Starting phenix.real_space_refine
on Wed Mar  4 04:00:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qmb_4594/03_2026/6qmb_4594.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qmb_4594/03_2026/6qmb_4594.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qmb_4594/03_2026/6qmb_4594.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qmb_4594/03_2026/6qmb_4594.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qmb_4594/03_2026/6qmb_4594.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qmb_4594/03_2026/6qmb_4594.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.011
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
     Ca      4      9.91       5
     S      40      5.16       5
     C    6960      2.51       5
     N    1782      2.21       5
     O    1912      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10698
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5347
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 661, 5347
          Classifications: {'peptide': 661}
          Link IDs: {'PTRANS': 28, 'TRANS': 632}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.46, per 1000 atoms: 0.42
  Number of scatterers: 10698
  At special positions: 0
  Unit cell: (118.404, 109.296, 108.284, 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)
     Ca      4     19.99
     S      40     16.00
     O    1912      8.00
     N    1782      7.00
     C    6960      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: 0.87
  Conformation dependent library (CDL) restraints added in 485.8 milliseconds
  

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2508

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 4 sheets defined
      75.8% alpha, 2.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 31
      No H-bonds generated for 'chain 'A' and resid 29 through 31'
    Processing helix  chain 'A' and resid 32 through 50
      removed outlier: 3.796A  pdb=" N   VAL A  50 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 90
      removed outlier: 3.678A  pdb=" N   HIS A  90 " --> pdb=" O   GLY A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 105
      removed outlier: 4.118A  pdb=" N   ALA A 104 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 125
    Processing helix  chain 'A' and resid 126 through 130
    Processing helix  chain 'A' and resid 152 through 166
      removed outlier: 3.704A  pdb=" N   GLU A 158 " --> pdb=" O   SER A 154 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LYS A 166 " --> pdb=" O   LYS A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 182
      removed outlier: 3.838A  pdb=" N   ILE A 174 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LYS A 180 " --> pdb=" O   ASN A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 199
    Processing helix  chain 'A' and resid 199 through 212
    Processing helix  chain 'A' and resid 217 through 246
      removed outlier: 3.581A  pdb=" N   ALA A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   VAL A 240 " --> pdb=" O   LYS A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 254
    Processing helix  chain 'A' and resid 280 through 289
      removed outlier: 3.541A  pdb=" N   ARG A 284 " --> pdb=" O   PRO A 280 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   THR A 287 " --> pdb=" O   LYS A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 320
      removed outlier: 3.690A  pdb=" N   PHE A 294 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 329
    Processing helix  chain 'A' and resid 330 through 358
      Proline residue:  A 341  - end of helix
      removed outlier: 3.724A  pdb=" N   VAL A 346 " --> pdb=" O   THR A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 391
      removed outlier: 6.066A  pdb=" N   ALA A 385 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
      removed outlier: 5.340A  pdb=" N   LEU A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 399
      No H-bonds generated for 'chain 'A' and resid 397 through 399'
    Processing helix  chain 'A' and resid 400 through 416
      removed outlier: 3.917A  pdb=" N   THR A 413 " --> pdb=" O   ALA A 409 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE A 416 " --> pdb=" O   GLN A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 453
      removed outlier: 3.945A  pdb=" N   ASN A 435 " --> pdb=" O   ALA A 431 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL A 453 " --> pdb=" O   PHE A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 466
    Processing helix  chain 'A' and resid 482 through 494
      removed outlier: 4.041A  pdb=" N   THR A 494 " --> pdb=" O   ARG A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 518
      removed outlier: 4.516A  pdb=" N   ASP A 503 " --> pdb=" O   ASP A 499 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   MET A 507 " --> pdb=" O   ASP A 503 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   SER A 518 " --> pdb=" O   VAL A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 546
      removed outlier: 4.011A  pdb=" N   ARG A 537 " --> pdb=" O   TRP A 533 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ALA A 540 " --> pdb=" O   LEU A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 585
      removed outlier: 3.685A  pdb=" N   ALA A 564 " --> pdb=" O   PRO A 560 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE A 574 " --> pdb=" O   TRP A 570 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   SER A 577 " --> pdb=" O   SER A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 626
      removed outlier: 3.561A  pdb=" N   LEU A 602 " --> pdb=" O   LYS A 598 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU A 603 " --> pdb=" O   ALA A 599 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LEU A 604 " --> pdb=" O   TRP A 600 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LYS A 626 " --> pdb=" O   PHE A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 650
      removed outlier: 3.847A  pdb=" N   GLN A 633 " --> pdb=" O   SER A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 684
    Processing helix  chain 'A' and resid 689 through 696
    Processing helix  chain 'A' and resid 700 through 718
    Processing helix  chain 'B' and resid 29 through 31
      No H-bonds generated for 'chain 'B' and resid 29 through 31'
    Processing helix  chain 'B' and resid 32 through 50
      removed outlier: 3.797A  pdb=" N   VAL B  50 " --> pdb=" O   ALA B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 90
      removed outlier: 3.678A  pdb=" N   HIS B  90 " --> pdb=" O   GLY B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 105
      removed outlier: 4.119A  pdb=" N   ALA B 104 " --> pdb=" O   ILE B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 125
    Processing helix  chain 'B' and resid 126 through 130
    Processing helix  chain 'B' and resid 152 through 166
      removed outlier: 3.705A  pdb=" N   GLU B 158 " --> pdb=" O   SER B 154 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LYS B 166 " --> pdb=" O   LYS B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 182
      removed outlier: 3.838A  pdb=" N   ILE B 174 " --> pdb=" O   GLU B 170 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LYS B 180 " --> pdb=" O   ASN B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 199
    Processing helix  chain 'B' and resid 199 through 212
    Processing helix  chain 'B' and resid 217 through 246
      removed outlier: 3.580A  pdb=" N   ALA B 221 " --> pdb=" O   SER B 217 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   VAL B 240 " --> pdb=" O   LYS B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 254
    Processing helix  chain 'B' and resid 280 through 289
      removed outlier: 3.541A  pdb=" N   ARG B 284 " --> pdb=" O   PRO B 280 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   THR B 287 " --> pdb=" O   LYS B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 320
      removed outlier: 3.691A  pdb=" N   PHE B 294 " --> pdb=" O   LEU B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 329
    Processing helix  chain 'B' and resid 330 through 358
      Proline residue:  B 341  - end of helix
      removed outlier: 3.724A  pdb=" N   VAL B 346 " --> pdb=" O   THR B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 391
      removed outlier: 6.066A  pdb=" N   ALA B 385 " --> pdb=" O   THR B 381 " (cutoff:3.500A)
      removed outlier: 5.340A  pdb=" N   LEU B 386 " --> pdb=" O   SER B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 397 through 399
      No H-bonds generated for 'chain 'B' and resid 397 through 399'
    Processing helix  chain 'B' and resid 400 through 416
      removed outlier: 3.916A  pdb=" N   THR B 413 " --> pdb=" O   ALA B 409 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE B 416 " --> pdb=" O   GLN B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 453
      removed outlier: 3.946A  pdb=" N   ASN B 435 " --> pdb=" O   ALA B 431 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL B 453 " --> pdb=" O   PHE B 449 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 466
    Processing helix  chain 'B' and resid 482 through 494
      removed outlier: 4.041A  pdb=" N   THR B 494 " --> pdb=" O   ARG B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 499 through 518
      removed outlier: 4.515A  pdb=" N   ASP B 503 " --> pdb=" O   ASP B 499 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   MET B 507 " --> pdb=" O   ASP B 503 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   SER B 518 " --> pdb=" O   VAL B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 546
      removed outlier: 4.010A  pdb=" N   ARG B 537 " --> pdb=" O   TRP B 533 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ALA B 540 " --> pdb=" O   LEU B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 585
      removed outlier: 3.685A  pdb=" N   ALA B 564 " --> pdb=" O   PRO B 560 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE B 574 " --> pdb=" O   TRP B 570 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   SER B 577 " --> pdb=" O   SER B 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 598 through 626
      removed outlier: 3.561A  pdb=" N   LEU B 602 " --> pdb=" O   LYS B 598 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU B 603 " --> pdb=" O   ALA B 599 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LEU B 604 " --> pdb=" O   TRP B 600 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LYS B 626 " --> pdb=" O   PHE B 622 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 629 through 650
      removed outlier: 3.847A  pdb=" N   GLN B 633 " --> pdb=" O   SER B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 666 through 684
    Processing helix  chain 'B' and resid 689 through 696
    Processing helix  chain 'B' and resid 700 through 718
    Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 59
      removed outlier: 3.595A  pdb=" N   PHE A  22 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 266
      removed outlier: 3.542A  pdb=" N   HIS A 265 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 59
      removed outlier: 3.595A  pdb=" N   PHE B  22 " --> pdb=" O   VAL B  68 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 266
      removed outlier: 3.542A  pdb=" N   HIS B 265 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)

    730 hydrogen bonds defined for protein.
    2142 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: 1.67

  Time building geometry restraints manager: 1.19 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3326
        1.34 -     1.45: 1955
        1.45 -     1.57: 5627
        1.57 -     1.69: 0
        1.69 -     1.80: 66
  Bond restraints: 10974
  Sorted by residual:
  bond pdb=" CB  PRO A 202 "
       pdb=" CG  PRO A 202 "
    ideal  model  delta    sigma   weight residual
    1.492  1.397  0.095 5.00e-02 4.00e+02 3.58e+00
  bond pdb=" CB  PRO B 202 "
       pdb=" CG  PRO B 202 "
    ideal  model  delta    sigma   weight residual
    1.492  1.398  0.094 5.00e-02 4.00e+02 3.52e+00
  bond pdb=" CB  VAL B 229 "
       pdb=" CG2 VAL B 229 "
    ideal  model  delta    sigma   weight residual
    1.521  1.460  0.061 3.30e-02 9.18e+02 3.38e+00
  bond pdb=" CB  VAL A 229 "
       pdb=" CG2 VAL A 229 "
    ideal  model  delta    sigma   weight residual
    1.521  1.461  0.060 3.30e-02 9.18e+02 3.34e+00
  bond pdb=" C   THR B 689 "
       pdb=" N   PRO B 690 "
    ideal  model  delta    sigma   weight residual
    1.336  1.355 -0.019 1.20e-02 6.94e+03 2.53e+00
  ... (remaining 10969 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 14335
        1.99 -     3.99: 474
        3.99 -     5.98: 49
        5.98 -     7.97: 16
        7.97 -     9.97: 12
  Bond angle restraints: 14886
  Sorted by residual:
  angle pdb=" N   THR B 689 "
        pdb=" CA  THR B 689 "
        pdb=" C   THR B 689 "
      ideal   model   delta    sigma   weight residual
     109.81  119.37   -9.56 2.21e+00 2.05e-01 1.87e+01
  angle pdb=" N   THR A 689 "
        pdb=" CA  THR A 689 "
        pdb=" C   THR A 689 "
      ideal   model   delta    sigma   weight residual
     109.81  119.35   -9.54 2.21e+00 2.05e-01 1.86e+01
  angle pdb=" CA  THR A 689 "
        pdb=" C   THR A 689 "
        pdb=" N   PRO A 690 "
      ideal   model   delta    sigma   weight residual
     118.44  124.60   -6.16 1.59e+00 3.96e-01 1.50e+01
  angle pdb=" CA  THR B 689 "
        pdb=" C   THR B 689 "
        pdb=" N   PRO B 690 "
      ideal   model   delta    sigma   weight residual
     118.44  124.57   -6.13 1.59e+00 3.96e-01 1.49e+01
  angle pdb=" C   SER B 584 "
        pdb=" N   ASN B 585 "
        pdb=" CA  ASN B 585 "
      ideal   model   delta    sigma   weight residual
     121.70  128.29   -6.59 1.80e+00 3.09e-01 1.34e+01
  ... (remaining 14881 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 5749
       17.71 -    35.41: 571
       35.41 -    53.12: 94
       53.12 -    70.83: 26
       70.83 -    88.53: 8
  Dihedral angle restraints: 6448
    sinusoidal: 2586
      harmonic: 3862
  Sorted by residual:
  dihedral pdb=" CA  ILE B 271 "
           pdb=" C   ILE B 271 "
           pdb=" N   THR B 272 "
           pdb=" CA  THR B 272 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.18  -18.82     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  LEU A 212 "
           pdb=" C   LEU A 212 "
           pdb=" N   LEU A 213 "
           pdb=" CA  LEU A 213 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.20  -18.80     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  LEU B 212 "
           pdb=" C   LEU B 212 "
           pdb=" N   LEU B 213 "
           pdb=" CA  LEU B 213 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.21  -18.79     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 6445 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1330
       0.066 -    0.133: 249
       0.133 -    0.199: 47
       0.199 -    0.265: 0
       0.265 -    0.331: 4
  Chirality restraints: 1630
  Sorted by residual:
  chirality pdb=" CB  VAL B 248 "
            pdb=" CA  VAL B 248 "
            pdb=" CG1 VAL B 248 "
            pdb=" CG2 VAL B 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" CB  VAL A 248 "
            pdb=" CA  VAL A 248 "
            pdb=" CG1 VAL A 248 "
            pdb=" CG2 VAL A 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.66e+00
  chirality pdb=" CA  THR A 689 "
            pdb=" N   THR A 689 "
            pdb=" C   THR A 689 "
            pdb=" CB  THR A 689 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.26    0.27 2.00e-01 2.50e+01 1.82e+00
  ... (remaining 1627 not shown)

  Planarity restraints: 1890
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 401 "   -0.037 5.00e-02 4.00e+02   5.59e-02 5.01e+00
        pdb=" N   PRO B 402 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO B 402 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 402 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 401 "   -0.037 5.00e-02 4.00e+02   5.58e-02 4.98e+00
        pdb=" N   PRO A 402 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 402 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 402 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B 677 "   -0.011 2.00e-02 2.50e+03   2.17e-02 4.70e+00
        pdb=" CD  GLU B 677 "    0.038 2.00e-02 2.50e+03
        pdb=" OE1 GLU B 677 "   -0.014 2.00e-02 2.50e+03
        pdb=" OE2 GLU B 677 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1887 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 3096
        2.81 -     3.33: 10282
        3.33 -     3.85: 18138
        3.85 -     4.38: 19923
        4.38 -     4.90: 34980
  Nonbonded interactions: 86419
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 120 "
            pdb=" OG1 THR A 124 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   TYR B 120 "
            pdb=" OG1 THR B 124 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OH  TYR A  26 "
            pdb=" O   ALA A  36 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" OH  TYR B  26 "
            pdb=" O   ALA B  36 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" O   MET B 701 "
            pdb=" OG1 THR B 704 "
     model   vdw
     2.325 3.040
  ... (remaining 86414 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.930
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.940
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
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      :  0.008   0.095  10974  Z= 0.323
  Angle     :  0.866   9.968  14886  Z= 0.475
  Chirality :  0.055   0.331   1630
  Planarity :  0.007   0.056   1890
  Dihedral  : 14.676  88.534   3940
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  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: -3.44 (0.18), residues: 1298
  helix: -2.02 (0.12), residues: 898
  sheet: -2.70 (0.64), residues: 58
  loop : -2.33 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 549 
 TYR   0.015   0.003   TYR B 279 
 PHE   0.037   0.002   PHE A 396 
 TRP   0.020   0.002   TRP B 235 
 HIS   0.006   0.001   HIS B 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00752 (10974)
  covalent geometry    : angle       0.86648 (14886)
  hydrogen bonds       : bond        0.11322 (  730)
  hydrogen bonds       : angle       5.96671 ( 2142)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 LEU cc_start: 0.8680 (tt) cc_final: 0.7874 (mm)
REVERT: A  282 MET cc_start: 0.8864 (mmt) cc_final: 0.8626 (mpp)
REVERT: A  372 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8675 (tt0)
REVERT: A  457 TYR cc_start: 0.7527 (t80) cc_final: 0.7237 (t80)
REVERT: A  531 ASN cc_start: 0.9234 (t0) cc_final: 0.8572 (t160)
REVERT: A  598 LYS cc_start: 0.7976 (mttt) cc_final: 0.6674 (pttt)
REVERT: B  223 LEU cc_start: 0.8702 (tt) cc_final: 0.7937 (mm)
REVERT: B  320 TYR cc_start: 0.5945 (m-10) cc_final: 0.5732 (m-80)
REVERT: B  335 PHE cc_start: 0.8573 (m-80) cc_final: 0.8276 (t80)
REVERT: B  457 TYR cc_start: 0.7515 (t80) cc_final: 0.7230 (t80)
REVERT: B  531 ASN cc_start: 0.9256 (t0) cc_final: 0.8612 (t160)
REVERT: B  598 LYS cc_start: 0.8047 (mttt) cc_final: 0.6848 (pttt)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.1236
  time to fit residues: 25.0384
Evaluate side-chains
  93 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:   20.0000
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
A 138 ASN
A 355 ASN
A 510 GLN
A 531 ASN
A 633 GLN
A 641 GLN
A 666 HIS
A 715 GLN
B 138 ASN
B 326 GLN
B 355 ASN
B 372 GLN
B 401 HIS
B 510 GLN
B 531 ASN
B 633 GLN
B 641 GLN
B 715 GLN

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.108383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.081374 restraints weight = 23579.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.084062 restraints weight = 11883.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.085795 restraints weight = 8104.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.086739 restraints weight = 6560.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.087075 restraints weight = 5877.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10974  Z= 0.122
  Angle     :  0.530   6.510  14886  Z= 0.278
  Chirality :  0.039   0.146   1630
  Planarity :  0.004   0.039   1890
  Dihedral  :  4.382  16.577   1420
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.80 %
    Favored  : 86.44 %
  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: -0.80 (0.21), residues: 1298
  helix:  0.13 (0.15), residues: 902
  sheet: -2.42 (0.68), residues: 58
  loop : -1.72 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 249 
 TYR   0.015   0.002   TYR B 393 
 PHE   0.012   0.001   PHE A 396 
 TRP   0.013   0.001   TRP B 235 
 HIS   0.004   0.001   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (10974)
  covalent geometry    : angle       0.53038 (14886)
  hydrogen bonds       : bond        0.03903 (  730)
  hydrogen bonds       : angle       4.25143 ( 2142)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: A  372 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8697 (tt0)
REVERT: A  400 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7983 (pp)
REVERT: A  403 PHE cc_start: 0.7766 (m-80) cc_final: 0.7338 (m-80)
REVERT: A  463 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6889 (t80)
REVERT: A  598 LYS cc_start: 0.8258 (mttt) cc_final: 0.7470 (pttt)
REVERT: A  680 ARG cc_start: 0.6586 (mmp-170) cc_final: 0.5771 (tmm-80)
REVERT: B  400 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8100 (pp)
REVERT: B  463 PHE cc_start: 0.7229 (OUTLIER) cc_final: 0.6882 (t80)
REVERT: B  598 LYS cc_start: 0.8373 (mttt) cc_final: 0.7574 (pttt)
  outliers start: 20
  outliers final: 12
  residues processed: 130
  average time/residue: 0.0988
  time to fit residues: 18.8823
Evaluate side-chains
  116 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  463 PHE
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  357 MET
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  463 PHE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 83 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 129 optimal weight:    0.9980
   chunk 117 optimal weight:    0.5980
   chunk 107 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 326 GLN
B 479 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.108973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.081794 restraints weight = 23700.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.084503 restraints weight = 11946.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.086233 restraints weight = 8139.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.087219 restraints weight = 6592.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.087409 restraints weight = 5896.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10974  Z= 0.120
  Angle     :  0.524  10.734  14886  Z= 0.266
  Chirality :  0.038   0.141   1630
  Planarity :  0.004   0.033   1890
  Dihedral  :  4.009  15.326   1420
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 15.05 %
    Favored  : 82.66 %
  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:  0.35 (0.22), residues: 1298
  helix:  1.07 (0.16), residues: 904
  sheet: -2.18 (0.72), residues: 58
  loop : -1.51 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 699 
 TYR   0.016   0.002   TYR B 457 
 PHE   0.024   0.001   PHE A 315 
 TRP   0.012   0.001   TRP A 235 
 HIS   0.004   0.001   HIS A 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (10974)
  covalent geometry    : angle       0.52395 (14886)
  hydrogen bonds       : bond        0.03654 (  730)
  hydrogen bonds       : angle       3.89036 ( 2142)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 125
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.8959 (t) cc_final: 0.8295 (p)
REVERT: A  315 PHE cc_start: 0.8030 (t80) cc_final: 0.7818 (t80)
REVERT: A  372 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8678 (tt0)
REVERT: A  463 PHE cc_start: 0.6954 (OUTLIER) cc_final: 0.6669 (t80)
REVERT: B  203 SER cc_start: 0.8939 (t) cc_final: 0.8317 (p)
REVERT: B  463 PHE cc_start: 0.6930 (OUTLIER) cc_final: 0.6626 (t80)
REVERT: B  598 LYS cc_start: 0.8306 (mttt) cc_final: 0.7591 (pttt)
  outliers start: 26
  outliers final: 12
  residues processed: 142
  average time/residue: 0.0879
  time to fit residues: 18.9312
Evaluate side-chains
  115 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  463 PHE
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  463 PHE
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   chunk 4 optimal weight:    6.9990
   chunk 119 optimal weight:    0.9990
   chunk 87 optimal weight:    2.9990
   chunk 127 optimal weight:    0.3980
   chunk 74 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0770
   chunk 69 optimal weight:    5.9990
   chunk 114 optimal weight:    0.9990
   overall best weight:    0.6944

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

Flipped N/Q/H residues before XYZ refinement:
B 715 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.110192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.083247 restraints weight = 23698.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.085944 restraints weight = 11877.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.087649 restraints weight = 8121.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.088640 restraints weight = 6595.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.088896 restraints weight = 5901.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  10974  Z= 0.107
  Angle     :  0.513  10.302  14886  Z= 0.257
  Chirality :  0.038   0.145   1630
  Planarity :  0.003   0.030   1890
  Dihedral  :  3.811  15.017   1420
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.58 %
    Favored  : 81.95 %
  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:  0.99 (0.23), residues: 1298
  helix:  1.55 (0.16), residues: 904
  sheet: -1.95 (0.74), residues: 58
  loop : -1.30 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 699 
 TYR   0.015   0.001   TYR B 457 
 PHE   0.033   0.001   PHE B 315 
 TRP   0.011   0.001   TRP B 407 
 HIS   0.002   0.000   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (10974)
  covalent geometry    : angle       0.51264 (14886)
  hydrogen bonds       : bond        0.03412 (  730)
  hydrogen bonds       : angle       3.75863 ( 2142)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 115
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.8944 (t) cc_final: 0.8280 (p)
REVERT: A  372 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8650 (tt0)
REVERT: A  463 PHE cc_start: 0.6765 (OUTLIER) cc_final: 0.6533 (t80)
REVERT: A  531 ASN cc_start: 0.9099 (t0) cc_final: 0.8599 (t160)
REVERT: B  203 SER cc_start: 0.8896 (t) cc_final: 0.8267 (p)
REVERT: B  463 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.6629 (t80)
REVERT: B  531 ASN cc_start: 0.9081 (t0) cc_final: 0.8569 (t160)
  outliers start: 28
  outliers final: 20
  residues processed: 132
  average time/residue: 0.0798
  time to fit residues: 16.4929
Evaluate side-chains
  127 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  463 PHE
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  463 PHE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 23 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 39 optimal weight:    9.9990
   chunk 25 optimal weight:    6.9990
   chunk 104 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 123 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    2.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 479 HIS
B  99 ASN
B 715 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.105964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.078488 restraints weight = 23678.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.081144 restraints weight = 12081.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.082768 restraints weight = 8322.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.083739 restraints weight = 6807.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.084091 restraints weight = 6106.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  10974  Z= 0.234
  Angle     :  0.597   9.275  14886  Z= 0.309
  Chirality :  0.042   0.144   1630
  Planarity :  0.004   0.029   1890
  Dihedral  :  4.046  17.626   1420
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 15.49 %
    Favored  : 81.51 %
  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:  0.80 (0.23), residues: 1298
  helix:  1.49 (0.16), residues: 904
  sheet: -1.93 (0.71), residues: 58
  loop : -1.65 (0.32), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 699 
 TYR   0.016   0.002   TYR A 327 
 PHE   0.021   0.002   PHE A 315 
 TRP   0.011   0.001   TRP A 210 
 HIS   0.004   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 (10974)
  covalent geometry    : angle       0.59721 (14886)
  hydrogen bonds       : bond        0.04086 (  730)
  hydrogen bonds       : angle       3.92458 ( 2142)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 98
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.9155 (t) cc_final: 0.8505 (p)
REVERT: A  348 MET cc_start: 0.9158 (mmt) cc_final: 0.8917 (mmm)
REVERT: A  372 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8725 (tt0)
REVERT: A  463 PHE cc_start: 0.6862 (OUTLIER) cc_final: 0.6630 (t80)
REVERT: B  203 SER cc_start: 0.9164 (t) cc_final: 0.8529 (p)
REVERT: B  348 MET cc_start: 0.9151 (mmt) cc_final: 0.8934 (mmm)
REVERT: B  403 PHE cc_start: 0.7624 (m-80) cc_final: 0.7177 (m-80)
REVERT: B  463 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6605 (t80)
  outliers start: 34
  outliers final: 22
  residues processed: 121
  average time/residue: 0.0792
  time to fit residues: 15.2184
Evaluate side-chains
  116 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  463 PHE
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  463 PHE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 17 optimal weight:    0.7980
   chunk 34 optimal weight:    4.9990
   chunk 60 optimal weight:    9.9990
   chunk 72 optimal weight:    7.9990
   chunk 13 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 116 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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 = 0.3576 r_free = 0.3576 target = 0.107935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.080701 restraints weight = 23529.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.083424 restraints weight = 11834.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.085122 restraints weight = 8076.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.086117 restraints weight = 6563.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.086541 restraints weight = 5875.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10974  Z= 0.145
  Angle     :  0.538  10.061  14886  Z= 0.273
  Chirality :  0.039   0.142   1630
  Planarity :  0.003   0.028   1890
  Dihedral  :  3.930  15.434   1420
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 17.43 %
    Favored  : 80.02 %
  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:  1.03 (0.23), residues: 1298
  helix:  1.66 (0.16), residues: 902
  sheet: -1.83 (0.72), residues: 58
  loop : -1.53 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 699 
 TYR   0.016   0.002   TYR B 327 
 PHE   0.012   0.001   PHE B 379 
 TRP   0.014   0.001   TRP A 407 
 HIS   0.003   0.000   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (10974)
  covalent geometry    : angle       0.53777 (14886)
  hydrogen bonds       : bond        0.03689 (  730)
  hydrogen bonds       : angle       3.79180 ( 2142)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.9096 (t) cc_final: 0.8442 (p)
REVERT: A  372 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8704 (tt0)
REVERT: A  403 PHE cc_start: 0.7625 (m-80) cc_final: 0.7118 (m-80)
REVERT: A  463 PHE cc_start: 0.6765 (OUTLIER) cc_final: 0.6546 (t80)
REVERT: B  203 SER cc_start: 0.9114 (t) cc_final: 0.8493 (p)
REVERT: B  463 PHE cc_start: 0.6815 (OUTLIER) cc_final: 0.6591 (t80)
  outliers start: 29
  outliers final: 24
  residues processed: 129
  average time/residue: 0.0820
  time to fit residues: 16.7842
Evaluate side-chains
  124 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  463 PHE
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  463 PHE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 93 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 34 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 62 optimal weight:    8.9990
   chunk 61 optimal weight:    6.9990
   chunk 125 optimal weight:    5.9990
   overall best weight:    1.3382

-------------------------------------------------------------------------------
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 = 0.3583 r_free = 0.3583 target = 0.108469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.081260 restraints weight = 23479.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.084009 restraints weight = 11781.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.085689 restraints weight = 8045.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.086424 restraints weight = 6541.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.087150 restraints weight = 5920.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.2595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10974  Z= 0.135
  Angle     :  0.532  10.104  14886  Z= 0.269
  Chirality :  0.039   0.140   1630
  Planarity :  0.003   0.028   1890
  Dihedral  :  3.862  14.436   1420
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 17.43 %
    Favored  : 79.67 %
  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:  1.11 (0.23), residues: 1298
  helix:  1.70 (0.16), residues: 902
  sheet: -1.72 (0.73), residues: 58
  loop : -1.48 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 699 
 TYR   0.016   0.002   TYR B 457 
 PHE   0.021   0.001   PHE A 315 
 TRP   0.011   0.001   TRP A 235 
 HIS   0.003   0.000   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (10974)
  covalent geometry    : angle       0.53169 (14886)
  hydrogen bonds       : bond        0.03589 (  730)
  hydrogen bonds       : angle       3.75259 ( 2142)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 107
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.9097 (t) cc_final: 0.8440 (p)
REVERT: A  372 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8730 (tt0)
REVERT: A  463 PHE cc_start: 0.6779 (OUTLIER) cc_final: 0.6571 (t80)
REVERT: B  203 SER cc_start: 0.9072 (t) cc_final: 0.8442 (p)
REVERT: B  463 PHE cc_start: 0.6776 (OUTLIER) cc_final: 0.6572 (t80)
  outliers start: 33
  outliers final: 28
  residues processed: 128
  average time/residue: 0.0803
  time to fit residues: 16.1994
Evaluate side-chains
  131 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 101
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  463 PHE
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  357 MET
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  463 PHE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 82 optimal weight:    0.9990
   chunk 59 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 25 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 118 optimal weight:    0.6980
   chunk 86 optimal weight:    0.0570
   chunk 70 optimal weight:    2.9990
   chunk 123 optimal weight:    3.9990
   overall best weight:    1.5504

-------------------------------------------------------------------------------
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 = 0.3577 r_free = 0.3577 target = 0.108268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.081031 restraints weight = 23470.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.083754 restraints weight = 11809.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.085478 restraints weight = 8078.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.086480 restraints weight = 6556.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.087014 restraints weight = 5857.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.2678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10974  Z= 0.147
  Angle     :  0.553  10.365  14886  Z= 0.277
  Chirality :  0.039   0.142   1630
  Planarity :  0.003   0.028   1890
  Dihedral  :  3.855  14.711   1420
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 18.13 %
    Favored  : 78.96 %
  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:  1.12 (0.23), residues: 1298
  helix:  1.71 (0.16), residues: 902
  sheet: -1.67 (0.72), residues: 58
  loop : -1.48 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 699 
 TYR   0.016   0.002   TYR B 457 
 PHE   0.013   0.001   PHE A 379 
 TRP   0.010   0.001   TRP B 235 
 HIS   0.003   0.000   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (10974)
  covalent geometry    : angle       0.55329 (14886)
  hydrogen bonds       : bond        0.03598 (  730)
  hydrogen bonds       : angle       3.76737 ( 2142)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 100
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.9109 (t) cc_final: 0.8449 (p)
REVERT: A  372 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8681 (tt0)
REVERT: A  645 ARG cc_start: 0.7714 (mmp80) cc_final: 0.7347 (mmp80)
REVERT: B  203 SER cc_start: 0.9106 (t) cc_final: 0.8467 (p)
REVERT: B  645 ARG cc_start: 0.7724 (mmp80) cc_final: 0.7317 (mmp80)
  outliers start: 33
  outliers final: 30
  residues processed: 122
  average time/residue: 0.0815
  time to fit residues: 15.6704
Evaluate side-chains
  129 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 99
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  187 PHE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  187 PHE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  357 MET
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0670
   chunk 47 optimal weight:    0.8980
   chunk 67 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   chunk 108 optimal weight:    8.9990
   chunk 63 optimal weight:    7.9990
   chunk 44 optimal weight:    9.9990
   chunk 77 optimal weight:    0.4980
   overall best weight:    1.0720

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

Flipped N/Q/H residues before XYZ refinement:
A 715 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.109444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.082368 restraints weight = 23360.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.085136 restraints weight = 11752.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.086836 restraints weight = 8043.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.087847 restraints weight = 6540.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.088022 restraints weight = 5848.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  10974  Z= 0.123
  Angle     :  0.539  10.616  14886  Z= 0.267
  Chirality :  0.039   0.140   1630
  Planarity :  0.003   0.029   1890
  Dihedral  :  3.778  14.614   1420
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.84 %
    Favored  : 78.70 %
  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:  1.26 (0.23), residues: 1298
  helix:  1.80 (0.16), residues: 902
  sheet: -1.54 (0.74), residues: 58
  loop : -1.41 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 699 
 TYR   0.016   0.001   TYR B 457 
 PHE   0.014   0.001   PHE B 379 
 TRP   0.011   0.001   TRP A 235 
 HIS   0.003   0.000   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (10974)
  covalent geometry    : angle       0.53942 (14886)
  hydrogen bonds       : bond        0.03438 (  730)
  hydrogen bonds       : angle       3.72694 ( 2142)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 101
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.9117 (t) cc_final: 0.8471 (p)
REVERT: A  372 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8695 (tt0)
REVERT: A  531 ASN cc_start: 0.9104 (t0) cc_final: 0.8606 (t160)
REVERT: B  203 SER cc_start: 0.9070 (t) cc_final: 0.8434 (p)
REVERT: B  531 ASN cc_start: 0.9110 (t0) cc_final: 0.8608 (t160)
  outliers start: 28
  outliers final: 26
  residues processed: 122
  average time/residue: 0.0825
  time to fit residues: 15.9483
Evaluate side-chains
  125 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  597 LEU
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 100 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 62 optimal weight:    9.9990
   chunk 115 optimal weight:    0.9980
   chunk 101 optimal weight:    0.8980
   chunk 111 optimal weight:    3.9990
   chunk 55 optimal weight:    0.3980
   chunk 93 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B 715 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.110194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.083213 restraints weight = 23138.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.085916 restraints weight = 11688.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.087669 restraints weight = 8002.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.088698 restraints weight = 6503.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.089036 restraints weight = 5786.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.2917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10974  Z= 0.113
  Angle     :  0.539  10.434  14886  Z= 0.264
  Chirality :  0.038   0.138   1630
  Planarity :  0.003   0.029   1890
  Dihedral  :  3.699  14.572   1420
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.01 %
    Favored  : 78.61 %
  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 (0.23), residues: 1298
  helix:  1.89 (0.16), residues: 900
  sheet: -1.48 (0.75), residues: 58
  loop : -1.42 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 645 
 TYR   0.016   0.001   TYR B 457 
 PHE   0.013   0.001   PHE B 379 
 TRP   0.012   0.001   TRP B 235 
 HIS   0.003   0.000   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (10974)
  covalent geometry    : angle       0.53872 (14886)
  hydrogen bonds       : bond        0.03342 (  730)
  hydrogen bonds       : angle       3.67495 ( 2142)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.9031 (t) cc_final: 0.8389 (p)
REVERT: A  372 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8628 (tt0)
REVERT: A  531 ASN cc_start: 0.9093 (t0) cc_final: 0.8616 (t160)
REVERT: A  645 ARG cc_start: 0.7697 (mmp80) cc_final: 0.7381 (mmp80)
REVERT: B  203 SER cc_start: 0.9053 (t) cc_final: 0.8400 (p)
REVERT: B  531 ASN cc_start: 0.9094 (t0) cc_final: 0.8615 (t160)
REVERT: B  645 ARG cc_start: 0.7725 (mmp80) cc_final: 0.7409 (mmp80)
  outliers start: 27
  outliers final: 23
  residues processed: 123
  average time/residue: 0.0795
  time to fit residues: 15.5675
Evaluate side-chains
  124 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  151 HIS
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  265 HIS
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  362 THR
Chi-restraints excluded: chain B residue  384 MET
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 95 optimal weight:    7.9990
   chunk 0 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 122 optimal weight:    2.9990
   chunk 130 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 118 optimal weight:    0.0060
   chunk 57 optimal weight:    2.9990
   chunk 9 optimal weight:    0.3980
   chunk 102 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    1.2802

-------------------------------------------------------------------------------
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 = 0.3593 r_free = 0.3593 target = 0.109225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.082134 restraints weight = 23296.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.084829 restraints weight = 11750.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.086557 restraints weight = 8053.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.087577 restraints weight = 6540.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.088027 restraints weight = 5828.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10974  Z= 0.131
  Angle     :  0.540  10.148  14886  Z= 0.265
  Chirality :  0.039   0.147   1630
  Planarity :  0.003   0.028   1890
  Dihedral  :  3.715  14.494   1420
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 19.19 %
    Favored  : 78.61 %
  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:  1.36 (0.23), residues: 1298
  helix:  1.85 (0.16), residues: 910
  sheet: -1.43 (0.74), residues: 58
  loop : -1.38 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 645 
 TYR   0.016   0.001   TYR B 457 
 PHE   0.014   0.001   PHE B 379 
 TRP   0.010   0.001   TRP A 600 
 HIS   0.004   0.000   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10974)
  covalent geometry    : angle       0.53981 (14886)
  hydrogen bonds       : bond        0.03403 (  730)
  hydrogen bonds       : angle       3.65430 ( 2142)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1639.01 seconds
wall clock time: 29 minutes 9.20 seconds (1749.20 seconds total)