Starting phenix.real_space_refine
on Wed Feb  4 09:20:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9sgy_54882/02_2026/9sgy_54882.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9sgy_54882/02_2026/9sgy_54882.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.34
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9sgy_54882/02_2026/9sgy_54882.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9sgy_54882/02_2026/9sgy_54882.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9sgy_54882/02_2026/9sgy_54882.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9sgy_54882/02_2026/9sgy_54882.map"
  }
  resolution = 2.34
  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=   0.000 sd=   0.006
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
     Fe      1      7.16       5
     S      32      5.16       5
     C    6161      2.51       5
     N    1661      2.21       5
     O    1821      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  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: 9676
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 5337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 700, 5337
          Classifications: {'peptide': 700}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 44, 'TRANS': 655}
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 51
          Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "A"
      Number of atoms: 4296
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4296
          Classifications: {'peptide': 565}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 30, 'TRANS': 534}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 109
          Unresolved non-hydrogen angles: 133
          Unresolved non-hydrogen dihedrals: 100
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 4, 'GLU:plan': 4, 'ASP:plan': 2, 'HIS:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 70
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.23, per 1000 atoms: 0.23
  Number of scatterers: 9676
  At special positions: 0
  Unit cell: (84.048, 95.584, 124.424, 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)
     Fe      1     26.01
     S      32     16.00
     O    1821      8.00
     N    1661      7.00
     C    6161      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.62
  Conformation dependent library (CDL) restraints added in 423.7 milliseconds
  

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2278

  Finding SS restraints...
    Secondary structure from input PDB file:
      73 helices and 5 sheets defined
      57.2% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'B' and resid 44 through 50
      removed outlier: 3.660A  pdb=" N   VAL B  47 " --> pdb=" O   ASN B  44 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   GLN B  50 " --> pdb=" O   VAL B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 56
    Processing helix  chain 'B' and resid 63 through 70
      removed outlier: 3.795A  pdb=" N   THR B  70 " --> pdb=" O   ALA B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 85
    Processing helix  chain 'B' and resid 93 through 97
    Processing helix  chain 'B' and resid 98 through 111
    Processing helix  chain 'B' and resid 125 through 128
      removed outlier: 3.552A  pdb=" N   ARG B 128 " --> pdb=" O   GLY B 125 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 125 through 128'
    Processing helix  chain 'B' and resid 129 through 134
      removed outlier: 3.836A  pdb=" N   SER B 134 " --> pdb=" O   ALA B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 148
      removed outlier: 3.604A  pdb=" N   ALA B 144 " --> pdb=" O   SER B 140 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU B 148 " --> pdb=" O   ALA B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 156
    Processing helix  chain 'B' and resid 157 through 159
      No H-bonds generated for 'chain 'B' and resid 157 through 159'
    Processing helix  chain 'B' and resid 160 through 176
      removed outlier: 3.699A  pdb=" N   VAL B 166 " --> pdb=" O   ALA B 162 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLY B 169 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 234 through 238
    Processing helix  chain 'B' and resid 240 through 254
      removed outlier: 3.835A  pdb=" N   VAL B 246 " --> pdb=" O   MET B 242 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ASP B 247 " --> pdb=" O   ALA B 243 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 272
      removed outlier: 4.104A  pdb=" N   PHE B 272 " --> pdb=" O   GLY B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 284
      removed outlier: 3.584A  pdb=" N   LEU B 283 " --> pdb=" O   PRO B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 291
    Processing helix  chain 'B' and resid 292 through 296
    Processing helix  chain 'B' and resid 308 through 312
    Processing helix  chain 'B' and resid 330 through 339
      removed outlier: 3.779A  pdb=" N   GLU B 334 " --> pdb=" O   ASN B 330 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   TYR B 339 " --> pdb=" O   ILE B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 387
    Processing helix  chain 'B' and resid 387 through 399
      removed outlier: 4.160A  pdb=" N   GLU B 399 " --> pdb=" O   ARG B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 417
      removed outlier: 3.567A  pdb=" N   LEU B 404 " --> pdb=" O   HIS B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 426
    Processing helix  chain 'B' and resid 436 through 440
    Processing helix  chain 'B' and resid 451 through 464
    Processing helix  chain 'B' and resid 468 through 481
    Processing helix  chain 'B' and resid 495 through 498
      removed outlier: 3.887A  pdb=" N   ARG B 498 " --> pdb=" O   GLY B 495 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 495 through 498'
    Processing helix  chain 'B' and resid 499 through 504
      removed outlier: 3.610A  pdb=" N   GLY B 504 " --> pdb=" O   GLN B 500 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 530
    Processing helix  chain 'B' and resid 539 through 559
    Processing helix  chain 'B' and resid 580 through 586
      removed outlier: 4.288A  pdb=" N   VAL B 586 " --> pdb=" O   GLU B 582 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 605 through 617
    Processing helix  chain 'B' and resid 620 through 635
      removed outlier: 3.523A  pdb=" N   VAL B 633 " --> pdb=" O   GLY B 629 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLY B 635 " --> pdb=" O   LEU B 631 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 637 through 641
    Processing helix  chain 'B' and resid 655 through 662
    Processing helix  chain 'B' and resid 692 through 701
      removed outlier: 3.940A  pdb=" N   PHE B 698 " --> pdb=" O   VAL B 694 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   GLY B 699 " --> pdb=" O   ASP B 695 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 701 through 712
    Processing helix  chain 'B' and resid 716 through 733
    Processing helix  chain 'A' and resid 28 through 32
    Processing helix  chain 'A' and resid 44 through 50
      removed outlier: 3.533A  pdb=" N   VAL A  47 " --> pdb=" O   ASN A  44 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLN A  50 " --> pdb=" O   VAL A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 56
    Processing helix  chain 'A' and resid 63 through 69
    Processing helix  chain 'A' and resid 72 through 86
    Processing helix  chain 'A' and resid 93 through 97
    Processing helix  chain 'A' and resid 98 through 111
    Processing helix  chain 'A' and resid 141 through 148
      removed outlier: 3.528A  pdb=" N   LEU A 148 " --> pdb=" O   ALA A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 156
      removed outlier: 3.740A  pdb=" N   LYS A 154 " --> pdb=" O   PRO A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 159
      No H-bonds generated for 'chain 'A' and resid 157 through 159'
    Processing helix  chain 'A' and resid 160 through 176
      removed outlier: 3.584A  pdb=" N   VAL A 166 " --> pdb=" O   ALA A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 258 through 273
    Processing helix  chain 'A' and resid 330 through 337
    Processing helix  chain 'A' and resid 382 through 387
    Processing helix  chain 'A' and resid 387 through 400
      removed outlier: 3.829A  pdb=" N   GLU A 399 " --> pdb=" O   ARG A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 417
      removed outlier: 3.542A  pdb=" N   LEU A 404 " --> pdb=" O   HIS A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 426
    Processing helix  chain 'A' and resid 436 through 440
    Processing helix  chain 'A' and resid 453 through 464
      removed outlier: 3.804A  pdb=" N   SER A 457 " --> pdb=" O   ALA A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 481
    Processing helix  chain 'A' and resid 495 through 498
      removed outlier: 3.865A  pdb=" N   ARG A 498 " --> pdb=" O   GLY A 495 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 495 through 498'
    Processing helix  chain 'A' and resid 499 through 504
      removed outlier: 3.610A  pdb=" N   GLY A 504 " --> pdb=" O   GLN A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 530
    Processing helix  chain 'A' and resid 539 through 560
    Processing helix  chain 'A' and resid 580 through 585
    Processing helix  chain 'A' and resid 586 through 588
      No H-bonds generated for 'chain 'A' and resid 586 through 588'
    Processing helix  chain 'A' and resid 605 through 617
    Processing helix  chain 'A' and resid 620 through 634
    Processing helix  chain 'A' and resid 637 through 641
    Processing helix  chain 'A' and resid 655 through 662
    Processing helix  chain 'A' and resid 693 through 701
      removed outlier: 3.954A  pdb=" N   PHE A 698 " --> pdb=" O   VAL A 694 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   GLY A 699 " --> pdb=" O   ASP A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 701 through 712
    Processing helix  chain 'A' and resid 716 through 733
    Processing sheet with id=AA1, first strand: chain 'B' and resid 341 through 345
    Processing sheet with id=AA2, first strand: chain 'B' and resid 591 through 592
    Processing sheet with id=AA3, first strand: chain 'B' and resid 667 through 670
    Processing sheet with id=AA4, first strand: chain 'A' and resid 591 through 592
    Processing sheet with id=AA5, first strand: chain 'A' and resid 667 through 670

    446 hydrogen bonds defined for protein.
    1218 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.16

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.23 -     1.39: 4053
        1.39 -     1.56: 5811
        1.56 -     1.72: 2
        1.72 -     1.89: 60
        1.89 -     2.05: 4
  Bond restraints: 9930
  Sorted by residual:
  bond pdb=" CB  PRO B 533 "
       pdb=" CG  PRO B 533 "
    ideal  model  delta    sigma   weight residual
    1.492  1.572 -0.080 5.00e-02 4.00e+02 2.56e+00
  bond pdb=" CG  PRO B 533 "
       pdb=" CD  PRO B 533 "
    ideal  model  delta    sigma   weight residual
    1.503  1.553 -0.050 3.40e-02 8.65e+02 2.14e+00
  bond pdb=" CB  GLU B 526 "
       pdb=" CG  GLU B 526 "
    ideal  model  delta    sigma   weight residual
    1.520  1.562 -0.042 3.00e-02 1.11e+03 1.95e+00
  bond pdb=" CB  TRP B 107 "
       pdb=" CG  TRP B 107 "
    ideal  model  delta    sigma   weight residual
    1.498  1.469  0.029 3.10e-02 1.04e+03 8.97e-01
  bond pdb=" CB  GLU A 582 "
       pdb=" CG  GLU A 582 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.85e-01
  ... (remaining 9925 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 13376
        1.80 -     3.60: 142
        3.60 -     5.40: 24
        5.40 -     7.20: 3
        7.20 -     9.00: 1
  Bond angle restraints: 13546
  Sorted by residual:
  angle pdb=" CA  GLU B 526 "
        pdb=" CB  GLU B 526 "
        pdb=" CG  GLU B 526 "
      ideal   model   delta    sigma   weight residual
     114.10  120.18   -6.08 2.00e+00 2.50e-01 9.23e+00
  angle pdb=" CB  GLU B 526 "
        pdb=" CG  GLU B 526 "
        pdb=" CD  GLU B 526 "
      ideal   model   delta    sigma   weight residual
     112.60  117.53   -4.93 1.70e+00 3.46e-01 8.39e+00
  angle pdb=" CA  PRO B 533 "
        pdb=" N   PRO B 533 "
        pdb=" CD  PRO B 533 "
      ideal   model   delta    sigma   weight residual
     112.00  108.12    3.88 1.40e+00 5.10e-01 7.67e+00
  angle pdb=" CB  MET A  58 "
        pdb=" CG  MET A  58 "
        pdb=" SD  MET A  58 "
      ideal   model   delta    sigma   weight residual
     112.70  119.25   -6.55 3.00e+00 1.11e-01 4.76e+00
  angle pdb=" CB  GLU A 582 "
        pdb=" CG  GLU A 582 "
        pdb=" CD  GLU A 582 "
      ideal   model   delta    sigma   weight residual
     112.60  116.06   -3.46 1.70e+00 3.46e-01 4.15e+00
  ... (remaining 13541 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 5165
       17.91 -    35.83: 462
       35.83 -    53.74: 119
       53.74 -    71.65: 28
       71.65 -    89.57: 8
  Dihedral angle restraints: 5782
    sinusoidal: 2211
      harmonic: 3571
  Sorted by residual:
  dihedral pdb=" CA  PHE B 129 "
           pdb=" C   PHE B 129 "
           pdb=" N   ALA B 130 "
           pdb=" CA  ALA B 130 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.44  -20.56     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  ASP A 511 "
           pdb=" CB  ASP A 511 "
           pdb=" CG  ASP A 511 "
           pdb=" OD1 ASP A 511 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.58   59.58     1      2.00e+01 2.50e-03 1.18e+01
  dihedral pdb=" CA  MET B 255 "
           pdb=" C   MET B 255 "
           pdb=" N   ALA B 256 "
           pdb=" CA  ALA B 256 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.30   16.70     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 5779 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 849
       0.026 -    0.052: 368
       0.052 -    0.078: 140
       0.078 -    0.103: 69
       0.103 -    0.129: 27
  Chirality restraints: 1453
  Sorted by residual:
  chirality pdb=" CA  MET B 255 "
            pdb=" N   MET B 255 "
            pdb=" C   MET B 255 "
            pdb=" CB  MET B 255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.18e-01
  chirality pdb=" CA  ILE B 364 "
            pdb=" N   ILE B 364 "
            pdb=" C   ILE B 364 "
            pdb=" CB  ILE B 364 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.05e-01
  chirality pdb=" CA  GLN B 500 "
            pdb=" N   GLN B 500 "
            pdb=" C   GLN B 500 "
            pdb=" CB  GLN B 500 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.13 2.00e-01 2.50e+01 3.92e-01
  ... (remaining 1450 not shown)

  Planarity restraints: 1780
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B 526 "    0.010 2.00e-02 2.50e+03   2.11e-02 4.47e+00
        pdb=" CD  GLU B 526 "   -0.037 2.00e-02 2.50e+03
        pdb=" OE1 GLU B 526 "    0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU B 526 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 532 "   -0.030 5.00e-02 4.00e+02   4.36e-02 3.04e+00
        pdb=" N   PRO B 533 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B 533 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 533 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 149 "   -0.026 5.00e-02 4.00e+02   3.84e-02 2.36e+00
        pdb=" N   PRO A 150 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 150 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 150 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1777 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 805
        2.74 -     3.28: 9584
        3.28 -     3.82: 17194
        3.82 -     4.36: 20687
        4.36 -     4.90: 35058
  Nonbonded interactions: 83328
  Sorted by model distance:
  nonbonded pdb=" O   TRP A  91 "
            pdb=" OH  TYR A  98 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" N   GLU A 582 "
            pdb=" OE1 GLU A 582 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" O   TRP B  91 "
            pdb=" OH  TYR B  98 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OH  TYR B 337 "
            pdb=" OG1 THR B 394 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OH  TYR A 337 "
            pdb=" OG1 THR A 394 "
     model   vdw
     2.230 3.040
  ... (remaining 83323 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.270
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.910
  Find NCS groups from input model:        0.050
  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:6.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8759
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   0.098   9931  Z= 0.105
  Angle     :  0.474   9.001  13546  Z= 0.233
  Chirality :  0.039   0.129   1453
  Planarity :  0.004   0.044   1780
  Dihedral  : 15.343  89.567   3504
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 16.84 %
    Favored  : 82.85 %
  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:  1.25 (0.23), residues: 1253
  helix:  1.98 (0.21), residues: 575
  sheet:  3.09 (1.06), residues: 20
  loop : -0.27 (0.23), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 249 
 TYR   0.018   0.001   TYR B 229 
 PHE   0.006   0.001   PHE A 720 
 TRP   0.015   0.001   TRP B 191 
 HIS   0.004   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 9930)
  covalent geometry    : angle       0.47433 (13546)
  hydrogen bonds       : bond        0.12834 (  446)
  hydrogen bonds       : angle       4.46641 ( 1218)
  Misc. bond           : bond        0.09759 (    1)

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 42
  time to evaluate  : 0.309 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 45
  average time/residue: 0.7224
  time to fit residues: 34.4540
Evaluate side-chains
  43 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  301 LYS
Chi-restraints excluded: chain B residue  611 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    7.9990
   chunk 123 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    2.2786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.074747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.055754 restraints weight = 17563.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.2666 rms_B_bonded: 2.35
r_work: 0.2535 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2413 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8786
moved from start:          0.0704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   9931  Z= 0.230
  Angle     :  0.543  10.740  13546  Z= 0.272
  Chirality :  0.043   0.150   1453
  Planarity :  0.004   0.047   1780
  Dihedral  :  4.916  69.421   1372
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 14.36 %
    Favored  : 83.99 %
  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:  1.04 (0.23), residues: 1253
  helix:  1.61 (0.21), residues: 582
  sheet:  2.99 (1.08), residues: 20
  loop : -0.19 (0.24), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 146 
 TYR   0.021   0.002   TYR B 229 
 PHE   0.011   0.001   PHE A 408 
 TRP   0.013   0.001   TRP B 191 
 HIS   0.006   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 9930)
  covalent geometry    : angle       0.54344 (13546)
  hydrogen bonds       : bond        0.04746 (  446)
  hydrogen bonds       : angle       4.04447 ( 1218)
  Misc. bond           : bond        0.01098 (    1)

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 44
  time to evaluate  : 0.379 
Fit side-chains
  outliers start: 16
  outliers final: 3
  residues processed: 58
  average time/residue: 0.6054
  time to fit residues: 37.7405
Evaluate side-chains
  43 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  611 LEU
Chi-restraints excluded: chain B residue  700 SER
Chi-restraints excluded: chain A residue  248 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 105 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 112 optimal weight:    5.9990
   chunk 87 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 110 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A 562 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.075734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.056671 restraints weight = 17569.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.2686 rms_B_bonded: 2.37
r_work: 0.2556 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2434 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8790
moved from start:          0.0718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9931  Z= 0.157
  Angle     :  0.503  10.220  13546  Z= 0.250
  Chirality :  0.041   0.134   1453
  Planarity :  0.004   0.048   1780
  Dihedral  :  4.742  68.971   1368
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 14.77 %
    Favored  : 83.88 %
  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:  1.06 (0.23), residues: 1253
  helix:  1.60 (0.21), residues: 583
  sheet:  2.86 (1.04), residues: 20
  loop : -0.15 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 146 
 TYR   0.016   0.001   TYR A 155 
 PHE   0.008   0.001   PHE A 408 
 TRP   0.015   0.001   TRP B 191 
 HIS   0.005   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 9930)
  covalent geometry    : angle       0.50277 (13546)
  hydrogen bonds       : bond        0.04099 (  446)
  hydrogen bonds       : angle       3.96541 ( 1218)
  Misc. bond           : bond        0.05260 (    1)

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.385 
Fit side-chains
REVERT: B  700 SER cc_start: 0.9010 (OUTLIER) cc_final: 0.8690 (m)
  outliers start: 13
  outliers final: 2
  residues processed: 56
  average time/residue: 0.5991
  time to fit residues: 36.0429
Evaluate side-chains
  43 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue  700 SER
Chi-restraints excluded: chain A residue  486 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 562 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.076470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.057525 restraints weight = 17603.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.2705 rms_B_bonded: 2.36
r_work: 0.2576 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2455 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8780
moved from start:          0.0751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   9931  Z= 0.126
  Angle     :  0.486   9.546  13546  Z= 0.240
  Chirality :  0.040   0.126   1453
  Planarity :  0.004   0.047   1780
  Dihedral  :  4.505  69.674   1366
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 14.88 %
    Favored  : 83.68 %
  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:  1.14 (0.23), residues: 1253
  helix:  1.66 (0.21), residues: 584
  sheet:  2.86 (1.04), residues: 20
  loop : -0.10 (0.24), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 254 
 TYR   0.016   0.001   TYR A 155 
 PHE   0.007   0.001   PHE A 408 
 TRP   0.015   0.001   TRP B 191 
 HIS   0.005   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9930)
  covalent geometry    : angle       0.48578 (13546)
  hydrogen bonds       : bond        0.03775 (  446)
  hydrogen bonds       : angle       3.87427 ( 1218)
  Misc. bond           : bond        0.07749 (    1)

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A  557 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8563 (ttmm)
  outliers start: 14
  outliers final: 5
  residues processed: 55
  average time/residue: 0.6050
  time to fit residues: 35.4877
Evaluate side-chains
  47 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue  137 ASP
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain A residue  140 SER
Chi-restraints excluded: chain A residue  486 SER
Chi-restraints excluded: chain A residue  557 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 19 optimal weight:    0.3980
   chunk 28 optimal weight:    1.9990
   chunk 114 optimal weight:    2.9990
   chunk 124 optimal weight:    0.9990
   chunk 31 optimal weight:    0.4980
   chunk 18 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 119 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.6984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.077568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.058664 restraints weight = 17648.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.2729 rms_B_bonded: 2.37
r_work: 0.2600 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2480 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8765
moved from start:          0.0757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.100   9931  Z= 0.104
  Angle     :  0.473   9.450  13546  Z= 0.232
  Chirality :  0.039   0.124   1453
  Planarity :  0.004   0.044   1780
  Dihedral  :  4.373  69.583   1366
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 14.98 %
    Favored  : 83.68 %
  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:  1.24 (0.23), residues: 1253
  helix:  1.74 (0.21), residues: 585
  sheet:  2.88 (1.03), residues: 20
  loop : -0.05 (0.24), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 254 
 TYR   0.015   0.001   TYR A 155 
 PHE   0.006   0.001   PHE A 408 
 TRP   0.014   0.001   TRP B 191 
 HIS   0.005   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 9930)
  covalent geometry    : angle       0.47306 (13546)
  hydrogen bonds       : bond        0.03441 (  446)
  hydrogen bonds       : angle       3.80122 ( 1218)
  Misc. bond           : bond        0.10033 (    1)

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 44
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A  557 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8528 (ttmm)
  outliers start: 13
  outliers final: 5
  residues processed: 55
  average time/residue: 0.6213
  time to fit residues: 36.6885
Evaluate side-chains
  49 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  137 ASP
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain A residue  140 SER
Chi-restraints excluded: chain A residue  486 SER
Chi-restraints excluded: chain A residue  557 LYS
Chi-restraints excluded: chain A residue  572 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 37 optimal weight:    0.0970
   chunk 118 optimal weight:    2.9990
   chunk 99 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 101 optimal weight:    5.9990
   chunk 81 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9990
   chunk 95 optimal weight:    0.0050
   overall best weight:    0.4392

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.078713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.059958 restraints weight = 17606.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.2759 rms_B_bonded: 2.38
r_work: 0.2632 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2512 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8750
moved from start:          0.0844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.119   9931  Z= 0.090
  Angle     :  0.475  10.036  13546  Z= 0.228
  Chirality :  0.038   0.124   1453
  Planarity :  0.004   0.041   1780
  Dihedral  :  4.228  69.136   1366
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 15.70 %
    Favored  : 83.26 %
  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:  1.35 (0.24), residues: 1253
  helix:  1.85 (0.21), residues: 585
  sheet:  3.02 (1.06), residues: 20
  loop : -0.02 (0.25), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 146 
 TYR   0.014   0.001   TYR A 155 
 PHE   0.004   0.001   PHE A 167 
 TRP   0.014   0.001   TRP B 191 
 HIS   0.004   0.001   HIS B  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 9930)
  covalent geometry    : angle       0.47511 (13546)
  hydrogen bonds       : bond        0.03129 (  446)
  hydrogen bonds       : angle       3.71320 ( 1218)
  Misc. bond           : bond        0.11884 (    1)

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.429 
Fit side-chains
REVERT: A  557 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8532 (ttmm)
  outliers start: 10
  outliers final: 3
  residues processed: 55
  average time/residue: 0.7636
  time to fit residues: 44.7284
Evaluate side-chains
  48 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  108 HIS
Chi-restraints excluded: chain B residue  137 ASP
Chi-restraints excluded: chain A residue  557 LYS
Chi-restraints excluded: chain A residue  572 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9980
   chunk 111 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 23 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 48 optimal weight:    0.5980
   chunk 108 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   overall best weight:    2.3186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.074907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.055789 restraints weight = 17659.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.2672 rms_B_bonded: 2.38
r_work: 0.2541 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2418 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8803
moved from start:          0.0887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   9931  Z= 0.230
  Angle     :  0.545  10.282  13546  Z= 0.269
  Chirality :  0.043   0.150   1453
  Planarity :  0.004   0.044   1780
  Dihedral  :  4.693  69.786   1366
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 15.91 %
    Favored  : 83.06 %
  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:  1.13 (0.23), residues: 1253
  helix:  1.66 (0.21), residues: 585
  sheet:  3.05 (1.09), residues: 20
  loop : -0.13 (0.24), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 146 
 TYR   0.025   0.002   TYR B 229 
 PHE   0.011   0.001   PHE A 408 
 TRP   0.013   0.001   TRP B 107 
 HIS   0.007   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00561 ( 9930)
  covalent geometry    : angle       0.54472 (13546)
  hydrogen bonds       : bond        0.04342 (  446)
  hydrogen bonds       : angle       3.85852 ( 1218)
  Misc. bond           : bond        0.03670 (    1)

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.261 
Fit side-chains
REVERT: B  107 TRP cc_start: 0.8878 (OUTLIER) cc_final: 0.8236 (t-100)
REVERT: B  700 SER cc_start: 0.8992 (OUTLIER) cc_final: 0.8743 (m)
  outliers start: 10
  outliers final: 2
  residues processed: 51
  average time/residue: 0.6578
  time to fit residues: 35.9146
Evaluate side-chains
  46 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  107 TRP
Chi-restraints excluded: chain B residue  611 LEU
Chi-restraints excluded: chain B residue  700 SER
Chi-restraints excluded: chain A residue  486 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 68 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 91 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9980
   chunk 93 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0000
   chunk 29 optimal weight:    0.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.6384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.077546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.058598 restraints weight = 17459.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.2732 rms_B_bonded: 2.38
r_work: 0.2604 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2483 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8765
moved from start:          0.0844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.100   9931  Z= 0.101
  Angle     :  0.490   9.778  13546  Z= 0.238
  Chirality :  0.039   0.126   1453
  Planarity :  0.004   0.042   1780
  Dihedral  :  4.378  69.396   1366
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 16.63 %
    Favored  : 82.85 %
  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:  1.26 (0.24), residues: 1253
  helix:  1.78 (0.21), residues: 584
  sheet:  3.01 (1.05), residues: 20
  loop : -0.06 (0.24), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 254 
 TYR   0.017   0.001   TYR B 229 
 PHE   0.006   0.001   PHE B 252 
 TRP   0.015   0.001   TRP B 191 
 HIS   0.004   0.001   HIS B  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 9930)
  covalent geometry    : angle       0.48993 (13546)
  hydrogen bonds       : bond        0.03393 (  446)
  hydrogen bonds       : angle       3.78413 ( 1218)
  Misc. bond           : bond        0.09986 (    1)

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.276 
Fit side-chains
  outliers start: 5
  outliers final: 0
  residues processed: 49
  average time/residue: 0.6793
  time to fit residues: 35.5525
Evaluate side-chains
  43 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 117 optimal weight:    0.9990
   chunk 95 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 42 optimal weight:    0.5980
   chunk 115 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9980
   chunk 122 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.078082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.059495 restraints weight = 17403.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.2732 rms_B_bonded: 2.34
r_work: 0.2606 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2485 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8775
moved from start:          0.0862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.090   9931  Z= 0.111
  Angle     :  0.497   9.903  13546  Z= 0.242
  Chirality :  0.039   0.125   1453
  Planarity :  0.004   0.043   1780
  Dihedral  :  4.350  67.769   1366
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 16.74 %
    Favored  : 82.85 %
  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:  1.30 (0.24), residues: 1253
  helix:  1.81 (0.21), residues: 585
  sheet:  3.11 (1.08), residues: 20
  loop : -0.04 (0.24), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 146 
 TYR   0.015   0.001   TYR A 155 
 PHE   0.006   0.001   PHE A 408 
 TRP   0.014   0.001   TRP B 191 
 HIS   0.004   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 9930)
  covalent geometry    : angle       0.49728 (13546)
  hydrogen bonds       : bond        0.03422 (  446)
  hydrogen bonds       : angle       3.72724 ( 1218)
  Misc. bond           : bond        0.09044 (    1)

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.458 
Fit side-chains
  outliers start: 4
  outliers final: 1
  residues processed: 47
  average time/residue: 0.6988
  time to fit residues: 35.3027
Evaluate side-chains
  45 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  137 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 84 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 112 optimal weight:    0.0070
   chunk 40 optimal weight:    0.2980
   chunk 24 optimal weight:    0.5980
   chunk 106 optimal weight:    0.7980
   chunk 100 optimal weight:    0.5980
   overall best weight:    0.4598

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.078727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.059993 restraints weight = 17423.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.2759 rms_B_bonded: 2.36
r_work: 0.2633 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2512 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8749
moved from start:          0.0913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.108   9931  Z= 0.094
  Angle     :  0.482  10.036  13546  Z= 0.234
  Chirality :  0.039   0.129   1453
  Planarity :  0.004   0.041   1780
  Dihedral  :  4.243  66.891   1366
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 17.05 %
    Favored  : 82.64 %
  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:  1.38 (0.24), residues: 1253
  helix:  1.89 (0.21), residues: 585
  sheet:  3.21 (1.09), residues: 20
  loop : -0.02 (0.25), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 146 
 TYR   0.014   0.001   TYR A 155 
 PHE   0.011   0.001   PHE B 252 
 TRP   0.023   0.001   TRP B 107 
 HIS   0.004   0.001   HIS B  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 9930)
  covalent geometry    : angle       0.48247 (13546)
  hydrogen bonds       : bond        0.03147 (  446)
  hydrogen bonds       : angle       3.68107 ( 1218)
  Misc. bond           : bond        0.10846 (    1)

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

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

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2506 Ramachandran restraints generated.
    1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.396 
Fit side-chains
REVERT: A   26 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.7275 (mmt)
  outliers start: 3
  outliers final: 1
  residues processed: 46
  average time/residue: 0.6675
  time to fit residues: 32.9069
Evaluate side-chains
  46 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 44
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  137 ASP
Chi-restraints excluded: chain A residue   26 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 112 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 101 optimal weight:    6.9990
   chunk 82 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0000
   chunk 87 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.1388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.077621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.058930 restraints weight = 17434.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.2723 rms_B_bonded: 2.35
r_work: 0.2595 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2474 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8782
moved from start:          0.0876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079   9931  Z= 0.136
  Angle     :  0.506  10.016  13546  Z= 0.248
  Chirality :  0.040   0.155   1453
  Planarity :  0.004   0.043   1780
  Dihedral  :  4.394  67.631   1366
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  : 16.94 %
    Favored  : 82.95 %
  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:  1.33 (0.23), residues: 1253
  helix:  1.85 (0.21), residues: 584
  sheet:  3.11 (1.09), residues: 20
  loop : -0.05 (0.24), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 519 
 TYR   0.016   0.001   TYR A 155 
 PHE   0.010   0.001   PHE B 252 
 TRP   0.016   0.001   TRP B 107 
 HIS   0.005   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 9930)
  covalent geometry    : angle       0.50642 (13546)
  hydrogen bonds       : bond        0.03595 (  446)
  hydrogen bonds       : angle       3.71489 ( 1218)
  Misc. bond           : bond        0.07922 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3077.36 seconds
wall clock time: 53 minutes 4.65 seconds (3184.65 seconds total)