Starting phenix.real_space_refine
on Mon Mar 11 02:33:42 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dro_27679/03_2024/8dro_27679.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dro_27679/03_2024/8dro_27679.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dro_27679/03_2024/8dro_27679.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dro_27679/03_2024/8dro_27679.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dro_27679/03_2024/8dro_27679.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dro_27679/03_2024/8dro_27679.pdb"
  }
  resolution = 4.06
  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=   0.049
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: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    4270      2.51       5
     N    1166      2.21       5
     O    1190      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B ASP  444": "OD1" <-> "OD2"
    Residue "B GLU  447": "OE1" <-> "OE2"
    Residue "B GLU  449": "OE1" <-> "OE2"
    Residue "B GLU  519": "OE1" <-> "OE2"
    Residue "B GLU  675": "OE1" <-> "OE2"
    Residue "B GLU  775": "OE1" <-> "OE2"
    Residue "B GLU  797": "OE1" <-> "OE2"
    Residue "C GLU  429": "OE1" <-> "OE2"
    Residue "C ASP  444": "OD1" <-> "OD2"
    Residue "C GLU  519": "OE1" <-> "OE2"
    Residue "C GLU  618": "OE1" <-> "OE2"
    Residue "C GLU  726": "OE1" <-> "OE2"
    Residue "C GLU  767": "OE1" <-> "OE2"
    Residue "C GLU  788": "OE1" <-> "OE2"
    Residue "C GLU  797": "OE1" <-> "OE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 6642
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 3321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3321
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 18, 'TRANS': 388}
    Chain: "C"
      Number of atoms: 3321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3321
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 18, 'TRANS': 388}
  Time building chain proxies: 4.00, per 1000 atoms: 0.60
  Number of scatterers: 6642
  At special positions: 0
  Unit cell: (89.08, 100.608, 90.128, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      16     16.00
     O    1190      8.00
     N    1166      7.00
     C    4270      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  - 3.50
        Amino acid           : False - 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: 2.52
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1576

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 5 sheets defined
      32.9% alpha, 11.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'B' and resid 402 through 411
    Processing helix  chain 'B' and resid 412 through 419
    Processing helix  chain 'B' and resid 439 through 445
      removed outlier: 3.844A  pdb=" N   PHE B 443 " --> pdb=" O   PRO B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 462 through 467
    Processing helix  chain 'B' and resid 484 through 495
      removed outlier: 3.740A  pdb=" N   GLU B 493 " --> pdb=" O   ALA B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 503 through 508
      removed outlier: 3.854A  pdb=" N   GLU B 507 " --> pdb=" O   ASP B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 515
      removed outlier: 4.280A  pdb=" N   SER B 514 " --> pdb=" O   LEU B 510 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU B 515 " --> pdb=" O   TRP B 511 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 510 through 515'
    Processing helix  chain 'B' and resid 535 through 543
      removed outlier: 3.532A  pdb=" N   ASP B 538 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   GLY B 539 " --> pdb=" O   VAL B 536 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ARG B 541 " --> pdb=" O   ASP B 538 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   GLU B 542 " --> pdb=" O   GLY B 539 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 566
    Processing helix  chain 'B' and resid 567 through 569
      No H-bonds generated for 'chain 'B' and resid 567 through 569'
    Processing helix  chain 'B' and resid 634 through 638
    Processing helix  chain 'B' and resid 655 through 661
      removed outlier: 3.684A  pdb=" N   ILE B 658 " --> pdb=" O   PRO B 655 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 684
      removed outlier: 3.508A  pdb=" N   TYR B 683 " --> pdb=" O   GLN B 680 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   CYS B 684 " --> pdb=" O   LEU B 681 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 701 through 707
    Processing helix  chain 'B' and resid 724 through 730
      removed outlier: 3.637A  pdb=" N   CYS B 730 " --> pdb=" O   GLU B 726 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 747 through 752
      removed outlier: 3.508A  pdb=" N   GLY B 751 " --> pdb=" O   PRO B 747 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 770 through 774
      removed outlier: 3.775A  pdb=" N   LEU B 773 " --> pdb=" O   PRO B 770 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 787 through 792
      removed outlier: 3.557A  pdb=" N   SER B 792 " --> pdb=" O   GLU B 788 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 795 through 808
    Processing helix  chain 'C' and resid 403 through 411
    Processing helix  chain 'C' and resid 412 through 419
      removed outlier: 4.003A  pdb=" N   GLN C 418 " --> pdb=" O   ASP C 414 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ARG C 419 " --> pdb=" O   LYS C 415 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 439 through 444
      removed outlier: 3.634A  pdb=" N   PHE C 443 " --> pdb=" O   PRO C 439 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 462 through 468
    Processing helix  chain 'C' and resid 484 through 494
    Processing helix  chain 'C' and resid 535 through 541
      removed outlier: 3.755A  pdb=" N   ASP C 538 " --> pdb=" O   ILE C 535 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   GLY C 539 " --> pdb=" O   VAL C 536 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ARG C 541 " --> pdb=" O   ASP C 538 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 559 through 566
    Processing helix  chain 'C' and resid 607 through 612
      removed outlier: 4.247A  pdb=" N   PHE C 611 " --> pdb=" O   PRO C 607 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 629 through 638
      removed outlier: 3.526A  pdb=" N   ILE C 632 " --> pdb=" O   ILE C 629 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ILE C 633 " --> pdb=" O   GLU C 630 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLN C 636 " --> pdb=" O   ILE C 633 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   HIS C 637 " --> pdb=" O   SER C 634 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 656 through 661
      removed outlier: 3.823A  pdb=" N   LEU C 661 " --> pdb=" O   ILE C 658 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 678 through 684
      removed outlier: 3.751A  pdb=" N   CYS C 684 " --> pdb=" O   LEU C 681 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 701 through 707
      removed outlier: 3.662A  pdb=" N   ILE C 704 " --> pdb=" O   PRO C 701 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 725 through 730
      removed outlier: 3.763A  pdb=" N   CYS C 730 " --> pdb=" O   LEU C 727 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 747 through 753
    Processing helix  chain 'C' and resid 770 through 775
    Processing helix  chain 'C' and resid 787 through 792
    Processing helix  chain 'C' and resid 795 through 807
    Processing sheet with id=AA1, first strand: chain 'B' and resid 420 through 422
      removed outlier: 6.965A  pdb=" N   LEU B 451 " --> pdb=" O   TRP B 475 " (cutoff:3.500A)
      removed outlier: 7.181A  pdb=" N   TYR B 477 " --> pdb=" O   LEU B 451 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   LEU B 453 " --> pdb=" O   TYR B 477 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   LEU B 474 " --> pdb=" O   HIS B 499 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   LYS B 501 " --> pdb=" O   LEU B 474 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   LEU B 476 " --> pdb=" O   LYS B 501 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ARG B 550 " --> pdb=" O   LEU B 521 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU B 523 " --> pdb=" O   ARG B 550 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LYS B 552 " --> pdb=" O   LEU B 523 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   SER B 573 " --> pdb=" O   LEU B 549 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASP B 620 " --> pdb=" O   LEU B 596 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ILE B 619 " --> pdb=" O   CYS B 643 " (cutoff:3.500A)
      removed outlier: 7.803A  pdb=" N   LEU B 644 " --> pdb=" O   TYR B 668 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 736 through 737
      removed outlier: 6.611A  pdb=" N   LEU B 736 " --> pdb=" O   GLU B 760 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 421 through 422
      removed outlier: 5.953A  pdb=" N   LEU C 451 " --> pdb=" O   TRP C 475 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   TYR C 477 " --> pdb=" O   LEU C 451 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   LEU C 453 " --> pdb=" O   TYR C 477 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   HIS C 522 " --> pdb=" O   LEU C 498 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   SER C 573 " --> pdb=" O   LEU C 549 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   LEU C 572 " --> pdb=" O   GLU C 595 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LYS C 645 " --> pdb=" O   ILE C 619 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   LEU C 644 " --> pdb=" O   TYR C 668 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 459 through 461
      removed outlier: 6.032A  pdb=" N   VAL C 459 " --> pdb=" O   LYS C 482 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 735 through 736
      removed outlier: 8.155A  pdb=" N   LEU C 736 " --> pdb=" O   GLU C 760 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   ILE C 759 " --> pdb=" O   VAL C 785 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5

    163 hydrogen bonds defined for protein.
    351 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: 1.69

  Time building geometry restraints manager: 2.72 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1247
        1.33 -     1.45: 1433
        1.45 -     1.57: 4054
        1.57 -     1.69: 2
        1.69 -     1.81: 20
  Bond restraints: 6756
  Sorted by residual:
  bond pdb=" CA  HIS C 522 "
       pdb=" CB  HIS C 522 "
    ideal  model  delta    sigma   weight residual
    1.533  1.597 -0.064 2.29e-02 1.91e+03 7.69e+00
  bond pdb=" C   ILE C 508 "
       pdb=" N   PRO C 509 "
    ideal  model  delta    sigma   weight residual
    1.329  1.358 -0.029 1.20e-02 6.94e+03 5.90e+00
  bond pdb=" CB  PRO B 509 "
       pdb=" CG  PRO B 509 "
    ideal  model  delta    sigma   weight residual
    1.492  1.590 -0.098 5.00e-02 4.00e+02 3.83e+00
  bond pdb=" CG  LEU B 681 "
       pdb=" CD1 LEU B 681 "
    ideal  model  delta    sigma   weight residual
    1.521  1.459  0.062 3.30e-02 9.18e+02 3.51e+00
  bond pdb=" N   GLY C 437 "
       pdb=" CA  GLY C 437 "
    ideal  model  delta    sigma   weight residual
    1.445  1.459 -0.014 9.90e-03 1.02e+04 2.04e+00
  ... (remaining 6751 not shown)

  Histogram of bond angle deviations from ideal:
       99.21 -   106.19: 179
      106.19 -   113.17: 3799
      113.17 -   120.15: 2347
      120.15 -   127.13: 2762
      127.13 -   134.11: 73
  Bond angle restraints: 9160
  Sorted by residual:
  angle pdb=" C   ASP B 703 "
        pdb=" CA  ASP B 703 "
        pdb=" CB  ASP B 703 "
      ideal   model   delta    sigma   weight residual
     110.01  117.18   -7.17 1.80e+00 3.09e-01 1.59e+01
  angle pdb=" N   HIS C 522 "
        pdb=" CA  HIS C 522 "
        pdb=" CB  HIS C 522 "
      ideal   model   delta    sigma   weight residual
     110.83  117.61   -6.78 1.74e+00 3.30e-01 1.52e+01
  angle pdb=" CA  LYS B 472 "
        pdb=" CB  LYS B 472 "
        pdb=" CG  LYS B 472 "
      ideal   model   delta    sigma   weight residual
     114.10  121.86   -7.76 2.00e+00 2.50e-01 1.51e+01
  angle pdb=" CB  LYS B 472 "
        pdb=" CG  LYS B 472 "
        pdb=" CD  LYS B 472 "
      ideal   model   delta    sigma   weight residual
     111.30  119.95   -8.65 2.30e+00 1.89e-01 1.41e+01
  angle pdb=" CB  ARG B 781 "
        pdb=" CG  ARG B 781 "
        pdb=" CD  ARG B 781 "
      ideal   model   delta    sigma   weight residual
     111.30  119.83   -8.53 2.30e+00 1.89e-01 1.37e+01
  ... (remaining 9155 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.47: 3633
       16.47 -    32.94: 429
       32.94 -    49.41: 97
       49.41 -    65.88: 25
       65.88 -    82.35: 4
  Dihedral angle restraints: 4188
    sinusoidal: 1784
      harmonic: 2404
  Sorted by residual:
  dihedral pdb=" CA  LYS B 589 "
           pdb=" C   LYS B 589 "
           pdb=" N   MET B 590 "
           pdb=" CA  MET B 590 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.55  -24.45     0      5.00e+00 4.00e-02 2.39e+01
  dihedral pdb=" CA  GLY B 774 "
           pdb=" C   GLY B 774 "
           pdb=" N   GLU B 775 "
           pdb=" CA  GLU B 775 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.85  -23.15     0      5.00e+00 4.00e-02 2.14e+01
  dihedral pdb=" CA  THR B 679 "
           pdb=" C   THR B 679 "
           pdb=" N   GLN B 680 "
           pdb=" CA  GLN B 680 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.42  -22.58     0      5.00e+00 4.00e-02 2.04e+01
  ... (remaining 4185 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 708
       0.040 -    0.080: 298
       0.080 -    0.120: 76
       0.120 -    0.159: 10
       0.159 -    0.199: 6
  Chirality restraints: 1098
  Sorted by residual:
  chirality pdb=" CB  ILE B 677 "
            pdb=" CA  ILE B 677 "
            pdb=" CG1 ILE B 677 "
            pdb=" CG2 ILE B 677 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.92e-01
  chirality pdb=" CG  LEU C 416 "
            pdb=" CB  LEU C 416 "
            pdb=" CD1 LEU C 416 "
            pdb=" CD2 LEU C 416 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 8.86e-01
  chirality pdb=" CG  LEU B 491 "
            pdb=" CB  LEU B 491 "
            pdb=" CD1 LEU B 491 "
            pdb=" CD2 LEU B 491 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.18 2.00e-01 2.50e+01 8.55e-01
  ... (remaining 1095 not shown)

  Planarity restraints: 1156
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 462 "    0.062 5.00e-02 4.00e+02   9.29e-02 1.38e+01
        pdb=" N   PRO C 463 "   -0.161 5.00e-02 4.00e+02
        pdb=" CA  PRO C 463 "    0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO C 463 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 724 "   -0.055 5.00e-02 4.00e+02   8.34e-02 1.11e+01
        pdb=" N   PRO B 725 "    0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO B 725 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO B 725 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 682 "    0.014 2.00e-02 2.50e+03   1.78e-02 5.53e+00
        pdb=" CG  PHE B 682 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 682 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 682 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 682 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 682 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 682 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1153 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1486
        2.79 -     3.32: 6256
        3.32 -     3.85: 11128
        3.85 -     4.37: 13749
        4.37 -     4.90: 21659
  Nonbonded interactions: 54278
  Sorted by model distance:
  nonbonded pdb=" O   GLN C 560 "
            pdb=" OG1 THR C 563 "
     model   vdw
     2.265 2.440
  nonbonded pdb=" O   ARG B 492 "
            pdb=" OG1 THR B 517 "
     model   vdw
     2.271 2.440
  nonbonded pdb=" O   PRO B 777 "
            pdb=" NZ  LYS B 780 "
     model   vdw
     2.296 2.520
  nonbonded pdb=" OE2 GLU B 493 "
            pdb=" NZ  LYS C 501 "
     model   vdw
     2.320 2.520
  nonbonded pdb=" O   GLN B 560 "
            pdb=" OG1 THR B 563 "
     model   vdw
     2.325 2.440
  ... (remaining 54273 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}

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:             5.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          14.900
  Check model and map are aligned:         0.100
  Set scattering table:                    0.100
  Process input model:                     21.300
  Find NCS groups from input model:        0.460
  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:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5410
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      :  0.004   0.098   6756  Z= 0.273
  Angle     :  0.957   9.695   9160  Z= 0.519
  Chirality :  0.046   0.199   1098
  Planarity :  0.007   0.093   1156
  Dihedral  : 15.273  82.350   2612
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 19.44 %
    Favored  : 80.16 %
  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: -3.39 (0.27), residues: 810
  helix: -2.86 (0.29), residues: 220
  sheet: -2.57 (0.54), residues: 90
  loop : -1.93 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP B 475 
 HIS   0.007   0.001   HIS C 522 
 PHE   0.039   0.002   PHE B 682 
 TYR   0.009   0.001   TYR C 668 
 ARG   0.007   0.001   ARG B 731 

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 233
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  453 LEU cc_start: 0.9064 (pp) cc_final: 0.8813 (pp)
REVERT: B  519 GLU cc_start: 0.6964 (tp30) cc_final: 0.5596 (tp30)
REVERT: B  551 LEU cc_start: 0.8119 (mt) cc_final: 0.6990 (pp)
REVERT: B  595 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7358 (mp0)
REVERT: B  675 GLU cc_start: 0.6095 (mm-30) cc_final: 0.5844 (mp0)
REVERT: B  690 LEU cc_start: 0.8504 (mp) cc_final: 0.8216 (mp)
REVERT: B  710 LEU cc_start: 0.7860 (mt) cc_final: 0.7508 (mp)
REVERT: B  804 ARG cc_start: 0.3552 (tpt170) cc_final: 0.3153 (tpt-90)
REVERT: C  412 THR cc_start: 0.5060 (p) cc_final: 0.4828 (t)
REVERT: C  433 PHE cc_start: 0.6844 (t80) cc_final: 0.6068 (t80)
REVERT: C  443 PHE cc_start: 0.6891 (m-80) cc_final: 0.5619 (m-80)
REVERT: C  503 THR cc_start: 0.7434 (m) cc_final: 0.7172 (m)
REVERT: C  744 GLN cc_start: 0.5638 (OUTLIER) cc_final: 0.5210 (pm20)
  outliers start: 3
  outliers final: 1
  residues processed: 236
  average time/residue: 0.2444
  time to fit residues: 71.8529
Evaluate side-chains
  124 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 122
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    9.9990
   chunk 60 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 20 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 32 optimal weight:    7.9990
   chunk 62 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   chunk 38 optimal weight:    0.0050
   chunk 46 optimal weight:    7.9990
   chunk 72 optimal weight:    3.9990
   overall best weight:    4.0002

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

Flipped N/Q/H residues before XYZ refinement:
** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 478 HIS
** B 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 614 HIS
B 694 HIS
C 404 GLN
** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 576 ASN
C 650 HIS
C 657 GLN
C 711 GLN
** C 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5840
moved from start:          0.5049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.084   6756  Z= 0.444
  Angle     :  1.033  12.309   9160  Z= 0.512
  Chirality :  0.052   0.245   1098
  Planarity :  0.008   0.075   1156
  Dihedral  :  6.759  24.661    878
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 33.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  7.28 %
    Favored  : 92.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.46 (0.27), residues: 810
  helix: -3.03 (0.28), residues: 220
  sheet: -2.85 (0.44), residues: 122
  loop : -1.72 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.004   TRP C 411 
 HIS   0.010   0.003   HIS B 499 
 PHE   0.020   0.003   PHE B 682 
 TYR   0.031   0.004   TYR C 513 
 ARG   0.011   0.001   ARG B 496 

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 158
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  647 TRP cc_start: 0.5343 (p90) cc_final: 0.4756 (p90)
REVERT: B  657 GLN cc_start: 0.0525 (OUTLIER) cc_final: 0.0042 (mm-40)
REVERT: B  690 LEU cc_start: 0.8585 (mp) cc_final: 0.8363 (mt)
REVERT: B  729 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8208 (tm-30)
REVERT: B  755 ASN cc_start: 0.5386 (t0) cc_final: 0.4394 (m-40)
REVERT: B  804 ARG cc_start: 0.4095 (tpp-160) cc_final: 0.3652 (tpt-90)
REVERT: C  403 ARG cc_start: 0.4706 (OUTLIER) cc_final: 0.3626 (mtm180)
REVERT: C  443 PHE cc_start: 0.7418 (m-80) cc_final: 0.6553 (m-80)
REVERT: C  473 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7289 (mt-10)
REVERT: C  590 MET cc_start: 0.5377 (mmm) cc_final: 0.5067 (mmm)
REVERT: C  596 LEU cc_start: 0.8392 (mt) cc_final: 0.8043 (pt)
REVERT: C  613 LEU cc_start: 0.5062 (tp) cc_final: 0.4821 (tp)
REVERT: C  618 GLU cc_start: 0.8337 (tp30) cc_final: 0.8067 (tp30)
  outliers start: 5
  outliers final: 0
  residues processed: 162
  average time/residue: 0.2015
  time to fit residues: 42.5130
Evaluate side-chains
  105 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0070
   chunk 72 optimal weight:    5.9990
   chunk 78 optimal weight:    0.0870
   chunk 64 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.5176

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

Flipped N/Q/H residues before XYZ refinement:
** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 467 GLN
C 576 ASN
C 737 HIS
C 764 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5683
moved from start:          0.5328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6756  Z= 0.199
  Angle     :  0.693   9.276   9160  Z= 0.346
  Chirality :  0.044   0.158   1098
  Planarity :  0.005   0.063   1156
  Dihedral  :  5.913  21.372    878
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 19.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.97 (0.29), residues: 810
  helix: -2.50 (0.32), residues: 225
  sheet: -2.79 (0.43), residues: 131
  loop : -1.34 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP C 411 
 HIS   0.004   0.001   HIS C 522 
 PHE   0.016   0.002   PHE B 635 
 TYR   0.019   0.002   TYR C 513 
 ARG   0.008   0.001   ARG C 600 

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  456 ILE cc_start: 0.8432 (tt) cc_final: 0.8183 (tt)
REVERT: B  500 ILE cc_start: 0.7690 (mm) cc_final: 0.7293 (mp)
REVERT: B  548 VAL cc_start: 0.7000 (t) cc_final: 0.6764 (t)
REVERT: B  729 GLN cc_start: 0.7848 (tm-30) cc_final: 0.7585 (tm-30)
REVERT: C  455 LEU cc_start: 0.8789 (mt) cc_final: 0.8545 (mt)
REVERT: C  473 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7129 (mt-10)
REVERT: C  618 GLU cc_start: 0.8293 (tp30) cc_final: 0.8043 (tp30)
REVERT: C  646 LEU cc_start: 0.7611 (tp) cc_final: 0.7407 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.2051
  time to fit residues: 38.7928
Evaluate side-chains
  102 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0970
   chunk 8 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 48 optimal weight:    7.9990
   chunk 73 optimal weight:    9.9990
   chunk 77 optimal weight:    0.3980
   chunk 38 optimal weight:    0.9990
   chunk 69 optimal weight:    0.0370
   chunk 20 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   overall best weight:    0.5060

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

Flipped N/Q/H residues before XYZ refinement:
** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 711 GLN
C 409 ASN
** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 639 HIS
C 657 GLN
C 737 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5664
moved from start:          0.5738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6756  Z= 0.174
  Angle     :  0.665  11.749   9160  Z= 0.328
  Chirality :  0.043   0.176   1098
  Planarity :  0.005   0.058   1156
  Dihedral  :  5.551  21.342    878
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 17.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  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: -2.67 (0.30), residues: 810
  helix: -2.11 (0.35), residues: 211
  sheet: -2.51 (0.45), residues: 126
  loop : -1.34 (0.30), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 411 
 HIS   0.004   0.001   HIS C 431 
 PHE   0.021   0.002   PHE C 433 
 TYR   0.019   0.002   TYR C 513 
 ARG   0.004   0.000   ARG B 765 

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  456 ILE cc_start: 0.8557 (tt) cc_final: 0.8238 (tt)
REVERT: B  500 ILE cc_start: 0.7633 (mm) cc_final: 0.7296 (mp)
REVERT: B  647 TRP cc_start: 0.5093 (p90) cc_final: 0.4583 (p90)
REVERT: B  695 ASN cc_start: 0.4165 (m-40) cc_final: 0.3413 (p0)
REVERT: B  729 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7796 (tm-30)
REVERT: B  755 ASN cc_start: 0.5333 (t0) cc_final: 0.4696 (m-40)
REVERT: C  473 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7166 (mt-10)
REVERT: C  503 THR cc_start: 0.7097 (m) cc_final: 0.6860 (t)
REVERT: C  618 GLU cc_start: 0.8279 (tp30) cc_final: 0.7973 (tp30)
REVERT: C  646 LEU cc_start: 0.7639 (tp) cc_final: 0.7394 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1971
  time to fit residues: 36.9718
Evaluate side-chains
  99 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 31 optimal weight:    9.9990
   chunk 65 optimal weight:    8.9990
   chunk 53 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 69 optimal weight:    7.9990
   chunk 19 optimal weight:    9.9990
   chunk 26 optimal weight:    0.0970
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 494 ASN
C 409 ASN
** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 737 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5720
moved from start:          0.6193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6756  Z= 0.186
  Angle     :  0.667   9.911   9160  Z= 0.333
  Chirality :  0.044   0.180   1098
  Planarity :  0.005   0.057   1156
  Dihedral  :  5.487  20.677    878
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 19.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  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: -2.64 (0.30), residues: 810
  helix: -2.36 (0.32), residues: 218
  sheet: -2.23 (0.45), residues: 138
  loop : -1.18 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP C 411 
 HIS   0.006   0.001   HIS C 478 
 PHE   0.017   0.002   PHE B 791 
 TYR   0.018   0.001   TYR C 513 
 ARG   0.006   0.000   ARG C 600 

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  500 ILE cc_start: 0.7569 (mm) cc_final: 0.7323 (mp)
REVERT: B  647 TRP cc_start: 0.4969 (p90) cc_final: 0.4417 (p90)
REVERT: B  695 ASN cc_start: 0.4042 (m-40) cc_final: 0.3533 (p0)
REVERT: B  729 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7803 (tm-30)
REVERT: B  755 ASN cc_start: 0.5589 (t0) cc_final: 0.4942 (m-40)
REVERT: B  804 ARG cc_start: 0.4255 (tpp-160) cc_final: 0.3220 (tpt-90)
REVERT: C  618 GLU cc_start: 0.8320 (tp30) cc_final: 0.7938 (tp30)
REVERT: C  646 LEU cc_start: 0.7652 (tp) cc_final: 0.7416 (mm)
REVERT: C  704 ILE cc_start: 0.6666 (tt) cc_final: 0.6452 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1912
  time to fit residues: 34.9239
Evaluate side-chains
  98 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 69 optimal weight:    0.2980
   chunk 15 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 19 optimal weight:    9.9990
   chunk 77 optimal weight:    0.4980
   chunk 64 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0050
   chunk 40 optimal weight:    4.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.8996

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

Flipped N/Q/H residues before XYZ refinement:
** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 576 ASN
C 657 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5724
moved from start:          0.6452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6756  Z= 0.176
  Angle     :  0.657   9.352   9160  Z= 0.326
  Chirality :  0.043   0.141   1098
  Planarity :  0.005   0.055   1156
  Dihedral  :  5.344  24.126    878
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 19.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  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: -2.60 (0.30), residues: 810
  helix: -2.24 (0.33), residues: 218
  sheet: -2.50 (0.44), residues: 129
  loop : -1.15 (0.31), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 411 
 HIS   0.003   0.001   HIS C 522 
 PHE   0.022   0.002   PHE B 682 
 TYR   0.016   0.001   TYR C 513 
 ARG   0.003   0.000   ARG B 801 

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  647 TRP cc_start: 0.4927 (p90) cc_final: 0.4326 (p90)
REVERT: B  695 ASN cc_start: 0.4045 (m-40) cc_final: 0.3552 (p0)
REVERT: B  729 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7681 (tm-30)
REVERT: B  755 ASN cc_start: 0.5755 (t0) cc_final: 0.5017 (m-40)
REVERT: C  618 GLU cc_start: 0.8345 (tp30) cc_final: 0.7928 (tp30)
REVERT: C  646 LEU cc_start: 0.7728 (tp) cc_final: 0.7496 (mm)
REVERT: C  704 ILE cc_start: 0.6625 (tt) cc_final: 0.6416 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1879
  time to fit residues: 33.6978
Evaluate side-chains
  95 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 8 optimal weight:    9.9990
   chunk 44 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   chunk 65 optimal weight:    6.9990
   chunk 77 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 708 GLN
** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 657 GLN
** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5874
moved from start:          0.7260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6756  Z= 0.261
  Angle     :  0.789  10.072   9160  Z= 0.390
  Chirality :  0.046   0.177   1098
  Planarity :  0.006   0.081   1156
  Dihedral  :  5.883  24.593    878
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 25.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.25 %
    Favored  : 89.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.97 (0.29), residues: 810
  helix: -2.66 (0.30), residues: 215
  sheet: -2.66 (0.42), residues: 133
  loop : -1.33 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP C 411 
 HIS   0.022   0.002   HIS C 499 
 PHE   0.020   0.003   PHE B 682 
 TYR   0.018   0.002   TYR C 513 
 ARG   0.008   0.001   ARG C 492 

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  647 TRP cc_start: 0.4587 (p90) cc_final: 0.3856 (p90)
REVERT: B  695 ASN cc_start: 0.4119 (m-40) cc_final: 0.3837 (p0)
REVERT: B  729 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7880 (tm-30)
REVERT: B  755 ASN cc_start: 0.5856 (t0) cc_final: 0.4928 (m110)
REVERT: C  596 LEU cc_start: 0.8095 (mt) cc_final: 0.7890 (pt)
REVERT: C  683 TYR cc_start: 0.7064 (m-10) cc_final: 0.6527 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1932
  time to fit residues: 32.1031
Evaluate side-chains
  81 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0770
   chunk 70 optimal weight:    0.0980
   chunk 73 optimal weight:    2.9990
   chunk 67 optimal weight:    7.9990
   overall best weight:    1.0342

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

Flipped N/Q/H residues before XYZ refinement:
** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 406 ASN
** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 575 ASN
** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 708 GLN
** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5799
moved from start:          0.7386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6756  Z= 0.193
  Angle     :  0.705  10.812   9160  Z= 0.348
  Chirality :  0.045   0.145   1098
  Planarity :  0.006   0.075   1156
  Dihedral  :  5.654  23.697    878
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 20.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  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: -2.82 (0.29), residues: 810
  helix: -2.40 (0.32), residues: 213
  sheet: -2.50 (0.42), residues: 136
  loop : -1.33 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 411 
 HIS   0.021   0.001   HIS C 499 
 PHE   0.018   0.002   PHE B 682 
 TYR   0.015   0.001   TYR C 513 
 ARG   0.003   0.000   ARG B 801 

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  429 GLU cc_start: 0.6502 (pt0) cc_final: 0.6251 (pm20)
REVERT: B  647 TRP cc_start: 0.4826 (p90) cc_final: 0.4089 (p90)
REVERT: B  729 GLN cc_start: 0.7883 (tm-30) cc_final: 0.7640 (tm-30)
REVERT: B  755 ASN cc_start: 0.6087 (t0) cc_final: 0.5196 (m110)
REVERT: C  503 THR cc_start: 0.7160 (m) cc_final: 0.6931 (t)
REVERT: C  683 TYR cc_start: 0.7099 (m-10) cc_final: 0.6682 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1903
  time to fit residues: 32.7923
Evaluate side-chains
  83 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 73 optimal weight:    5.9990
   chunk 43 optimal weight:    0.7980
   chunk 31 optimal weight:    6.9990
   chunk 56 optimal weight:    7.9990
   chunk 22 optimal weight:    5.9990
   chunk 64 optimal weight:    7.9990
   chunk 67 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0060
   overall best weight:    1.1198

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

Flipped N/Q/H residues before XYZ refinement:
** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 406 ASN
B 494 ASN
** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5798
moved from start:          0.7605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6756  Z= 0.193
  Angle     :  0.711  11.675   9160  Z= 0.347
  Chirality :  0.045   0.145   1098
  Planarity :  0.006   0.079   1156
  Dihedral  :  5.566  21.242    878
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 20.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.63 %
    Favored  : 90.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  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: -2.72 (0.29), residues: 810
  helix: -2.27 (0.33), residues: 206
  sheet: -2.47 (0.41), residues: 143
  loop : -1.28 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 411 
 HIS   0.018   0.001   HIS C 499 
 PHE   0.019   0.002   PHE C 443 
 TYR   0.015   0.002   TYR C 513 
 ARG   0.003   0.000   ARG B 640 

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  429 GLU cc_start: 0.6807 (pt0) cc_final: 0.6390 (pm20)
REVERT: B  647 TRP cc_start: 0.4848 (p90) cc_final: 0.3855 (p90)
REVERT: C  431 HIS cc_start: 0.7245 (t70) cc_final: 0.6185 (p90)
REVERT: C  683 TYR cc_start: 0.7056 (m-10) cc_final: 0.6657 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1900
  time to fit residues: 31.6760
Evaluate side-chains
  85 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 36 optimal weight:    0.0570
   chunk 52 optimal weight:    9.9990
   chunk 79 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 63 optimal weight:    9.9990
   chunk 6 optimal weight:    0.0060
   chunk 49 optimal weight:   10.0000
   chunk 38 optimal weight:    0.8980
   chunk 50 optimal weight:    0.1980
   chunk 67 optimal weight:    8.9990
   chunk 19 optimal weight:    9.9990
   overall best weight:    0.6316

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

Flipped N/Q/H residues before XYZ refinement:
** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 406 ASN
B 708 GLN
B 758 GLN
** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 478 HIS
** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5747
moved from start:          0.7740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6756  Z= 0.175
  Angle     :  0.699  11.841   9160  Z= 0.338
  Chirality :  0.044   0.147   1098
  Planarity :  0.005   0.069   1156
  Dihedral  :  5.420  22.124    878
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 18.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.63 %
    Favored  : 90.37 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.53 %
    Favored  : 99.34 %
  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: -2.60 (0.30), residues: 810
  helix: -2.08 (0.34), residues: 212
  sheet: -2.35 (0.42), residues: 140
  loop : -1.26 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 511 
 HIS   0.016   0.001   HIS C 499 
 PHE   0.025   0.002   PHE B 682 
 TYR   0.013   0.001   TYR C 513 
 ARG   0.003   0.000   ARG B 640 

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  519 GLU cc_start: 0.6216 (tp30) cc_final: 0.5519 (pt0)
REVERT: B  647 TRP cc_start: 0.4938 (p90) cc_final: 0.3943 (p90)
REVERT: C  431 HIS cc_start: 0.7353 (t70) cc_final: 0.6196 (p-80)
REVERT: C  477 TYR cc_start: 0.6454 (m-10) cc_final: 0.5731 (m-10)
REVERT: C  596 LEU cc_start: 0.8118 (mm) cc_final: 0.7733 (pp)
REVERT: C  683 TYR cc_start: 0.7084 (m-10) cc_final: 0.6649 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1838
  time to fit residues: 31.1244
Evaluate side-chains
  86 residues out of total 756 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 58 optimal weight:    0.0030
   chunk 9 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   chunk 63 optimal weight:    7.9990
   chunk 26 optimal weight:    0.2980
   chunk 65 optimal weight:    0.8980
   chunk 8 optimal weight:    9.9990
   chunk 11 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   overall best weight:    0.4990

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

Flipped N/Q/H residues before XYZ refinement:
** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 406 ASN
** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 478 HIS
** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.167746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.158225 restraints weight = 27960.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.159289 restraints weight = 23136.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.160471 restraints weight = 16539.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.4585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5309
moved from start:          0.7848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6756  Z= 0.171
  Angle     :  0.689  11.988   9160  Z= 0.335
  Chirality :  0.044   0.144   1098
  Planarity :  0.005   0.062   1156
  Dihedral  :  5.286  20.457    878
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 19.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.14 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.44 (0.30), residues: 810
  helix: -1.98 (0.35), residues: 204
  sheet: -2.16 (0.43), residues: 140
  loop : -1.20 (0.30), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 511 
 HIS   0.015   0.001   HIS C 499 
 PHE   0.022   0.002   PHE B 682 
 TYR   0.012   0.001   TYR C 513 
 ARG   0.008   0.000   ARG C 492 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1911.83 seconds
wall clock time: 35 minutes 33.10 seconds (2133.10 seconds total)