Starting phenix.real_space_refine
on Thu Mar 14 16:27:12 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n59_24183/03_2024/7n59_24183_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n59_24183/03_2024/7n59_24183.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n59_24183/03_2024/7n59_24183_ligands.cif

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 {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n59_24183/03_2024/7n59_24183_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n59_24183/03_2024/7n59_24183_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n59_24183/03_2024/7n59_24183.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n59_24183/03_2024/7n59_24183.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n59_24183/03_2024/7n59_24183_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n59_24183/03_2024/7n59_24183_updated.pdb"
  }
  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=   0.021
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      36      5.16       5
     C    5892      2.51       5
     N    1584      2.21       5
     O    1726      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  205": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  313": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  355": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  567": "OD1" <-> "OD2"
    Residue "A GLU  596": "OE1" <-> "OE2"
    Residue "B PHE  355": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  373": "OE1" <-> "OE2"
    Residue "B PHE  500": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 9238
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 590, 4599
          Classifications: {'peptide': 590}
          Link IDs: {'PTRANS': 13, 'TRANS': 576}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 590, 4599
          Classifications: {'peptide': 590}
          Link IDs: {'PTRANS': 13, 'TRANS': 576}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 40
          Unusual residues: {'GDS': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" CB1 GDS A 801 " occ=0.50
      ... (38 atoms not shown)
      pdb=" SG5 GDS A 801 " occ=0.50
  Time building chain proxies: 4.98, per 1000 atoms: 0.54
  Number of scatterers: 9238
  At special positions: 0
  Unit cell: (81.225, 98.325, 142.785, 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      36     16.00
     O    1726      8.00
     N    1584      7.00
     C    5892      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: 3.38
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2208

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      44 helices and 6 sheets defined
      62.9% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 118 through 132
    Processing helix  chain 'A' and resid 137 through 174
      removed outlier: 3.771A  pdb=" N   ARG A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
      Proline residue:  A 161  - end of helix
      removed outlier: 3.602A  pdb=" N   PHE A 164 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 244
      removed outlier: 3.689A  pdb=" N   GLY A 206 " --> pdb=" O   LEU A 202 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   VAL A 226 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ARG A 232 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASP A 244 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 252
    Processing helix  chain 'A' and resid 257 through 278
    Processing helix  chain 'A' and resid 280 through 293
    Processing helix  chain 'A' and resid 301 through 347
      removed outlier: 4.034A  pdb=" N   VAL A 310 " --> pdb=" O   THR A 306 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   LYS A 333 " --> pdb=" O   LYS A 329 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   ALA A 334 " --> pdb=" O   ALA A 330 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ASP A 335 " --> pdb=" O   MET A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 354
    Processing helix  chain 'A' and resid 360 through 411
    Processing helix  chain 'A' and resid 419 through 434
      removed outlier: 3.592A  pdb=" N   LEU A 431 " --> pdb=" O   PHE A 427 " (cutoff:3.500A)
      Proline residue:  A 432  - end of helix
    Processing helix  chain 'A' and resid 436 through 456
    Processing helix  chain 'A' and resid 514 through 516
      No H-bonds generated for 'chain 'A' and resid 514 through 516'
    Processing helix  chain 'A' and resid 521 through 526
    Processing helix  chain 'A' and resid 548 through 553
    Processing helix  chain 'A' and resid 569 through 576
      removed outlier: 4.539A  pdb=" N   GLY A 576 " --> pdb=" O   ASN A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 591
    Processing helix  chain 'A' and resid 595 through 600
      removed outlier: 3.881A  pdb=" N   ASN A 600 " --> pdb=" O   GLU A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 618 through 632
    Processing helix  chain 'A' and resid 648 through 661
    Processing helix  chain 'A' and resid 674 through 676
      No H-bonds generated for 'chain 'A' and resid 674 through 676'
    Processing helix  chain 'A' and resid 697 through 703
    Processing helix  chain 'A' and resid 706 through 712
    Processing helix  chain 'B' and resid 118 through 132
    Processing helix  chain 'B' and resid 137 through 174
      Proline residue:  B 161  - end of helix
    Processing helix  chain 'B' and resid 198 through 244
      removed outlier: 3.945A  pdb=" N   VAL B 226 " --> pdb=" O   VAL B 222 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ASP B 244 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 252
    Processing helix  chain 'B' and resid 257 through 278
    Processing helix  chain 'B' and resid 280 through 295
    Processing helix  chain 'B' and resid 301 through 347
      removed outlier: 4.586A  pdb=" N   LYS B 326 " --> pdb=" O   GLN B 322 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   PHE B 327 " --> pdb=" O   TRP B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 354
    Processing helix  chain 'B' and resid 361 through 411
    Processing helix  chain 'B' and resid 418 through 434
      removed outlier: 3.631A  pdb=" N   LEU B 431 " --> pdb=" O   PHE B 427 " (cutoff:3.500A)
      Proline residue:  B 432  - end of helix
    Processing helix  chain 'B' and resid 436 through 456
    Processing helix  chain 'B' and resid 514 through 516
      No H-bonds generated for 'chain 'B' and resid 514 through 516'
    Processing helix  chain 'B' and resid 521 through 525
    Processing helix  chain 'B' and resid 548 through 553
    Processing helix  chain 'B' and resid 569 through 576
      removed outlier: 4.477A  pdb=" N   GLY B 576 " --> pdb=" O   ASN B 572 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 582 through 591
    Processing helix  chain 'B' and resid 595 through 600
      removed outlier: 3.675A  pdb=" N   ASN B 600 " --> pdb=" O   GLU B 596 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 618 through 632
    Processing helix  chain 'B' and resid 648 through 661
    Processing helix  chain 'B' and resid 674 through 679
      removed outlier: 4.204A  pdb=" N   MET B 678 " --> pdb=" O   THR B 675 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLN B 679 " --> pdb=" O   THR B 676 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 697 through 703
    Processing helix  chain 'B' and resid 706 through 712
    Processing sheet with id=  A, first strand: chain 'A' and resid 479 through 482
    Processing sheet with id=  B, first strand: chain 'A' and resid 691 through 694
      removed outlier: 7.135A  pdb=" N   VAL A 685 " --> pdb=" O   VAL A 692 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   GLN A 694 " --> pdb=" O   ILE A 683 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ILE A 683 " --> pdb=" O   GLN A 694 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   SER A 667 " --> pdb=" O   VAL A 508 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   ILE A 510 " --> pdb=" O   SER A 667 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   PHE A 669 " --> pdb=" O   ILE A 510 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE A 670 " --> pdb=" O   CYS A 639 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 484 through 486
      removed outlier: 3.607A  pdb=" N   VAL A 484 " --> pdb=" O   ILE A 498 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ILE A 498 " --> pdb=" O   VAL A 484 " (cutoff:3.500A)
      removed outlier: 7.548A  pdb=" N   PHE A 486 " --> pdb=" O   ASP A 496 " (cutoff:3.500A)
      removed outlier: 5.205A  pdb=" N   ASP A 496 " --> pdb=" O   PHE A 486 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  C
    Processing sheet with id=  D, first strand: chain 'B' and resid 479 through 482
      removed outlier: 3.808A  pdb=" N   ASN B 535 " --> pdb=" O   GLU B 482 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 690 through 695
      removed outlier: 7.117A  pdb=" N   VAL B 685 " --> pdb=" O   VAL B 692 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   GLN B 694 " --> pdb=" O   ILE B 683 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ILE B 683 " --> pdb=" O   GLN B 694 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   SER B 667 " --> pdb=" O   VAL B 508 " (cutoff:3.500A)
      removed outlier: 8.200A  pdb=" N   ILE B 510 " --> pdb=" O   SER B 667 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   PHE B 669 " --> pdb=" O   ILE B 510 " (cutoff:3.500A)
      removed outlier: 8.720A  pdb=" N   GLY B 512 " --> pdb=" O   PHE B 669 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   CYS B 639 " --> pdb=" O   ILE B 668 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 484 through 486
      removed outlier: 3.578A  pdb=" N   VAL B 484 " --> pdb=" O   ILE B 498 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ILE B 498 " --> pdb=" O   VAL B 484 " (cutoff:3.500A)
      removed outlier: 8.023A  pdb=" N   PHE B 486 " --> pdb=" O   ASP B 496 " (cutoff:3.500A)
      removed outlier: 5.757A  pdb=" N   ASP B 496 " --> pdb=" O   PHE B 486 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  F

    567 hydrogen bonds defined for protein.
    1686 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: 2.55

  Time building geometry restraints manager: 3.70 seconds

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

  Histogram of bond lengths:
        1.18 -     1.37: 3059
        1.37 -     1.55: 6273
        1.55 -     1.73: 0
        1.73 -     1.92: 64
        1.92 -     2.10: 1
  Bond restraints: 9397
  Sorted by residual:
  bond pdb=" C   ALA B 221 "
       pdb=" O   ALA B 221 "
    ideal  model  delta    sigma   weight residual
    1.236  1.251 -0.014 1.15e-02 7.56e+03 1.57e+00
  bond pdb=" N   ASN A 356 "
       pdb=" CA  ASN A 356 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.015 1.29e-02 6.01e+03 1.29e+00
  bond pdb=" C   ALA A 221 "
       pdb=" O   ALA A 221 "
    ideal  model  delta    sigma   weight residual
    1.236  1.249 -0.012 1.15e-02 7.56e+03 1.18e+00
  bond pdb=" N   HIS B 243 "
       pdb=" CA  HIS B 243 "
    ideal  model  delta    sigma   weight residual
    1.458  1.470 -0.013 1.33e-02 5.65e+03 9.24e-01
  bond pdb=" C   GLU B 217 "
       pdb=" O   GLU B 217 "
    ideal  model  delta    sigma   weight residual
    1.236  1.247 -0.011 1.16e-02 7.43e+03 9.09e-01
  ... (remaining 9392 not shown)

  Histogram of bond angle deviations from ideal:
       99.47 -   106.37: 156
      106.37 -   113.27: 5237
      113.27 -   120.17: 3363
      120.17 -   127.07: 3885
      127.07 -   133.97: 67
  Bond angle restraints: 12708
  Sorted by residual:
  angle pdb=" C   LEU B 242 "
        pdb=" N   HIS B 243 "
        pdb=" CA  HIS B 243 "
      ideal   model   delta    sigma   weight residual
     120.72  116.57    4.15 1.67e+00 3.59e-01 6.18e+00
  angle pdb=" CB  MET A 121 "
        pdb=" CG  MET A 121 "
        pdb=" SD  MET A 121 "
      ideal   model   delta    sigma   weight residual
     112.70  119.79   -7.09 3.00e+00 1.11e-01 5.58e+00
  angle pdb=" CA  TRP A 323 "
        pdb=" CB  TRP A 323 "
        pdb=" CG  TRP A 323 "
      ideal   model   delta    sigma   weight residual
     113.60  118.03   -4.43 1.90e+00 2.77e-01 5.43e+00
  angle pdb=" CA  ALA A 295 "
        pdb=" C   ALA A 295 "
        pdb=" N   TYR A 296 "
      ideal   model   delta    sigma   weight residual
     118.87  116.13    2.74 1.18e+00 7.18e-01 5.40e+00
  angle pdb=" C   PHE B 355 "
        pdb=" N   ASN B 356 "
        pdb=" CA  ASN B 356 "
      ideal   model   delta    sigma   weight residual
     121.54  125.86   -4.32 1.91e+00 2.74e-01 5.11e+00
  ... (remaining 12703 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.16: 5017
       17.16 -    34.32: 493
       34.32 -    51.49: 98
       51.49 -    68.65: 9
       68.65 -    85.81: 8
  Dihedral angle restraints: 5625
    sinusoidal: 2209
      harmonic: 3416
  Sorted by residual:
  dihedral pdb=" CA  ILE A 543 "
           pdb=" C   ILE A 543 "
           pdb=" N   LYS A 544 "
           pdb=" CA  LYS A 544 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.14  -15.86     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CB6 GDS A 801 "
           pdb=" CD6 GDS A 801 "
           pdb=" CG6 GDS A 801 "
           pdb=" N5  GDS A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     135.82 -138.37  -85.81     1      3.00e+01 1.11e-03 9.89e+00
  dihedral pdb=" CG  ARG A 537 "
           pdb=" CD  ARG A 537 "
           pdb=" NE  ARG A 537 "
           pdb=" CZ  ARG A 537 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -131.54   41.54     2      1.50e+01 4.44e-03 9.38e+00
  ... (remaining 5622 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 992
       0.032 -    0.064: 335
       0.064 -    0.095: 101
       0.095 -    0.127: 51
       0.127 -    0.159: 7
  Chirality restraints: 1486
  Sorted by residual:
  chirality pdb=" CB  ILE B 538 "
            pdb=" CA  ILE B 538 "
            pdb=" CG1 ILE B 538 "
            pdb=" CG2 ILE B 538 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.30e-01
  chirality pdb=" CG  LEU B 245 "
            pdb=" CB  LEU B 245 "
            pdb=" CD1 LEU B 245 "
            pdb=" CD2 LEU B 245 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.16 2.00e-01 2.50e+01 6.01e-01
  chirality pdb=" CA  ILE B 636 "
            pdb=" N   ILE B 636 "
            pdb=" C   ILE B 636 "
            pdb=" CB  ILE B 636 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.98e-01
  ... (remaining 1483 not shown)

  Planarity restraints: 1614
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 711 "    0.021 2.00e-02 2.50e+03   1.76e-02 7.75e+00
        pdb=" CG  TRP B 711 "   -0.047 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 711 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 711 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 711 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 711 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 711 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 711 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 711 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 711 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 323 "    0.019 2.00e-02 2.50e+03   1.55e-02 6.03e+00
        pdb=" CG  TRP A 323 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 323 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 323 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 323 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 323 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 323 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 323 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 323 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 323 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 711 "   -0.010 2.00e-02 2.50e+03   9.38e-03 2.20e+00
        pdb=" CG  TRP A 711 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 711 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 711 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 711 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 711 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 711 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 711 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 711 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 711 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1611 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1400
        2.76 -     3.29: 9494
        3.29 -     3.83: 15202
        3.83 -     4.36: 15757
        4.36 -     4.90: 27879
  Nonbonded interactions: 69732
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 358 "
            pdb=" OG  SER B 240 "
     model   vdw
     2.221 2.440
  nonbonded pdb=" ND1 HIS A 243 "
            pdb=" OE2 GLU B 358 "
     model   vdw
     2.261 2.520
  nonbonded pdb=" O   GLN B 709 "
            pdb=" OG1 THR B 712 "
     model   vdw
     2.287 2.440
  nonbonded pdb=" OD2 ASP A 366 "
            pdb=" NH1 ARG B 236 "
     model   vdw
     2.319 2.520
  nonbonded pdb=" O   LEU B 661 "
            pdb=" NH2 ARG B 665 "
     model   vdw
     2.333 2.520
  ... (remaining 69727 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 'A' and resid 117 through 716)
  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=0.50 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:             1.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          5.900
  Check model and map are aligned:         0.140
  Set scattering table:                    0.100
  Process input model:                     26.850
  Find NCS groups from input model:        0.550
  Set up NCS constraints:                  0.050
  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:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9397  Z= 0.187
  Angle     :  0.559   7.089  12708  Z= 0.297
  Chirality :  0.039   0.159   1486
  Planarity :  0.003   0.028   1614
  Dihedral  : 13.838  85.810   3417
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.20 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.69 (0.25), residues: 1172
  helix:  2.28 (0.18), residues: 780
  sheet:  0.15 (0.66), residues: 72
  loop : -1.70 (0.29), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.003   TRP B 711 
 HIS   0.005   0.001   HIS B 241 
 PHE   0.018   0.001   PHE A 394 
 TYR   0.020   0.001   TYR B 707 
 ARG   0.004   0.000   ARG B 341 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 996 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 1.107 
Fit side-chains
REVERT: A  121 MET cc_start: 0.7833 (tmm) cc_final: 0.7621 (tpt)
REVERT: A  286 GLU cc_start: 0.8134 (tp30) cc_final: 0.7613 (tt0)
REVERT: A  396 THR cc_start: 0.8851 (t) cc_final: 0.8596 (m)
REVERT: B  506 LYS cc_start: 0.7965 (mmtt) cc_final: 0.7619 (mmtm)
REVERT: B  541 GLN cc_start: 0.7751 (tp40) cc_final: 0.7379 (tp40)
REVERT: B  688 ASN cc_start: 0.8255 (m-40) cc_final: 0.7903 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1883
  time to fit residues: 35.2171
Evaluate side-chains
  97 residues out of total 996 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    5.9990
   chunk 89 optimal weight:    0.0370
   chunk 49 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 60 optimal weight:    0.4980
   chunk 47 optimal weight:    7.9990
   chunk 92 optimal weight:    0.5980
   chunk 35 optimal weight:    0.1980
   chunk 56 optimal weight:    0.3980
   chunk 68 optimal weight:    0.6980
   chunk 107 optimal weight:    8.9990
   overall best weight:    0.3458

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

Flipped N/Q/H residues before XYZ refinement:
A 485 HIS
** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 390 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.0785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9397  Z= 0.146
  Angle     :  0.497   7.918  12708  Z= 0.258
  Chirality :  0.038   0.154   1486
  Planarity :  0.003   0.026   1614
  Dihedral  :  5.015  78.525   1295
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  7.93 %
    Favored  : 91.06 %
  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:  2.05 (0.25), residues: 1172
  helix:  2.58 (0.19), residues: 780
  sheet:  0.19 (0.64), residues: 72
  loop : -1.60 (0.29), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 323 
 HIS   0.003   0.001   HIS A 485 
 PHE   0.017   0.001   PHE B 394 
 TYR   0.018   0.001   TYR B 205 
 ARG   0.014   0.000   ARG B 253 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 996 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 1.128 
Fit side-chains
REVERT: A  286 GLU cc_start: 0.8052 (tp30) cc_final: 0.7664 (tt0)
REVERT: A  697 HIS cc_start: 0.7688 (p-80) cc_final: 0.7395 (p-80)
REVERT: B  396 THR cc_start: 0.9008 (t) cc_final: 0.8705 (m)
REVERT: B  506 LYS cc_start: 0.7818 (mmtt) cc_final: 0.7427 (mmtm)
REVERT: B  541 GLN cc_start: 0.7895 (tp40) cc_final: 0.7661 (tp40)
REVERT: B  688 ASN cc_start: 0.8231 (m-40) cc_final: 0.8029 (p0)
  outliers start: 10
  outliers final: 5
  residues processed: 111
  average time/residue: 0.1863
  time to fit residues: 30.3659
Evaluate side-chains
  107 residues out of total 996 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  637 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 89 optimal weight:    0.0470
   chunk 72 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 107 optimal weight:    5.9990
   chunk 115 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0170
   chunk 36 optimal weight:   10.0000
   chunk 86 optimal weight:    0.5980
   overall best weight:    0.7320

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.0990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9397  Z= 0.161
  Angle     :  0.473   7.162  12708  Z= 0.250
  Chirality :  0.038   0.156   1486
  Planarity :  0.003   0.025   1614
  Dihedral  :  4.882  74.337   1295
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 11.45 %
    Favored  : 87.05 %
  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:  2.12 (0.25), residues: 1172
  helix:  2.64 (0.19), residues: 780
  sheet:  0.35 (0.65), residues: 72
  loop : -1.62 (0.29), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 323 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.017   0.001   PHE A 394 
 TYR   0.017   0.001   TYR B 205 
 ARG   0.003   0.000   ARG A 341 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 996 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 1.025 
Fit side-chains
REVERT: A  286 GLU cc_start: 0.8097 (tp30) cc_final: 0.7695 (tt0)
REVERT: A  697 HIS cc_start: 0.7669 (p-80) cc_final: 0.7405 (p-80)
REVERT: B  217 GLU cc_start: 0.6194 (OUTLIER) cc_final: 0.5806 (tt0)
REVERT: B  506 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7427 (mmtm)
REVERT: B  688 ASN cc_start: 0.8228 (m-40) cc_final: 0.7975 (p0)
  outliers start: 15
  outliers final: 11
  residues processed: 109
  average time/residue: 0.1758
  time to fit residues: 28.6826
Evaluate side-chains
  109 residues out of total 996 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain B residue  217 GLU
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  637 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 106 optimal weight:    0.8980
   chunk 80 optimal weight:    0.5980
   chunk 55 optimal weight:    0.2980
   chunk 11 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 107 optimal weight:    0.7980
   chunk 114 optimal weight:    9.9990
   chunk 56 optimal weight:    2.9990
   chunk 102 optimal weight:    8.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.1137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9397  Z= 0.178
  Angle     :  0.476   8.279  12708  Z= 0.251
  Chirality :  0.038   0.148   1486
  Planarity :  0.003   0.024   1614
  Dihedral  :  4.847  72.574   1295
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 13.05 %
    Favored  : 84.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.15 (0.25), residues: 1172
  helix:  2.65 (0.19), residues: 780
  sheet:  0.34 (0.65), residues: 72
  loop : -1.59 (0.29), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 323 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.016   0.001   PHE A 394 
 TYR   0.017   0.001   TYR B 205 
 ARG   0.003   0.000   ARG A 341 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 996 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 1.037 
Fit side-chains
REVERT: A  286 GLU cc_start: 0.8181 (tp30) cc_final: 0.7711 (tt0)
REVERT: A  541 GLN cc_start: 0.8167 (tp40) cc_final: 0.7859 (tp40)
REVERT: A  601 PHE cc_start: 0.6998 (m-80) cc_final: 0.6643 (m-80)
REVERT: A  697 HIS cc_start: 0.7683 (p-80) cc_final: 0.7414 (p-80)
REVERT: B  498 ILE cc_start: 0.8256 (mm) cc_final: 0.7911 (mm)
REVERT: B  506 LYS cc_start: 0.7923 (mmtt) cc_final: 0.7695 (mmtm)
  outliers start: 23
  outliers final: 16
  residues processed: 113
  average time/residue: 0.1874
  time to fit residues: 31.2909
Evaluate side-chains
  114 residues out of total 996 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  506 LYS
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  637 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   chunk 97 optimal weight:    9.9990
   chunk 78 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   chunk 58 optimal weight:    3.9990
   chunk 102 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    1.0784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.1292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9397  Z= 0.203
  Angle     :  0.505  12.245  12708  Z= 0.263
  Chirality :  0.038   0.182   1486
  Planarity :  0.003   0.025   1614
  Dihedral  :  4.887  72.466   1295
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 14.26 %
    Favored  : 83.33 %
  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:  2.11 (0.25), residues: 1172
  helix:  2.63 (0.19), residues: 780
  sheet:  0.30 (0.64), residues: 72
  loop : -1.61 (0.29), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 323 
 HIS   0.005   0.001   HIS B 697 
 PHE   0.016   0.001   PHE A 394 
 TYR   0.017   0.001   TYR B 205 
 ARG   0.003   0.000   ARG A 341 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 996 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A  601 PHE cc_start: 0.7124 (m-80) cc_final: 0.6752 (m-80)
REVERT: A  697 HIS cc_start: 0.7708 (p-80) cc_final: 0.7417 (p-80)
REVERT: B  498 ILE cc_start: 0.8212 (mm) cc_final: 0.7895 (mm)
REVERT: B  506 LYS cc_start: 0.7942 (mmtt) cc_final: 0.7702 (mmtm)
  outliers start: 24
  outliers final: 19
  residues processed: 111
  average time/residue: 0.1929
  time to fit residues: 31.2496
Evaluate side-chains
  113 residues out of total 996 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  506 LYS
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  711 TRP
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  637 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 38 optimal weight:    8.9990
   chunk 102 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 114 optimal weight:    2.9990
   chunk 94 optimal weight:    0.6980
   chunk 52 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 59 optimal weight:   10.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 243 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9397  Z= 0.173
  Angle     :  0.476  10.142  12708  Z= 0.251
  Chirality :  0.038   0.180   1486
  Planarity :  0.003   0.026   1614
  Dihedral  :  4.833  70.637   1295
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 16.47 %
    Favored  : 81.63 %
  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:  2.19 (0.25), residues: 1172
  helix:  2.70 (0.19), residues: 780
  sheet:  0.14 (0.63), residues: 72
  loop : -1.55 (0.29), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 711 
 HIS   0.005   0.001   HIS B 697 
 PHE   0.017   0.001   PHE A 394 
 TYR   0.017   0.001   TYR B 205 
 ARG   0.003   0.000   ARG A 341 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 996 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 1.112 
Fit side-chains
REVERT: A  286 GLU cc_start: 0.8204 (tp30) cc_final: 0.7733 (tt0)
REVERT: A  541 GLN cc_start: 0.8118 (tp40) cc_final: 0.7817 (tp40)
REVERT: A  601 PHE cc_start: 0.7131 (m-80) cc_final: 0.6771 (m-80)
REVERT: B  498 ILE cc_start: 0.8250 (mm) cc_final: 0.7986 (mm)
REVERT: B  506 LYS cc_start: 0.8006 (mmtt) cc_final: 0.7757 (mmtm)
REVERT: B  697 HIS cc_start: 0.7525 (p90) cc_final: 0.7258 (p-80)
  outliers start: 19
  outliers final: 18
  residues processed: 115
  average time/residue: 0.1876
  time to fit residues: 31.4108
Evaluate side-chains
  118 residues out of total 996 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  506 LYS
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  711 TRP
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  685 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 110 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   chunk 65 optimal weight:    0.5980
   chunk 83 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 96 optimal weight:    5.9990
   chunk 63 optimal weight:    0.4980
   chunk 113 optimal weight:    4.9990
   chunk 71 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B 390 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.1473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9397  Z= 0.202
  Angle     :  0.493   9.324  12708  Z= 0.260
  Chirality :  0.038   0.164   1486
  Planarity :  0.003   0.026   1614
  Dihedral  :  4.866  70.754   1295
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 17.27 %
    Favored  : 80.62 %
  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:  2.13 (0.25), residues: 1172
  helix:  2.64 (0.19), residues: 780
  sheet:  0.14 (0.63), residues: 72
  loop : -1.56 (0.29), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 711 
 HIS   0.011   0.001   HIS B 243 
 PHE   0.016   0.001   PHE A 394 
 TYR   0.017   0.001   TYR B 205 
 ARG   0.003   0.000   ARG A 341 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 996 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 1.318 
Fit side-chains
REVERT: A  541 GLN cc_start: 0.8157 (tp40) cc_final: 0.7867 (tp40)
REVERT: A  601 PHE cc_start: 0.7135 (m-80) cc_final: 0.6796 (m-80)
REVERT: A  697 HIS cc_start: 0.7703 (p-80) cc_final: 0.7425 (p-80)
REVERT: B  498 ILE cc_start: 0.8275 (mm) cc_final: 0.7927 (mm)
REVERT: B  506 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7749 (mmtm)
REVERT: B  541 GLN cc_start: 0.7931 (tp40) cc_final: 0.7595 (tp40)
REVERT: B  697 HIS cc_start: 0.7504 (p90) cc_final: 0.7277 (p-80)
  outliers start: 21
  outliers final: 21
  residues processed: 107
  average time/residue: 0.1833
  time to fit residues: 28.9145
Evaluate side-chains
  116 residues out of total 996 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  506 LYS
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  711 TRP
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  521 ILE
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  637 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 34 optimal weight:    9.9990
   chunk 22 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   chunk 56 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 103 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 356 ASN
B 243 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.1558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9397  Z= 0.177
  Angle     :  0.478   8.920  12708  Z= 0.252
  Chirality :  0.038   0.161   1486
  Planarity :  0.003   0.025   1614
  Dihedral  :  4.831  69.471   1295
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 17.97 %
    Favored  : 79.82 %
  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:  2.21 (0.25), residues: 1172
  helix:  2.70 (0.19), residues: 780
  sheet:  0.15 (0.64), residues: 72
  loop : -1.50 (0.30), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 711 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.017   0.001   PHE A 394 
 TYR   0.017   0.001   TYR B 205 
 ARG   0.003   0.000   ARG A 341 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 996 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.802 
Fit side-chains
REVERT: A  541 GLN cc_start: 0.8149 (tp40) cc_final: 0.7877 (tp40)
REVERT: A  601 PHE cc_start: 0.7159 (m-80) cc_final: 0.6830 (m-80)
REVERT: A  697 HIS cc_start: 0.7726 (p-80) cc_final: 0.7442 (p-80)
REVERT: B  506 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7745 (mmtm)
REVERT: B  541 GLN cc_start: 0.8035 (tp40) cc_final: 0.7742 (tp40)
REVERT: B  697 HIS cc_start: 0.7486 (p90) cc_final: 0.7187 (p-80)
  outliers start: 22
  outliers final: 16
  residues processed: 109
  average time/residue: 0.1862
  time to fit residues: 29.6427
Evaluate side-chains
  108 residues out of total 996 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  506 LYS
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  685 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 99 optimal weight:    0.8980
   chunk 105 optimal weight:    3.9990
   chunk 63 optimal weight:    0.6980
   chunk 46 optimal weight:    4.9990
   chunk 83 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 95 optimal weight:   10.0000
   chunk 100 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 112 optimal weight:    7.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 243 HIS
A 356 ASN
B 243 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9397  Z= 0.199
  Angle     :  0.499   9.076  12708  Z= 0.262
  Chirality :  0.038   0.157   1486
  Planarity :  0.003   0.026   1614
  Dihedral  :  4.866  69.618   1295
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 17.77 %
    Favored  : 79.82 %
  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:  2.18 (0.25), residues: 1172
  helix:  2.69 (0.19), residues: 778
  sheet:  0.16 (0.64), residues: 72
  loop : -1.54 (0.29), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 711 
 HIS   0.009   0.001   HIS B 243 
 PHE   0.016   0.001   PHE A 394 
 TYR   0.017   0.001   TYR B 205 
 ARG   0.003   0.000   ARG A 341 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 996 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 1.096 
Fit side-chains
REVERT: A  541 GLN cc_start: 0.8175 (tp40) cc_final: 0.7917 (tp40)
REVERT: A  601 PHE cc_start: 0.7198 (m-80) cc_final: 0.6875 (m-80)
REVERT: A  697 HIS cc_start: 0.7733 (p-80) cc_final: 0.7504 (p-80)
REVERT: B  506 LYS cc_start: 0.8011 (mmtt) cc_final: 0.7756 (mmtm)
REVERT: B  541 GLN cc_start: 0.8044 (tp40) cc_final: 0.7683 (tp40)
REVERT: B  697 HIS cc_start: 0.7466 (p90) cc_final: 0.7197 (p-80)
  outliers start: 24
  outliers final: 21
  residues processed: 109
  average time/residue: 0.1869
  time to fit residues: 29.8609
Evaluate side-chains
  115 residues out of total 996 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  506 LYS
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  711 TRP
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  521 ILE
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  637 LEU
Chi-restraints excluded: chain B residue  685 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 68 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 77 optimal weight:    0.5980
   chunk 117 optimal weight:    0.6980
   chunk 108 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0040
   chunk 74 optimal weight:    0.5980
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
B 243 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.1696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9397  Z= 0.151
  Angle     :  0.477   9.307  12708  Z= 0.249
  Chirality :  0.037   0.162   1486
  Planarity :  0.003   0.026   1614
  Dihedral  :  4.773  66.770   1295
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 18.67 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.31 (0.25), residues: 1172
  helix:  2.80 (0.19), residues: 778
  sheet: -0.01 (0.60), residues: 78
  loop : -1.49 (0.30), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 711 
 HIS   0.010   0.001   HIS B 243 
 PHE   0.017   0.001   PHE A 394 
 TYR   0.017   0.001   TYR B 205 
 ARG   0.003   0.000   ARG A 341 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 996 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A  286 GLU cc_start: 0.8169 (tp30) cc_final: 0.7634 (tt0)
REVERT: A  541 GLN cc_start: 0.8203 (tp40) cc_final: 0.7970 (tp40)
REVERT: A  601 PHE cc_start: 0.7345 (m-80) cc_final: 0.6950 (m-80)
REVERT: A  697 HIS cc_start: 0.7745 (p-80) cc_final: 0.7523 (p-80)
REVERT: B  506 LYS cc_start: 0.8008 (mmtt) cc_final: 0.7766 (mmtm)
REVERT: B  541 GLN cc_start: 0.8020 (tp40) cc_final: 0.7742 (tp40)
REVERT: B  697 HIS cc_start: 0.7429 (p90) cc_final: 0.7170 (p-80)
  outliers start: 16
  outliers final: 15
  residues processed: 109
  average time/residue: 0.1957
  time to fit residues: 31.0774
Evaluate side-chains
  113 residues out of total 996 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  506 LYS
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  711 TRP
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  243 HIS
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  637 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 28 optimal weight:    0.0870
   chunk 86 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 96 optimal weight:    0.0770
   chunk 11 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.5716

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

Flipped N/Q/H residues before XYZ refinement:
B 485 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.188175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.142939 restraints weight = 12154.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.146701 restraints weight = 6406.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.149257 restraints weight = 4253.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3904
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3904 r_free = 0.3904    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3900 r_free = 0.3900    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3900
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9397  Z= 0.155
  Angle     :  0.481   9.236  12708  Z= 0.251
  Chirality :  0.037   0.161   1486
  Planarity :  0.003   0.026   1614
  Dihedral  :  4.736  64.867   1295
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 19.28 %
    Favored  : 79.22 %
  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:  2.31 (0.25), residues: 1172
  helix:  2.82 (0.19), residues: 778
  sheet:  0.00 (0.60), residues: 78
  loop : -1.55 (0.30), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 711 
 HIS   0.006   0.001   HIS B 243 
 PHE   0.017   0.001   PHE A 394 
 TYR   0.017   0.001   TYR B 205 
 ARG   0.003   0.000   ARG A 341 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1770.66 seconds
wall clock time: 32 minutes 45.05 seconds (1965.05 seconds total)