0.017 2.00e-02 2.50e+03 7.44e-01
  bond pdb=" O4'  DG B   7 "
       pdb=" C1'  DG B   7 "
    ideal  model  delta    sigma   weight residual
    1.414  1.397  0.017 2.00e-02 2.50e+03 6.93e-01
  bond pdb=" C3'  DA B  27 "
       pdb=" C2'  DA B  27 "
    ideal  model  delta    sigma   weight residual
    1.525  1.541 -0.016 2.00e-02 2.50e+03 6.12e-01
  ... (remaining 11728 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.02: 15500
        1.02 -     2.04: 763
        2.04 -     3.07: 124
        3.07 -     4.09: 26
        4.09 -     5.11: 8
  Bond angle restraints: 16421
  Sorted by residual:
  angle pdb=" CA  VAL A1280 "
        pdb=" C   VAL A1280 "
        pdb=" N   ILE A1281 "
      ideal   model   delta    sigma   weight residual
     116.60  121.22   -4.62 1.45e+00 4.76e-01 1.01e+01
  angle pdb=" C   ARG A 494 "
        pdb=" N   MET A 495 "
        pdb=" CA  MET A 495 "
      ideal   model   delta    sigma   weight residual
     122.08  126.39   -4.31 1.47e+00 4.63e-01 8.58e+00
  angle pdb=" N   VAL A1280 "
        pdb=" CA  VAL A1280 "
        pdb=" C   VAL A1280 "
      ideal   model   delta    sigma   weight residual
     109.34  114.45   -5.11 2.08e+00 2.31e-01 6.04e+00
  angle pdb=" N   ASP A 585 "
        pdb=" CA  ASP A 585 "
        pdb=" CB  ASP A 585 "
      ideal   model   delta    sigma   weight residual
     113.65  110.18    3.47 1.47e+00 4.63e-01 5.59e+00
  angle pdb=" C3'  DT B   6 "
        pdb=" C2'  DT B   6 "
        pdb=" C1'  DT B   6 "
      ideal   model   delta    sigma   weight residual
     101.60   98.08    3.52 1.50e+00 4.44e-01 5.52e+00
  ... (remaining 16416 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.85: 6673
       30.85 -    61.70: 367
       61.70 -    92.55: 72
       92.55 -   123.40: 1
      123.40 -   154.25: 1
  Dihedral angle restraints: 7114
    sinusoidal: 4103
      harmonic: 3011
  Sorted by residual:
  dihedral pdb=" C4'  DG B   7 "
           pdb=" C3'  DG B   7 "
           pdb=" O3'  DG B   7 "
           pdb=" P    DA B   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   14.25 -154.25     1      3.50e+01 8.16e-04 1.49e+01
  dihedral pdb=" CA  PHE A 446 "
           pdb=" C   PHE A 446 "
           pdb=" N   ARG A 447 "
           pdb=" CA  ARG A 447 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.51   18.49     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  LEU A 625 "
           pdb=" C   LEU A 625 "
           pdb=" N   PHE A 626 "
           pdb=" CA  PHE A 626 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.97  -17.03     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 7111 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1369
       0.031 -    0.062: 355
       0.062 -    0.093: 114
       0.093 -    0.124: 49
       0.124 -    0.155: 7
  Chirality restraints: 1894
  Sorted by residual:
  chirality pdb=" C1'   A D  34 "
            pdb=" O4'   A D  34 "
            pdb=" C2'   A D  34 "
            pdb=" N9    A D  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.30    0.15 2.00e-01 2.50e+01 5.97e-01
  chirality pdb=" C1'   A D  42 "
            pdb=" O4'   A D  42 "
            pdb=" C2'   A D  42 "
            pdb=" N9    A D  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.31    0.15 2.00e-01 2.50e+01 5.79e-01
  chirality pdb=" C4'   U D  12 "
            pdb=" C5'   U D  12 "
            pdb=" O4'   U D  12 "
            pdb=" C3'   U D  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.35   -0.15 2.00e-01 2.50e+01 5.41e-01
  ... (remaining 1891 not shown)

  Planarity restraints: 1599
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  34 "   -0.026 2.00e-02 2.50e+03   1.20e-02 3.97e+00
        pdb=" N9    A D  34 "    0.028 2.00e-02 2.50e+03
        pdb=" C8    A D  34 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    A D  34 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    A D  34 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A D  34 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6    A D  34 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    A D  34 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A D  34 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A D  34 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A D  34 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  42 "    0.025 2.00e-02 2.50e+03   1.12e-02 3.43e+00
        pdb=" N9    A D  42 "   -0.025 2.00e-02 2.50e+03
        pdb=" C8    A D  42 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7    A D  42 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    A D  42 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    A D  42 "    0.005 2.00e-02 2.50e+03
        pdb=" N6    A D  42 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    A D  42 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    A D  42 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A D  42 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    A D  42 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U D  10 "    0.023 2.00e-02 2.50e+03   1.23e-02 3.40e+00
        pdb=" N1    U D  10 "   -0.026 2.00e-02 2.50e+03
        pdb=" C2    U D  10 "    0.002 2.00e-02 2.50e+03
        pdb=" O2    U D  10 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    U D  10 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    U D  10 "    0.007 2.00e-02 2.50e+03
        pdb=" O4    U D  10 "    0.006 2.00e-02 2.50e+03
        pdb=" C5    U D  10 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    U D  10 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1596 not shown)

  Histogram of nonbonded interaction distances:
        1.30 -     2.02: 5
        2.02 -     2.74: 936
        2.74 -     3.46: 15538
        3.46 -     4.18: 28453
        4.18 -     4.90: 45587
  Nonbonded interactions: 90519
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 742 "
            pdb=" OP1   C D  67 "
     model   vdw
     1.296 3.120
  nonbonded pdb=" NZ  LYS A  44 "
            pdb=" O6    G D  92 "
     model   vdw
     1.297 3.120
  nonbonded pdb=" ND2 ASN A  77 "
            pdb=" O2    U D  59 "
     model   vdw
     1.298 3.120
  nonbonded pdb=" NH1 ARG A 340 "
            pdb=" OP1   A D  41 "
     model   vdw
     1.298 3.120
  nonbonded pdb=" NH2 ARG A1122 "
            pdb=" N3    A D  49 "
     model   vdw
     1.353 3.200
  ... (remaining 90514 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.380
  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:                    0.030
  Process input model:                     11.630
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
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   0.037  11733  Z= 0.130
  Angle     :  0.517   5.111  16421  Z= 0.309
  Chirality :  0.035   0.155   1894
  Planarity :  0.003   0.035   1599
  Dihedral  : 17.165 154.251   5164
  Min Nonbonded Distance : 1.296

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.85 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.27), residues: 1017
  helix:  2.09 (0.24), residues: 511
  sheet:  1.02 (0.66), residues: 68
  loop :  0.29 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  71 
 TYR   0.008   0.001   TYR A 451 
 PHE   0.009   0.001   PHE A 491 
 TRP   0.015   0.002   TRP A1126 
 HIS   0.006   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (11733)
  covalent geometry    : angle       0.51690 (16421)
  hydrogen bonds       : bond        0.16176 (  521)
  hydrogen bonds       : angle       5.57888 ( 1394)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  517 TYR cc_start: 0.8381 (m-80) cc_final: 0.7870 (m-80)
REVERT: A  569 PHE cc_start: 0.9184 (m-80) cc_final: 0.8897 (m-80)
REVERT: A  651 LEU cc_start: 0.9346 (mt) cc_final: 0.8956 (pp)
REVERT: A  948 LYS cc_start: 0.9194 (tttt) cc_final: 0.8826 (mptt)
REVERT: A 1099 GLU cc_start: 0.7386 (mt-10) cc_final: 0.5567 (mt-10)
REVERT: A 1365 LEU cc_start: 0.9051 (mt) cc_final: 0.8699 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 231
  average time/residue: 0.1376
  time to fit residues: 41.4243
Evaluate side-chains
  137 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:   20.0000
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:   10.0000
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:   20.0000
   chunk 100 optimal weight:   10.0000
   overall best weight:    5.0990

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

Flipped N/Q/H residues before XYZ refinement:
** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 556 ASN
** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 933 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.057248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.038761 restraints weight = 76806.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.040254 restraints weight = 42393.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.041191 restraints weight = 29468.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.041861 restraints weight = 23486.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.042226 restraints weight = 20339.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.2916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11733  Z= 0.215
  Angle     :  0.658  10.152  16421  Z= 0.354
  Chirality :  0.041   0.211   1894
  Planarity :  0.005   0.052   1599
  Dihedral  : 20.046 178.656   2981
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  :  8.80 %
    Favored  : 89.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.26), residues: 1017
  helix:  1.55 (0.23), residues: 511
  sheet:  1.82 (0.75), residues: 55
  loop :  0.02 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 635 
 TYR   0.013   0.002   TYR A1326 
 PHE   0.024   0.002   PHE A1324 
 TRP   0.008   0.002   TRP A 659 
 HIS   0.007   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (11733)
  covalent geometry    : angle       0.65845 (16421)
  hydrogen bonds       : bond        0.05994 (  521)
  hydrogen bonds       : angle       4.67824 ( 1394)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 MET cc_start: 0.9471 (ttm) cc_final: 0.9212 (mmm)
REVERT: A  383 MET cc_start: 0.7962 (ttm) cc_final: 0.7740 (ttm)
REVERT: A  399 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8949 (tp)
REVERT: A  416 LEU cc_start: 0.9702 (OUTLIER) cc_final: 0.9309 (mt)
REVERT: A  484 LYS cc_start: 0.9667 (mtpt) cc_final: 0.9149 (mmtp)
REVERT: A  534 MET cc_start: 0.6551 (mtt) cc_final: 0.6124 (mtp)
REVERT: A  651 LEU cc_start: 0.9218 (mt) cc_final: 0.8936 (mt)
REVERT: A  746 GLU cc_start: 0.9513 (tp30) cc_final: 0.9099 (tp30)
REVERT: A  751 MET cc_start: 0.9084 (tpp) cc_final: 0.8799 (mtp)
REVERT: A 1089 MET cc_start: 0.7982 (tpp) cc_final: 0.7559 (tpp)
REVERT: A 1096 LYS cc_start: 0.9528 (tptt) cc_final: 0.9254 (tptm)
REVERT: A 1097 LYS cc_start: 0.9469 (tptp) cc_final: 0.8944 (tptt)
REVERT: A 1099 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8484 (mt-10)
REVERT: A 1213 MET cc_start: 0.9274 (ttm) cc_final: 0.8793 (tpp)
REVERT: A 1214 LEU cc_start: 0.9807 (tp) cc_final: 0.9445 (tp)
REVERT: A 1313 PHE cc_start: 0.9503 (m-80) cc_final: 0.9082 (m-10)
REVERT: A 1324 PHE cc_start: 0.8169 (p90) cc_final: 0.7926 (p90)
  outliers start: 19
  outliers final: 10
  residues processed: 149
  average time/residue: 0.1141
  time to fit residues: 22.9830
Evaluate side-chains
  121 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  590 SER
Chi-restraints excluded: chain A residue  667 ILE
Chi-restraints excluded: chain A residue  975 VAL
Chi-restraints excluded: chain A residue  978 ILE
Chi-restraints excluded: chain A residue 1083 VAL
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1318 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 82 optimal weight:    5.9990
   chunk 71 optimal weight:    9.9990
   chunk 69 optimal weight:    9.9990
   chunk 100 optimal weight:    9.9990
   chunk 5 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0000
   chunk 103 optimal weight:   10.0000
   chunk 41 optimal weight:   30.0000
   chunk 24 optimal weight:    9.9990
   chunk 112 optimal weight:   20.0000
   overall best weight:    5.3590

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

Flipped N/Q/H residues before XYZ refinement:
** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 407 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.055340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.037053 restraints weight = 78122.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.038481 restraints weight = 42871.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.039384 restraints weight = 29681.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.040021 restraints weight = 23703.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.040388 restraints weight = 20464.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.3707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11733  Z= 0.214
  Angle     :  0.614   8.781  16421  Z= 0.337
  Chirality :  0.039   0.219   1894
  Planarity :  0.004   0.051   1599
  Dihedral  : 20.160 177.570   2981
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 10.11 %
    Favored  : 87.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.26), residues: 1017
  helix:  1.37 (0.23), residues: 511
  sheet:  0.91 (0.66), residues: 65
  loop :  0.01 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1212 
 TYR   0.023   0.002   TYR A 517 
 PHE   0.016   0.002   PHE A 970 
 TRP   0.008   0.002   TRP A 659 
 HIS   0.006   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (11733)
  covalent geometry    : angle       0.61398 (16421)
  hydrogen bonds       : bond        0.05733 (  521)
  hydrogen bonds       : angle       4.62712 ( 1394)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLU cc_start: 0.9547 (pm20) cc_final: 0.9278 (pm20)
REVERT: A   90 MET cc_start: 0.9291 (tpt) cc_final: 0.9037 (tpp)
REVERT: A  321 MET cc_start: 0.9846 (mmp) cc_final: 0.9460 (mmm)
REVERT: A  399 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8958 (tp)
REVERT: A  484 LYS cc_start: 0.9703 (mtpt) cc_final: 0.9146 (mmtp)
REVERT: A  534 MET cc_start: 0.6553 (mtt) cc_final: 0.6140 (mtp)
REVERT: A  651 LEU cc_start: 0.9135 (mt) cc_final: 0.8909 (mt)
REVERT: A  746 GLU cc_start: 0.9551 (tp30) cc_final: 0.9160 (tp30)
REVERT: A  751 MET cc_start: 0.9114 (tpp) cc_final: 0.8711 (mtp)
REVERT: A  928 THR cc_start: 0.9754 (m) cc_final: 0.9490 (p)
REVERT: A  929 LYS cc_start: 0.9725 (mttt) cc_final: 0.9417 (mmtt)
REVERT: A 1089 MET cc_start: 0.7938 (tpp) cc_final: 0.7696 (tpp)
REVERT: A 1097 LYS cc_start: 0.9443 (tptp) cc_final: 0.8947 (tptt)
REVERT: A 1099 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8674 (mt-10)
REVERT: A 1268 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8717 (mp0)
REVERT: A 1313 PHE cc_start: 0.9535 (m-80) cc_final: 0.9060 (m-10)
  outliers start: 19
  outliers final: 10
  residues processed: 123
  average time/residue: 0.1115
  time to fit residues: 19.1589
Evaluate side-chains
  112 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  975 VAL
Chi-restraints excluded: chain A residue  978 ILE
Chi-restraints excluded: chain A residue 1197 LYS
Chi-restraints excluded: chain A residue 1263 LYS
Chi-restraints excluded: chain A residue 1318 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 40 optimal weight:   20.0000
   chunk 71 optimal weight:    0.8980
   chunk 52 optimal weight:   20.0000
   chunk 83 optimal weight:    7.9990
   chunk 76 optimal weight:    8.9990
   chunk 97 optimal weight:   10.0000
   chunk 17 optimal weight:    0.7980
   chunk 75 optimal weight:    9.9990
   chunk 6 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 43 optimal weight:    9.9990
   overall best weight:    5.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.053470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.035557 restraints weight = 81224.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.036975 restraints weight = 43945.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.037851 restraints weight = 30390.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.038479 restraints weight = 24264.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.038889 restraints weight = 20899.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.4535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11733  Z= 0.225
  Angle     :  0.628   8.562  16421  Z= 0.346
  Chirality :  0.040   0.220   1894
  Planarity :  0.004   0.049   1599
  Dihedral  : 20.388 177.930   2981
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 17.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 11.20 %
    Favored  : 85.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.26), residues: 1017
  helix:  1.04 (0.23), residues: 513
  sheet:  1.00 (0.70), residues: 56
  loop : -0.19 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 494 
 TYR   0.025   0.002   TYR A 517 
 PHE   0.016   0.002   PHE A 164 
 TRP   0.017   0.002   TRP A 659 
 HIS   0.006   0.002   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 (11733)
  covalent geometry    : angle       0.62763 (16421)
  hydrogen bonds       : bond        0.05901 (  521)
  hydrogen bonds       : angle       4.71084 ( 1394)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.9268 (OUTLIER) cc_final: 0.8632 (mm-30)
REVERT: A  321 MET cc_start: 0.9748 (mmp) cc_final: 0.9540 (mmm)
REVERT: A  379 ILE cc_start: 0.9586 (OUTLIER) cc_final: 0.9208 (mp)
REVERT: A  399 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9049 (tp)
REVERT: A  484 LYS cc_start: 0.9712 (mtpt) cc_final: 0.9328 (mttm)
REVERT: A  534 MET cc_start: 0.6661 (mtt) cc_final: 0.6166 (mtp)
REVERT: A  746 GLU cc_start: 0.9568 (tp30) cc_final: 0.9339 (tp30)
REVERT: A  751 MET cc_start: 0.9194 (tpp) cc_final: 0.8705 (mtp)
REVERT: A 1089 MET cc_start: 0.7988 (tpp) cc_final: 0.7541 (tpp)
REVERT: A 1097 LYS cc_start: 0.9432 (tptp) cc_final: 0.8738 (tptt)
REVERT: A 1099 GLU cc_start: 0.9319 (mt-10) cc_final: 0.8605 (mt-10)
REVERT: A 1313 PHE cc_start: 0.9550 (m-80) cc_final: 0.8962 (m-10)
  outliers start: 27
  outliers final: 13
  residues processed: 121
  average time/residue: 0.1010
  time to fit residues: 16.9151
Evaluate side-chains
  110 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  667 ILE
Chi-restraints excluded: chain A residue  975 VAL
Chi-restraints excluded: chain A residue  978 ILE
Chi-restraints excluded: chain A residue 1083 VAL
Chi-restraints excluded: chain A residue 1190 VAL
Chi-restraints excluded: chain A residue 1197 LYS
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain A residue 1342 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 54 optimal weight:    8.9990
   chunk 34 optimal weight:    9.9990
   chunk 32 optimal weight:    4.9990
   chunk 109 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9980
   chunk 95 optimal weight:    8.9990
   chunk 76 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   chunk 18 optimal weight:    8.9990
   chunk 52 optimal weight:    8.9990
   overall best weight:    6.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.052033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.034445 restraints weight = 81365.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.035784 restraints weight = 44535.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.036628 restraints weight = 30957.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.037229 restraints weight = 24821.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.037606 restraints weight = 21508.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.5134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  11733  Z= 0.251
  Angle     :  0.655   9.164  16421  Z= 0.358
  Chirality :  0.040   0.230   1894
  Planarity :  0.004   0.048   1599
  Dihedral  : 20.648 177.403   2981
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 19.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 12.93 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.26), residues: 1017
  helix:  0.80 (0.22), residues: 513
  sheet:  0.64 (0.69), residues: 56
  loop : -0.31 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 395 
 TYR   0.023   0.002   TYR A 517 
 PHE   0.024   0.002   PHE A 164 
 TRP   0.015   0.002   TRP A 659 
 HIS   0.007   0.002   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 (11733)
  covalent geometry    : angle       0.65454 (16421)
  hydrogen bonds       : bond        0.06135 (  521)
  hydrogen bonds       : angle       4.88886 ( 1394)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8535 (mm-30)
REVERT: A  321 MET cc_start: 0.9709 (mmp) cc_final: 0.9454 (mmm)
REVERT: A  383 MET cc_start: 0.9137 (mmm) cc_final: 0.8468 (ttt)
REVERT: A  399 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8993 (tp)
REVERT: A  484 LYS cc_start: 0.9726 (mtpt) cc_final: 0.9519 (ttmm)
REVERT: A  534 MET cc_start: 0.6801 (mtt) cc_final: 0.6293 (mtp)
REVERT: A  653 ARG cc_start: 0.9004 (ptp-170) cc_final: 0.8730 (ptt-90)
REVERT: A  746 GLU cc_start: 0.9632 (tp30) cc_final: 0.9401 (tp30)
REVERT: A  751 MET cc_start: 0.9233 (tpp) cc_final: 0.8750 (mtp)
REVERT: A 1089 MET cc_start: 0.7953 (tpp) cc_final: 0.7608 (tpp)
REVERT: A 1097 LYS cc_start: 0.9426 (tptp) cc_final: 0.8675 (tptt)
REVERT: A 1099 GLU cc_start: 0.9334 (mt-10) cc_final: 0.8568 (mt-10)
REVERT: A 1122 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8378 (mtm110)
REVERT: A 1197 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8790 (mmtm)
REVERT: A 1313 PHE cc_start: 0.9541 (m-80) cc_final: 0.9187 (m-10)
  outliers start: 21
  outliers final: 13
  residues processed: 108
  average time/residue: 0.1165
  time to fit residues: 17.0532
Evaluate side-chains
  107 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  440 ILE
Chi-restraints excluded: chain A residue  631 MET
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  978 ILE
Chi-restraints excluded: chain A residue 1083 VAL
Chi-restraints excluded: chain A residue 1122 ARG
Chi-restraints excluded: chain A residue 1166 ILE
Chi-restraints excluded: chain A residue 1190 VAL
Chi-restraints excluded: chain A residue 1197 LYS
Chi-restraints excluded: chain A residue 1318 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 42 optimal weight:   50.0000
   chunk 7 optimal weight:    5.9990
   chunk 48 optimal weight:   20.0000
   chunk 87 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 45 optimal weight:   30.0000
   chunk 79 optimal weight:   10.0000
   chunk 85 optimal weight:    3.9990
   chunk 101 optimal weight:    8.9990
   chunk 99 optimal weight:   20.0000
   chunk 33 optimal weight:    0.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 412 HIS
** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.052504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.034826 restraints weight = 81353.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.036229 restraints weight = 43365.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.037092 restraints weight = 29840.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.037710 restraints weight = 23807.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.037988 restraints weight = 20448.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.5369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  11733  Z= 0.201
  Angle     :  0.630  10.354  16421  Z= 0.340
  Chirality :  0.040   0.208   1894
  Planarity :  0.004   0.051   1599
  Dihedral  : 20.633 174.521   2981
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 16.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 13.91 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.26), residues: 1017
  helix:  0.97 (0.23), residues: 507
  sheet:  0.96 (0.72), residues: 54
  loop : -0.24 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 494 
 TYR   0.025   0.002   TYR A 517 
 PHE   0.018   0.002   PHE A 164 
 TRP   0.010   0.002   TRP A  18 
 HIS   0.007   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (11733)
  covalent geometry    : angle       0.62960 (16421)
  hydrogen bonds       : bond        0.05410 (  521)
  hydrogen bonds       : angle       4.71212 ( 1394)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8630 (mm-30)
REVERT: A  321 MET cc_start: 0.9724 (mmp) cc_final: 0.9473 (mmm)
REVERT: A  383 MET cc_start: 0.9214 (mmm) cc_final: 0.8564 (ttt)
REVERT: A  399 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8955 (tp)
REVERT: A  534 MET cc_start: 0.6755 (mtt) cc_final: 0.6284 (mtp)
REVERT: A  746 GLU cc_start: 0.9632 (tp30) cc_final: 0.9399 (tp30)
REVERT: A  751 MET cc_start: 0.9217 (tpp) cc_final: 0.8748 (mtp)
REVERT: A 1089 MET cc_start: 0.7973 (tpp) cc_final: 0.7634 (tpp)
REVERT: A 1097 LYS cc_start: 0.9442 (tptp) cc_final: 0.8682 (tptt)
REVERT: A 1099 GLU cc_start: 0.9339 (mt-10) cc_final: 0.8551 (mt-10)
REVERT: A 1122 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8396 (mtm110)
REVERT: A 1258 PHE cc_start: 0.9434 (OUTLIER) cc_final: 0.9097 (m-80)
REVERT: A 1313 PHE cc_start: 0.9513 (m-80) cc_final: 0.9203 (m-10)
  outliers start: 22
  outliers final: 10
  residues processed: 109
  average time/residue: 0.1091
  time to fit residues: 16.6772
Evaluate side-chains
  106 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  440 ILE
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  978 ILE
Chi-restraints excluded: chain A residue 1122 ARG
Chi-restraints excluded: chain A residue 1190 VAL
Chi-restraints excluded: chain A residue 1197 LYS
Chi-restraints excluded: chain A residue 1258 PHE
Chi-restraints excluded: chain A residue 1318 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 97 optimal weight:    9.9990
   chunk 89 optimal weight:    9.9990
   chunk 50 optimal weight:    5.9990
   chunk 81 optimal weight:   20.0000
   chunk 20 optimal weight:    8.9990
   chunk 56 optimal weight:   20.0000
   chunk 108 optimal weight:   20.0000
   chunk 33 optimal weight:    6.9990
   chunk 1 optimal weight:    7.9990
   chunk 34 optimal weight:   20.0000
   chunk 51 optimal weight:    6.9990
   overall best weight:    7.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 394 ASN
** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 754 HIS
** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.050424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.033050 restraints weight = 82685.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.034330 restraints weight = 45581.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.035182 restraints weight = 31234.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.035744 restraints weight = 24748.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.036080 restraints weight = 21420.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.5921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  11733  Z= 0.279
  Angle     :  0.710  13.340  16421  Z= 0.382
  Chirality :  0.042   0.214   1894
  Planarity :  0.005   0.048   1599
  Dihedral  : 20.965 176.643   2981
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 21.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.67 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.26), residues: 1017
  helix:  0.58 (0.22), residues: 509
  sheet:  0.65 (0.66), residues: 60
  loop : -0.45 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 765 
 TYR   0.024   0.002   TYR A 517 
 PHE   0.021   0.002   PHE A 164 
 TRP   0.017   0.002   TRP A 659 
 HIS   0.008   0.002   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 (11733)
  covalent geometry    : angle       0.71009 (16421)
  hydrogen bonds       : bond        0.06441 (  521)
  hydrogen bonds       : angle       5.08026 ( 1394)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8284 (t)
REVERT: A  125 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8384 (mm-30)
REVERT: A  321 MET cc_start: 0.9734 (mmp) cc_final: 0.9462 (mmm)
REVERT: A  383 MET cc_start: 0.9201 (mmm) cc_final: 0.8680 (ttt)
REVERT: A  399 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9016 (tp)
REVERT: A  534 MET cc_start: 0.6789 (mtt) cc_final: 0.6265 (mtp)
REVERT: A  742 LYS cc_start: 0.9712 (mttt) cc_final: 0.9476 (mtmm)
REVERT: A  751 MET cc_start: 0.9251 (tpp) cc_final: 0.8740 (mtp)
REVERT: A 1089 MET cc_start: 0.7945 (tpp) cc_final: 0.7572 (tpp)
REVERT: A 1097 LYS cc_start: 0.9418 (tptp) cc_final: 0.8661 (tptt)
REVERT: A 1099 GLU cc_start: 0.9292 (mt-10) cc_final: 0.8489 (mt-10)
REVERT: A 1122 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8374 (mtm110)
REVERT: A 1197 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8747 (mmtm)
REVERT: A 1213 MET cc_start: 0.9317 (ttm) cc_final: 0.8854 (tpt)
REVERT: A 1258 PHE cc_start: 0.9426 (OUTLIER) cc_final: 0.9098 (m-80)
REVERT: A 1313 PHE cc_start: 0.9498 (m-80) cc_final: 0.9089 (m-80)
  outliers start: 24
  outliers final: 12
  residues processed: 108
  average time/residue: 0.1170
  time to fit residues: 17.5138
Evaluate side-chains
  105 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  440 ILE
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  978 ILE
Chi-restraints excluded: chain A residue 1083 VAL
Chi-restraints excluded: chain A residue 1122 ARG
Chi-restraints excluded: chain A residue 1190 VAL
Chi-restraints excluded: chain A residue 1197 LYS
Chi-restraints excluded: chain A residue 1258 PHE
Chi-restraints excluded: chain A residue 1263 LYS
Chi-restraints excluded: chain A residue 1318 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 107 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   chunk 74 optimal weight:    8.9990
   chunk 61 optimal weight:   20.0000
   chunk 14 optimal weight:    0.9980
   chunk 109 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 113 optimal weight:   10.0000
   chunk 110 optimal weight:   10.0000
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.051587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.033948 restraints weight = 80530.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.035321 restraints weight = 43215.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.036217 restraints weight = 29755.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.036751 restraints weight = 23545.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.037045 restraints weight = 20483.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.5990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11733  Z= 0.189
  Angle     :  0.653  14.415  16421  Z= 0.347
  Chirality :  0.040   0.265   1894
  Planarity :  0.004   0.044   1599
  Dihedral  : 20.839 170.497   2981
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 16.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.98 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.26), residues: 1017
  helix:  0.87 (0.23), residues: 504
  sheet:  0.87 (0.71), residues: 54
  loop : -0.36 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 494 
 TYR   0.022   0.002   TYR A 517 
 PHE   0.016   0.002   PHE A 164 
 TRP   0.012   0.002   TRP A  18 
 HIS   0.008   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (11733)
  covalent geometry    : angle       0.65268 (16421)
  hydrogen bonds       : bond        0.05176 (  521)
  hydrogen bonds       : angle       4.83928 ( 1394)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8344 (t)
REVERT: A  125 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8542 (mm-30)
REVERT: A  321 MET cc_start: 0.9745 (mmp) cc_final: 0.9456 (mmm)
REVERT: A  383 MET cc_start: 0.9077 (mmm) cc_final: 0.8744 (ttt)
REVERT: A  399 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8875 (tp)
REVERT: A  534 MET cc_start: 0.7101 (mtt) cc_final: 0.6650 (mtp)
REVERT: A  653 ARG cc_start: 0.9035 (ptp-170) cc_final: 0.8734 (ptt-90)
REVERT: A  751 MET cc_start: 0.9272 (tpp) cc_final: 0.8780 (mtp)
REVERT: A 1089 MET cc_start: 0.8001 (tpp) cc_final: 0.7668 (tpp)
REVERT: A 1097 LYS cc_start: 0.9433 (tptp) cc_final: 0.8654 (tptt)
REVERT: A 1099 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8438 (mt-10)
REVERT: A 1122 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8354 (mtm110)
REVERT: A 1197 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8800 (mmtm)
REVERT: A 1213 MET cc_start: 0.9284 (ttm) cc_final: 0.8814 (tpt)
REVERT: A 1258 PHE cc_start: 0.9404 (OUTLIER) cc_final: 0.9033 (m-80)
REVERT: A 1313 PHE cc_start: 0.9510 (m-80) cc_final: 0.9155 (m-10)
  outliers start: 20
  outliers final: 8
  residues processed: 104
  average time/residue: 0.1298
  time to fit residues: 18.7514
Evaluate side-chains
  96 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  416 LEU
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  667 ILE
Chi-restraints excluded: chain A residue  978 ILE
Chi-restraints excluded: chain A residue 1122 ARG
Chi-restraints excluded: chain A residue 1190 VAL
Chi-restraints excluded: chain A residue 1197 LYS
Chi-restraints excluded: chain A residue 1258 PHE
Chi-restraints excluded: chain A residue 1318 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 79 optimal weight:    9.9990
   chunk 55 optimal weight:    0.7980
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 88 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 99 optimal weight:    8.9990
   chunk 76 optimal weight:   20.0000
   overall best weight:    2.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.053699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.035935 restraints weight = 78767.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.037386 restraints weight = 41745.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.038274 restraints weight = 28283.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.038918 restraints weight = 22328.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.039258 restraints weight = 19241.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.6030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11733  Z= 0.132
  Angle     :  0.654  15.148  16421  Z= 0.336
  Chirality :  0.040   0.300   1894
  Planarity :  0.004   0.043   1599
  Dihedral  : 20.609 167.686   2981
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 17.07 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.26), residues: 1017
  helix:  1.03 (0.23), residues: 511
  sheet:  1.09 (0.72), residues: 54
  loop : -0.23 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 494 
 TYR   0.026   0.001   TYR A 517 
 PHE   0.013   0.001   PHE A 164 
 TRP   0.010   0.001   TRP A  18 
 HIS   0.008   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (11733)
  covalent geometry    : angle       0.65399 (16421)
  hydrogen bonds       : bond        0.04400 (  521)
  hydrogen bonds       : angle       4.60070 ( 1394)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8713 (mm-30)
REVERT: A  321 MET cc_start: 0.9776 (mmp) cc_final: 0.9566 (mmm)
REVERT: A  534 MET cc_start: 0.6982 (mtt) cc_final: 0.6545 (mtp)
REVERT: A  653 ARG cc_start: 0.9017 (ptp-170) cc_final: 0.8708 (ptt-90)
REVERT: A  751 MET cc_start: 0.9222 (tpp) cc_final: 0.8739 (mtp)
REVERT: A 1089 MET cc_start: 0.8017 (tpp) cc_final: 0.7708 (tpp)
REVERT: A 1097 LYS cc_start: 0.9448 (tptp) cc_final: 0.8894 (tptt)
REVERT: A 1197 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8796 (mmtm)
REVERT: A 1213 MET cc_start: 0.9265 (ttm) cc_final: 0.8765 (tpp)
REVERT: A 1258 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.9037 (m-80)
  outliers start: 13
  outliers final: 5
  residues processed: 97
  average time/residue: 0.1106
  time to fit residues: 15.2331
Evaluate side-chains
  90 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  978 ILE
Chi-restraints excluded: chain A residue 1197 LYS
Chi-restraints excluded: chain A residue 1258 PHE
Chi-restraints excluded: chain A residue 1318 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 66 optimal weight:    8.9990
   chunk 107 optimal weight:   10.0000
   chunk 65 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 7 optimal weight:    7.9990
   chunk 44 optimal weight:    0.0770
   chunk 40 optimal weight:    5.9990
   chunk 46 optimal weight:   50.0000
   chunk 83 optimal weight:    9.9990
   overall best weight:    4.4146

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

Flipped N/Q/H residues before XYZ refinement:
** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 739 GLN
A 758 ASN
** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.052123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.034505 restraints weight = 81404.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.035878 restraints weight = 43284.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.036827 restraints weight = 29597.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.037170 restraints weight = 23319.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.037759 restraints weight = 20761.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.6216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11733  Z= 0.184
  Angle     :  0.674  15.376  16421  Z= 0.350
  Chirality :  0.040   0.272   1894
  Planarity :  0.004   0.044   1599
  Dihedral  : 20.760 171.381   2981
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 16.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 17.93 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.26), residues: 1017
  helix:  1.00 (0.23), residues: 504
  sheet:  1.08 (0.74), residues: 54
  loop : -0.35 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 494 
 TYR   0.028   0.002   TYR A 517 
 PHE   0.017   0.002   PHE A 164 
 TRP   0.010   0.001   TRP A  18 
 HIS   0.012   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (11733)
  covalent geometry    : angle       0.67399 (16421)
  hydrogen bonds       : bond        0.05100 (  521)
  hydrogen bonds       : angle       4.75653 ( 1394)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8565 (mm-30)
REVERT: A  321 MET cc_start: 0.9773 (mmp) cc_final: 0.9552 (mmm)
REVERT: A  383 MET cc_start: 0.9212 (mmp) cc_final: 0.8838 (tpp)
REVERT: A  534 MET cc_start: 0.7203 (mtt) cc_final: 0.6807 (mtp)
REVERT: A  653 ARG cc_start: 0.8995 (ptp-170) cc_final: 0.8708 (ptt-90)
REVERT: A  751 MET cc_start: 0.9219 (tpp) cc_final: 0.8650 (mtp)
REVERT: A 1089 MET cc_start: 0.7963 (tpp) cc_final: 0.7607 (tpp)
REVERT: A 1097 LYS cc_start: 0.9466 (tptp) cc_final: 0.8674 (tptt)
REVERT: A 1099 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8462 (mt-10)
REVERT: A 1213 MET cc_start: 0.9265 (ttm) cc_final: 0.8725 (tpp)
REVERT: A 1258 PHE cc_start: 0.9425 (OUTLIER) cc_final: 0.9065 (m-80)
REVERT: A 1327 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7883 (m-80)
  outliers start: 10
  outliers final: 4
  residues processed: 93
  average time/residue: 0.1136
  time to fit residues: 14.9772
Evaluate side-chains
  90 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  128 TYR
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue 1258 PHE
Chi-restraints excluded: chain A residue 1327 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 95 optimal weight:    6.9990
   chunk 89 optimal weight:   10.0000
   chunk 104 optimal weight:    8.9990
   chunk 102 optimal weight:   10.0000
   chunk 57 optimal weight:   40.0000
   chunk 77 optimal weight:    3.9990
   chunk 42 optimal weight:    7.9990
   chunk 81 optimal weight:    7.9990
   chunk 93 optimal weight:    2.9990
   chunk 85 optimal weight:    0.5980
   chunk 54 optimal weight:   10.0000
   overall best weight:    4.5188

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

Flipped N/Q/H residues before XYZ refinement:
** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.051908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.034091 restraints weight = 82400.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.035441 restraints weight = 44816.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.036288 restraints weight = 30254.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.036863 restraints weight = 24058.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.037260 restraints weight = 20756.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.6296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11733  Z= 0.187
  Angle     :  0.685  16.275  16421  Z= 0.356
  Chirality :  0.040   0.285   1894
  Planarity :  0.004   0.044   1599
  Dihedral  : 20.795 170.495   2981
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 16.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 18.37 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.26), residues: 1017
  helix:  0.92 (0.23), residues: 505
  sheet:  1.03 (0.75), residues: 54
  loop : -0.40 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 494 
 TYR   0.050   0.002   TYR A 517 
 PHE   0.016   0.002   PHE A 164 
 TRP   0.010   0.001   TRP A  18 
 HIS   0.010   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (11733)
  covalent geometry    : angle       0.68495 (16421)
  hydrogen bonds       : bond        0.05037 (  521)
  hydrogen bonds       : angle       4.75888 ( 1394)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1897.60 seconds
wall clock time: 33 minutes 37.30 seconds (2017.30 seconds total)