Starting phenix.real_space_refine
on Wed Sep 25 16:02:27 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qmb_4594/09_2024/6qmb_4594.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qmb_4594/09_2024/6qmb_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 {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qmb_4594/09_2024/6qmb_4594.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qmb_4594/09_2024/6qmb_4594.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qmb_4594/09_2024/6qmb_4594.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qmb_4594/09_2024/6qmb_4594.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.011
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 10.29, per 1000 atoms: 0.96
  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: 2.70
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 1.05
  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: 3.41

  Time building geometry restraints manager: 3.16 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: 0.00
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:                  0.010
  Normalize map: mean=0, sd=1:             1.140
  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:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     30.440
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.030
  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:2.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.980
-------------------------------------------------------------------------------
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= 0.477
  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 : 3.90
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.020   0.002   TRP B 235 
 HIS   0.006   0.001   HIS B 611 
 PHE   0.037   0.002   PHE A 396 
 TYR   0.015   0.003   TYR B 279 
 ARG   0.003   0.001   ARG B 549 

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.216 
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: 0.2735
  time to fit residues: 55.1757
Evaluate side-chains
  93 residues out of total 1136 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 1.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    0.7980
   chunk 100 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 40 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 77 optimal weight:    8.9990
   chunk 119 optimal weight:    0.8980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
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 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: 17

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.1676

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= 0.166
  Angle     :  0.531   6.532  14886  Z= 0.278
  Chirality :  0.039   0.149   1630
  Planarity :  0.004   0.039   1890
  Dihedral  :  4.369  16.575   1420
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.71 %
    Favored  : 86.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (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
 TRP   0.013   0.001   TRP B 235 
 HIS   0.004   0.001   HIS B  58 
 PHE   0.013   0.001   PHE A 396 
 TYR   0.017   0.002   TYR B 393 
 ARG   0.004   0.000   ARG B 249 

*********************** 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
  136 residues out of total 1136 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 1.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  372 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8704 (tt0)
REVERT: A  400 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7995 (pp)
REVERT: A  403 PHE cc_start: 0.7814 (m-80) cc_final: 0.7385 (m-80)
REVERT: A  463 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.6889 (t80)
REVERT: A  598 LYS cc_start: 0.8270 (mttt) cc_final: 0.7458 (pttt)
REVERT: A  680 ARG cc_start: 0.6579 (mmp-170) cc_final: 0.5766 (tmm-80)
REVERT: B  335 PHE cc_start: 0.8534 (m-80) cc_final: 0.8333 (t80)
REVERT: B  400 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8115 (pp)
REVERT: B  463 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.6887 (t80)
REVERT: B  598 LYS cc_start: 0.8360 (mttt) cc_final: 0.7549 (pttt)
  outliers start: 19
  outliers final: 12
  residues processed: 128
  average time/residue: 0.2180
  time to fit residues: 40.5559
Evaluate side-chains
  117 residues out of total 1136 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 1.290 
-------------------------------------------------------------------------------
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 66 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 99 optimal weight:    4.9990
   chunk 81 optimal weight:    0.0770
   chunk 33 optimal weight:    1.9990
   chunk 120 optimal weight:    1.9990
   chunk 129 optimal weight:    0.9980
   chunk 106 optimal weight:    0.0570
   chunk 119 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 96 optimal weight:    5.9990
   overall best weight:    1.0260

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

Flipped N/Q/H residues before XYZ refinement:
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 479 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10974  Z= 0.166
  Angle     :  0.523  10.440  14886  Z= 0.265
  Chirality :  0.038   0.142   1630
  Planarity :  0.004   0.033   1890
  Dihedral  :  4.006  15.321   1420
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 15.14 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.22), residues: 1298
  helix:  1.07 (0.16), residues: 904
  sheet: -2.15 (0.72), residues: 58
  loop : -1.52 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 235 
 HIS   0.004   0.001   HIS A 611 
 PHE   0.023   0.001   PHE A 315 
 TYR   0.016   0.002   TYR B 457 
 ARG   0.004   0.000   ARG B 249 

*********************** 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
  149 residues out of total 1136 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 1.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.8962 (t) cc_final: 0.8307 (p)
REVERT: A  315 PHE cc_start: 0.8065 (t80) cc_final: 0.7821 (t80)
REVERT: A  372 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8679 (tt0)
REVERT: A  463 PHE cc_start: 0.6967 (OUTLIER) cc_final: 0.6674 (t80)
REVERT: A  531 ASN cc_start: 0.9142 (t0) cc_final: 0.8594 (t160)
REVERT: B  203 SER cc_start: 0.8938 (t) cc_final: 0.8328 (p)
REVERT: B  315 PHE cc_start: 0.8040 (t80) cc_final: 0.7829 (t80)
REVERT: B  463 PHE cc_start: 0.6947 (OUTLIER) cc_final: 0.6632 (t80)
REVERT: B  598 LYS cc_start: 0.8301 (mttt) cc_final: 0.7565 (pttt)
  outliers start: 24
  outliers final: 12
  residues processed: 141
  average time/residue: 0.2034
  time to fit residues: 42.4101
Evaluate side-chains
  117 residues out of total 1136 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 1.241 
-------------------------------------------------------------------------------
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 118 optimal weight:    0.1980
   chunk 90 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 120 optimal weight:    0.9990
   chunk 127 optimal weight:   10.0000
   chunk 114 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 106 optimal weight:    9.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10974  Z= 0.164
  Angle     :  0.519  10.120  14886  Z= 0.261
  Chirality :  0.038   0.143   1630
  Planarity :  0.003   0.028   1890
  Dihedral  :  3.847  14.899   1420
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 15.23 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.23), residues: 1298
  helix:  1.52 (0.16), residues: 904
  sheet: -1.95 (0.74), residues: 58
  loop : -1.33 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 235 
 HIS   0.002   0.000   HIS A  58 
 PHE   0.018   0.001   PHE A 406 
 TYR   0.015   0.001   TYR A 457 
 ARG   0.002   0.000   ARG A  82 

*********************** 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
  140 residues out of total 1136 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 108
  time to evaluate  : 1.186 
Fit side-chains
REVERT: A  203 SER cc_start: 0.9003 (t) cc_final: 0.8330 (p)
REVERT: A  372 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8664 (tt0)
REVERT: A  463 PHE cc_start: 0.6856 (OUTLIER) cc_final: 0.6589 (t80)
REVERT: A  531 ASN cc_start: 0.9125 (t0) cc_final: 0.8585 (t160)
REVERT: B  203 SER cc_start: 0.8998 (t) cc_final: 0.8388 (p)
REVERT: B  463 PHE cc_start: 0.6938 (OUTLIER) cc_final: 0.6656 (t80)
REVERT: B  531 ASN cc_start: 0.9120 (t0) cc_final: 0.8579 (t160)
  outliers start: 32
  outliers final: 24
  residues processed: 127
  average time/residue: 0.1797
  time to fit residues: 35.2088
Evaluate side-chains
  128 residues out of total 1136 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
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  265 HIS
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  357 MET
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 72 optimal weight:    8.9990
   chunk 1 optimal weight:    5.9990
   chunk 95 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9990
   chunk 108 optimal weight:    4.9990
   chunk 88 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 65 optimal weight:    9.9990
   chunk 114 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0040
   chunk 42 optimal weight:    5.9990
   overall best weight:    2.3798

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 479 HIS
B  99 ASN
** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  10974  Z= 0.286
  Angle     :  0.569   9.550  14886  Z= 0.294
  Chirality :  0.041   0.157   1630
  Planarity :  0.004   0.028   1890
  Dihedral  :  4.001  16.778   1420
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 15.93 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.23), residues: 1298
  helix:  1.54 (0.16), residues: 900
  sheet: -1.92 (0.72), residues: 58
  loop : -1.38 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 210 
 HIS   0.003   0.000   HIS A 401 
 PHE   0.021   0.001   PHE B 315 
 TYR   0.016   0.002   TYR B 327 
 ARG   0.004   0.000   ARG B 645 

*********************** 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
  139 residues out of total 1136 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 105
  time to evaluate  : 1.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.9153 (t) cc_final: 0.8515 (p)
REVERT: A  372 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8711 (tt0)
REVERT: A  463 PHE cc_start: 0.6850 (OUTLIER) cc_final: 0.6622 (t80)
REVERT: B  203 SER cc_start: 0.9137 (t) cc_final: 0.8524 (p)
REVERT: B  348 MET cc_start: 0.9157 (mmt) cc_final: 0.8942 (mmm)
REVERT: B  463 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.6638 (t80)
  outliers start: 34
  outliers final: 25
  residues processed: 128
  average time/residue: 0.1776
  time to fit residues: 35.0903
Evaluate side-chains
  121 residues out of total 1136 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
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   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  308 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  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 114 optimal weight:    0.6980
   chunk 25 optimal weight:    6.9990
   chunk 74 optimal weight:    0.7980
   chunk 31 optimal weight:   10.0000
   chunk 127 optimal weight:    9.9990
   chunk 106 optimal weight:    3.9990
   chunk 59 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 123 optimal weight:    0.6980
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10974  Z= 0.181
  Angle     :  0.530  10.288  14886  Z= 0.267
  Chirality :  0.039   0.151   1630
  Planarity :  0.003   0.027   1890
  Dihedral  :  3.889  15.161   1420
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 17.17 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.23), residues: 1298
  helix:  1.70 (0.16), residues: 902
  sheet: -1.77 (0.73), residues: 58
  loop : -1.46 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 407 
 HIS   0.003   0.000   HIS A  58 
 PHE   0.019   0.001   PHE B 315 
 TYR   0.015   0.001   TYR B 327 
 ARG   0.004   0.000   ARG A 645 

*********************** 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
  140 residues out of total 1136 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 113
  time to evaluate  : 1.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.9110 (t) cc_final: 0.8481 (p)
REVERT: A  372 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8722 (tt0)
REVERT: A  463 PHE cc_start: 0.6848 (OUTLIER) cc_final: 0.6624 (t80)
REVERT: A  531 ASN cc_start: 0.9139 (t0) cc_final: 0.8620 (t160)
REVERT: B  203 SER cc_start: 0.9068 (t) cc_final: 0.8446 (p)
REVERT: B  463 PHE cc_start: 0.6869 (OUTLIER) cc_final: 0.6641 (t80)
REVERT: B  531 ASN cc_start: 0.9128 (t0) cc_final: 0.8601 (t160)
  outliers start: 27
  outliers final: 23
  residues processed: 131
  average time/residue: 0.1857
  time to fit residues: 37.5942
Evaluate side-chains
  129 residues out of total 1136 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 1.316 
-------------------------------------------------------------------------------
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  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 14 optimal weight:    5.9990
   chunk 72 optimal weight:    6.9990
   chunk 93 optimal weight:    5.9990
   chunk 107 optimal weight:    6.9990
   chunk 71 optimal weight:    0.8980
   chunk 127 optimal weight:    8.9990
   chunk 79 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 78 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  10974  Z= 0.329
  Angle     :  0.590   9.331  14886  Z= 0.305
  Chirality :  0.042   0.147   1630
  Planarity :  0.004   0.028   1890
  Dihedral  :  4.051  17.015   1420
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 17.87 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.23), residues: 1298
  helix:  1.59 (0.16), residues: 900
  sheet: -1.91 (0.70), residues: 58
  loop : -1.35 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 210 
 HIS   0.004   0.001   HIS A 401 
 PHE   0.016   0.001   PHE A 315 
 TYR   0.016   0.002   TYR B 327 
 ARG   0.002   0.000   ARG B 548 

*********************** 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
  137 residues out of total 1136 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 104
  time to evaluate  : 1.330 
Fit side-chains
REVERT: A  203 SER cc_start: 0.9177 (t) cc_final: 0.8539 (p)
REVERT: A  348 MET cc_start: 0.9157 (mmt) cc_final: 0.8929 (mmm)
REVERT: A  372 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8742 (tt0)
REVERT: A  463 PHE cc_start: 0.6803 (OUTLIER) cc_final: 0.6600 (t80)
REVERT: B  203 SER cc_start: 0.9183 (t) cc_final: 0.8562 (p)
REVERT: B  348 MET cc_start: 0.9151 (mmt) cc_final: 0.8932 (mmm)
REVERT: B  403 PHE cc_start: 0.7630 (m-80) cc_final: 0.7171 (m-80)
REVERT: B  463 PHE cc_start: 0.6900 (OUTLIER) cc_final: 0.6674 (t80)
  outliers start: 33
  outliers final: 26
  residues processed: 124
  average time/residue: 0.1928
  time to fit residues: 36.6798
Evaluate side-chains
  124 residues out of total 1136 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
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  328 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  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  187 PHE
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  308 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  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 75 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 86 optimal weight:    4.9990
   chunk 62 optimal weight:    9.9990
   chunk 11 optimal weight:    6.9990
   chunk 100 optimal weight:    3.9990
   chunk 115 optimal weight:    0.2980
   chunk 121 optimal weight:    5.9990
   chunk 111 optimal weight:    7.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  10974  Z= 0.309
  Angle     :  0.593   9.720  14886  Z= 0.303
  Chirality :  0.042   0.147   1630
  Planarity :  0.004   0.029   1890
  Dihedral  :  4.091  17.074   1420
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 18.13 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.23), residues: 1298
  helix:  1.53 (0.16), residues: 900
  sheet: -1.93 (0.68), residues: 58
  loop : -1.40 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 210 
 HIS   0.004   0.001   HIS A 401 
 PHE   0.015   0.001   PHE A 189 
 TYR   0.015   0.002   TYR B 457 
 ARG   0.003   0.000   ARG A 645 

*********************** 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
  131 residues out of total 1136 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 99
  time to evaluate  : 1.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.9176 (t) cc_final: 0.8538 (p)
REVERT: A  348 MET cc_start: 0.9145 (mmt) cc_final: 0.8924 (mmm)
REVERT: A  372 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8729 (tt0)
REVERT: A  384 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7629 (ttp)
REVERT: A  403 PHE cc_start: 0.7664 (m-80) cc_final: 0.7171 (m-80)
REVERT: B  203 SER cc_start: 0.9149 (t) cc_final: 0.8537 (p)
REVERT: B  403 PHE cc_start: 0.7613 (m-80) cc_final: 0.7186 (m-80)
  outliers start: 32
  outliers final: 25
  residues processed: 122
  average time/residue: 0.1817
  time to fit residues: 34.3728
Evaluate side-chains
  123 residues out of total 1136 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 97
  time to evaluate  : 1.184 
-------------------------------------------------------------------------------
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  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  308 THR
Chi-restraints excluded: chain A residue  328 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  384 MET
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  302 LEU
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  362 THR
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 118 optimal weight:    0.8980
   chunk 121 optimal weight:    0.7980
   chunk 71 optimal weight:    0.6980
   chunk 51 optimal weight:    0.0870
   chunk 93 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 107 optimal weight:    6.9990
   chunk 112 optimal weight:    3.9990
   chunk 77 optimal weight:    0.0870
   chunk 125 optimal weight:    0.8980
   chunk 76 optimal weight:    0.5980
   overall best weight:    0.4536

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

Flipped N/Q/H residues before XYZ refinement:
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 715 GLN
** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 715 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.059  10974  Z= 0.134
  Angle     :  0.539  11.418  14886  Z= 0.264
  Chirality :  0.038   0.201   1630
  Planarity :  0.003   0.029   1890
  Dihedral  :  3.795  14.852   1420
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 19.89 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.23), residues: 1298
  helix:  1.78 (0.16), residues: 906
  sheet: -1.70 (0.73), residues: 58
  loop : -1.42 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 235 
 HIS   0.002   0.000   HIS B  58 
 PHE   0.010   0.001   PHE B 379 
 TYR   0.015   0.001   TYR A 457 
 ARG   0.003   0.000   ARG B 645 

*********************** 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 fitting.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 1.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8669 (m-80)
REVERT: A  203 SER cc_start: 0.9045 (t) cc_final: 0.8385 (p)
REVERT: A  372 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8638 (tt0)
REVERT: A  531 ASN cc_start: 0.9087 (t0) cc_final: 0.8637 (t160)
REVERT: A  645 ARG cc_start: 0.7711 (mmp80) cc_final: 0.7346 (mmp80)
REVERT: B  203 SER cc_start: 0.9034 (t) cc_final: 0.8404 (p)
REVERT: B  531 ASN cc_start: 0.9074 (t0) cc_final: 0.8591 (t0)
REVERT: B  645 ARG cc_start: 0.7725 (mmp80) cc_final: 0.7355 (mmp80)
  outliers start: 19
  outliers final: 18
  residues processed: 125
  average time/residue: 0.1841
  time to fit residues: 35.7083
Evaluate side-chains
  121 residues out of total 1136 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 1.199 
-------------------------------------------------------------------------------
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  187 PHE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  265 HIS
Chi-restraints excluded: chain A residue  328 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  302 LEU
Chi-restraints excluded: chain B residue  342 THR
Chi-restraints excluded: chain B residue  400 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 59 optimal weight:    8.9990
   chunk 87 optimal weight:    2.9990
   chunk 131 optimal weight:    3.9990
   chunk 121 optimal weight:    0.0970
   chunk 104 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 80 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 111 optimal weight:    7.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10974  Z= 0.182
  Angle     :  0.560  11.248  14886  Z= 0.271
  Chirality :  0.040   0.302   1630
  Planarity :  0.003   0.028   1890
  Dihedral  :  3.757  14.328   1420
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 19.81 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.23), residues: 1298
  helix:  1.81 (0.16), residues: 904
  sheet: -1.56 (0.74), residues: 58
  loop : -1.30 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 235 
 HIS   0.003   0.001   HIS B 611 
 PHE   0.013   0.001   PHE A 379 
 TYR   0.016   0.002   TYR B 457 
 ARG   0.003   0.000   ARG B 645 

********************** 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
  123 residues out of total 1136 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 1.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 SER cc_start: 0.9081 (t) cc_final: 0.8422 (p)
REVERT: A  372 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8666 (tt0)
REVERT: A  531 ASN cc_start: 0.9102 (t0) cc_final: 0.8619 (t160)
REVERT: A  645 ARG cc_start: 0.7775 (mmp80) cc_final: 0.7364 (mmp80)
REVERT: B  203 SER cc_start: 0.9036 (t) cc_final: 0.8431 (p)
REVERT: B  388 PHE cc_start: 0.7574 (m-80) cc_final: 0.7372 (m-80)
REVERT: B  531 ASN cc_start: 0.9101 (t0) cc_final: 0.8613 (t160)
REVERT: B  645 ARG cc_start: 0.7808 (mmp80) cc_final: 0.7404 (mmp80)
  outliers start: 19
  outliers final: 16
  residues processed: 119
  average time/residue: 0.1858
  time to fit residues: 34.3670
Evaluate side-chains
  116 residues out of total 1136 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 1.236 
-------------------------------------------------------------------------------
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  265 HIS
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  342 THR
Chi-restraints excluded: chain B residue  400 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 96 optimal weight:    0.6980
   chunk 15 optimal weight:    5.9990
   chunk 29 optimal weight:   10.0000
   chunk 104 optimal weight:    0.5980
   chunk 43 optimal weight:    8.9990
   chunk 107 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 75 optimal weight:    6.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.110092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.083194 restraints weight = 23270.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.085913 restraints weight = 11745.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.087653 restraints weight = 8045.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10974  Z= 0.166
  Angle     :  0.556  11.421  14886  Z= 0.267
  Chirality :  0.039   0.290   1630
  Planarity :  0.003   0.028   1890
  Dihedral  :  3.723  14.825   1420
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 19.98 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.23), residues: 1298
  helix:  1.80 (0.16), residues: 920
  sheet: -1.48 (0.75), residues: 58
  loop : -1.37 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 235 
 HIS   0.003   0.000   HIS B  58 
 PHE   0.013   0.001   PHE A 379 
 TYR   0.016   0.001   TYR B 457 
 ARG   0.002   0.000   ARG B 645 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1900.07 seconds
wall clock time: 34 minutes 50.66 seconds (2090.66 seconds total)