Starting phenix.real_space_refine
on Thu Mar 14 23:37:20 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmw_13542/03_2024/7pmw_13542.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmw_13542/03_2024/7pmw_13542.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmw_13542/03_2024/7pmw_13542.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmw_13542/03_2024/7pmw_13542.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmw_13542/03_2024/7pmw_13542.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmw_13542/03_2024/7pmw_13542.pdb"
  }
  resolution = 4.1
  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=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    3298      2.51       5
     N     806      2.21       5
     O     894      1.98       5
     H    5123      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE  427": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  507": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  513": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  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: 10153
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 641, 10120
          Classifications: {'peptide': 641}
          Link IDs: {'PTRANS': 29, 'TRANS': 611}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Classifications: {'peptide': 2}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 1}
  Time building chain proxies: 4.83, per 1000 atoms: 0.48
  Number of scatterers: 10153
  At special positions: 0
  Unit cell: (82.41, 91.12, 120.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     O     894      8.00
     N     806      7.00
     C    3298      6.00
     H    5123      1.00
    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: 7.75
  Conformation dependent library (CDL) restraints added in 962.7 milliseconds
  

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1202

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 5 sheets defined
      60.8% alpha, 11.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 42
      removed outlier: 4.233A  pdb=" N   ILE A  16 " --> pdb=" O   TYR A  12 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   PHE A  18 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ILE A  19 " --> pdb=" O   SER A  15 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLY A  32 " --> pdb=" O   PHE A  28 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   MET A  33 " --> pdb=" O   SER A  29 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ARG A  34 " --> pdb=" O   TYR A  30 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ALA A  35 " --> pdb=" O   TYR A  31 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ILE A  36 " --> pdb=" O   GLY A  32 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ILE A  38 " --> pdb=" O   ARG A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 64
      removed outlier: 3.622A  pdb=" N   TYR A  64 " --> pdb=" O   VAL A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 77
      removed outlier: 3.905A  pdb=" N   LEU A  72 " --> pdb=" O   ILE A  68 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ILE A  73 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 108
      removed outlier: 3.630A  pdb=" N   LEU A 106 " --> pdb=" O   SER A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 149
      removed outlier: 3.784A  pdb=" N   SER A 125 " --> pdb=" O   HIS A 121 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLY A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LEU A 129 " --> pdb=" O   SER A 125 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ALA A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   GLY A 135 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   LYS A 140 " --> pdb=" O   THR A 136 " (cutoff:3.500A)
      Proline residue:  A 141  - end of helix
      removed outlier: 3.681A  pdb=" N   SER A 144 " --> pdb=" O   LYS A 140 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLY A 148 " --> pdb=" O   SER A 144 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASP A 149 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 181
      removed outlier: 3.718A  pdb=" N   ASN A 171 " --> pdb=" O   TYR A 167 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA A 172 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   SER A 174 " --> pdb=" O   ILE A 170 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ILE A 179 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 219
      Proline residue:  A 205  - end of helix
      removed outlier: 3.712A  pdb=" N   MET A 209 " --> pdb=" O   PRO A 205 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLY A 219 " --> pdb=" O   VAL A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 222
      No H-bonds generated for 'chain 'A' and resid 220 through 222'
    Processing helix  chain 'A' and resid 231 through 249
    Processing helix  chain 'A' and resid 261 through 266
      removed outlier: 3.661A  pdb=" N   ALA A 265 " --> pdb=" O   TRP A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 287
      removed outlier: 3.775A  pdb=" N   LEU A 286 " --> pdb=" O   ARG A 282 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   TYR A 287 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 298
      removed outlier: 4.126A  pdb=" N   TRP A 294 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ALA A 295 " --> pdb=" O   PRO A 291 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU A 296 " --> pdb=" O   MET A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 311
      removed outlier: 4.206A  pdb=" N   SER A 302 " --> pdb=" O   ASP A 298 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   TRP A 304 " --> pdb=" O   GLN A 300 " (cutoff:3.500A)
      removed outlier: 4.764A  pdb=" N   THR A 305 " --> pdb=" O   GLY A 301 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   THR A 310 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 325
    Processing helix  chain 'A' and resid 326 through 343
      removed outlier: 4.034A  pdb=" N   ALA A 330 " --> pdb=" O   GLN A 326 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ILE A 335 " --> pdb=" O   ILE A 331 " (cutoff:3.500A)
      Proline residue:  A 338  - end of helix
      removed outlier: 3.557A  pdb=" N   ASP A 341 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 351
    Processing helix  chain 'A' and resid 356 through 383
      removed outlier: 3.745A  pdb=" N   VAL A 366 " --> pdb=" O   ALA A 362 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU A 367 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA A 368 " --> pdb=" O   GLY A 364 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   PHE A 372 " --> pdb=" O   ALA A 368 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   VAL A 373 " --> pdb=" O   SER A 369 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   VAL A 374 " --> pdb=" O   MET A 370 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ALA A 375 " --> pdb=" O   ALA A 371 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ASP A 383 " --> pdb=" O   GLN A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 485
      removed outlier: 3.664A  pdb=" N   GLU A 485 " --> pdb=" O   GLU A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 582
      No H-bonds generated for 'chain 'A' and resid 580 through 582'
    Processing helix  chain 'A' and resid 583 through 610
      removed outlier: 4.698A  pdb=" N   GLN A 587 " --> pdb=" O   LEU A 583 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU A 590 " --> pdb=" O   PRO A 586 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   LEU A 591 " --> pdb=" O   GLN A 587 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   VAL A 597 " --> pdb=" O   CYS A 593 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL A 600 " --> pdb=" O   VAL A 596 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   THR A 601 " --> pdb=" O   VAL A 597 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLN A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ALA A 610 " --> pdb=" O   SER A 606 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 637
      removed outlier: 3.768A  pdb=" N   LEU A 618 " --> pdb=" O   MET A 614 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   GLN A 619 " --> pdb=" O   LYS A 615 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   VAL A 626 " --> pdb=" O   TRP A 622 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ALA A 627 " --> pdb=" O   LEU A 623 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   VAL A 628 " --> pdb=" O   LEU A 624 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ILE A 631 " --> pdb=" O   ALA A 627 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE A 632 " --> pdb=" O   VAL A 628 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL A 633 " --> pdb=" O   GLY A 629 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   ALA A 637 " --> pdb=" O   VAL A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 651
      removed outlier: 4.067A  pdb=" N   ALA A 647 " --> pdb=" O   SER A 643 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 668
    Processing helix  chain 'A' and resid 669 through 674
      removed outlier: 5.626A  pdb=" N   TYR A 672 " --> pdb=" O   PHE A 669 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASN A 674 " --> pdb=" O   THR A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 675 through 680
      removed outlier: 4.199A  pdb=" N   ALA A 680 " --> pdb=" O   ALA A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 683
      No H-bonds generated for 'chain 'A' and resid 681 through 683'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 422 through 423
    Processing sheet with id=AA2, first strand: chain 'A' and resid 422 through 423
      removed outlier: 6.845A  pdb=" N   HIS A 469 " --> pdb=" O   TRP A 465 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 414 through 418
    Processing sheet with id=AA4, first strand: chain 'A' and resid 519 through 521
      removed outlier: 6.614A  pdb=" N   GLY A 487 " --> pdb=" O   TYR A 554 " (cutoff:3.500A)
      removed outlier: 7.978A  pdb=" N   TYR A 556 " --> pdb=" O   GLY A 487 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ARG A 489 " --> pdb=" O   TYR A 556 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   VAL A 558 " --> pdb=" O   ARG A 489 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ALA A 553 " --> pdb=" O   ASP A 573 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 505 through 510
      removed outlier: 6.303A  pdb=" N   ILE A 498 " --> pdb=" O   ASN A 509 " (cutoff:3.500A)

    265 hydrogen bonds defined for protein.
    747 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: 4.03

  Time building geometry restraints manager: 8.13 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 5113
        1.03 -     1.23: 12
        1.23 -     1.42: 2135
        1.42 -     1.61: 2957
        1.61 -     1.81: 54
  Bond restraints: 10271
  Sorted by residual:
  bond pdb=" N   ASN A 329 "
       pdb=" CA  ASN A 329 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.23e-02 6.61e+03 7.80e+00
  bond pdb=" N   ASN A 329 "
       pdb=" H   ASN A 329 "
    ideal  model  delta    sigma   weight residual
    0.860  0.914 -0.054 2.00e-02 2.50e+03 7.25e+00
  bond pdb=" C   ASN A 329 "
       pdb=" O   ASN A 329 "
    ideal  model  delta    sigma   weight residual
    1.237  1.212  0.025 1.19e-02 7.06e+03 4.39e+00
  bond pdb=" C   ASN A 329 "
       pdb=" N   ALA A 330 "
    ideal  model  delta    sigma   weight residual
    1.335  1.310  0.025 1.36e-02 5.41e+03 3.25e+00
  bond pdb=" ND2 ASN A 329 "
       pdb="HD22 ASN A 329 "
    ideal  model  delta    sigma   weight residual
    0.860  0.885 -0.025 2.00e-02 2.50e+03 1.53e+00
  ... (remaining 10266 not shown)

  Histogram of bond angle deviations from ideal:
       73.89 -    85.92: 6
       85.92 -    97.94: 0
       97.94 -   109.97: 8830
      109.97 -   122.00: 8196
      122.00 -   134.03: 1560
  Bond angle restraints: 18592
  Sorted by residual:
  angle pdb=" C   LEU A  51 "
        pdb=" CA  LEU A  51 "
        pdb=" HA  LEU A  51 "
      ideal   model   delta    sigma   weight residual
     109.00   73.89   35.11 3.00e+00 1.11e-01 1.37e+02
  angle pdb=" C   GLN A 609 "
        pdb=" CA  GLN A 609 "
        pdb=" HA  GLN A 609 "
      ideal   model   delta    sigma   weight residual
     109.00   74.26   34.74 3.00e+00 1.11e-01 1.34e+02
  angle pdb=" N   GLN A 609 "
        pdb=" CA  GLN A 609 "
        pdb=" HA  GLN A 609 "
      ideal   model   delta    sigma   weight residual
     110.00   75.29   34.71 3.00e+00 1.11e-01 1.34e+02
  angle pdb=" N   LEU A  51 "
        pdb=" CA  LEU A  51 "
        pdb=" HA  LEU A  51 "
      ideal   model   delta    sigma   weight residual
     110.00   75.86   34.14 3.00e+00 1.11e-01 1.30e+02
  angle pdb=" CB  LEU A  51 "
        pdb=" CA  LEU A  51 "
        pdb=" HA  LEU A  51 "
      ideal   model   delta    sigma   weight residual
     109.00   75.27   33.73 3.00e+00 1.11e-01 1.26e+02
  ... (remaining 18587 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4572
       17.96 -    35.92: 191
       35.92 -    53.88: 65
       53.88 -    71.84: 26
       71.84 -    89.80: 5
  Dihedral angle restraints: 4859
    sinusoidal: 2592
      harmonic: 2267
  Sorted by residual:
  dihedral pdb=" C   LEU A  51 "
           pdb=" N   LEU A  51 "
           pdb=" CA  LEU A  51 "
           pdb=" CB  LEU A  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.99    9.39     0      2.50e+00 1.60e-01 1.41e+01
  dihedral pdb=" C   GLN A 609 "
           pdb=" N   GLN A 609 "
           pdb=" CA  GLN A 609 "
           pdb=" CB  GLN A 609 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.75    9.15     0      2.50e+00 1.60e-01 1.34e+01
  dihedral pdb=" C   ASN A 329 "
           pdb=" N   ASN A 329 "
           pdb=" CA  ASN A 329 "
           pdb=" CB  ASN A 329 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.57   -9.03     0      2.50e+00 1.60e-01 1.30e+01
  ... (remaining 4856 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 758
       0.078 -    0.156: 49
       0.156 -    0.234: 0
       0.234 -    0.311: 0
       0.311 -    0.389: 2
  Chirality restraints: 809
  Sorted by residual:
  chirality pdb=" CA  GLN A 609 "
            pdb=" N   GLN A 609 "
            pdb=" C   GLN A 609 "
            pdb=" CB  GLN A 609 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.79e+00
  chirality pdb=" CA  LEU A  51 "
            pdb=" N   LEU A  51 "
            pdb=" C   LEU A  51 "
            pdb=" CB  LEU A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.37e+00
  chirality pdb=" CA  ASN A 329 "
            pdb=" N   ASN A 329 "
            pdb=" C   ASN A 329 "
            pdb=" CB  ASN A 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 5.03e-01
  ... (remaining 806 not shown)

  Planarity restraints: 1482
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 329 "    0.107 2.00e-02 2.50e+03   1.13e-01 1.93e+02
        pdb=" CG  ASN A 329 "   -0.012 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 329 "   -0.101 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 329 "    0.004 2.00e-02 2.50e+03
        pdb="HD21 ASN A 329 "    0.168 2.00e-02 2.50e+03
        pdb="HD22 ASN A 329 "   -0.165 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 535 "    0.019 5.00e-02 4.00e+02   2.82e-02 1.28e+00
        pdb=" N   PRO A 536 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A 536 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 536 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 585 "   -0.017 5.00e-02 4.00e+02   2.55e-02 1.04e+00
        pdb=" N   PRO A 586 "    0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO A 586 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 586 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 1479 not shown)

  Histogram of nonbonded interaction distances:
        1.29 -     1.95: 70
        1.95 -     2.61: 11824
        2.61 -     3.28: 30968
        3.28 -     3.94: 36170
        3.94 -     4.60: 57202
  Nonbonded interactions: 136234
  Sorted by model distance:
  nonbonded pdb="HD22 ASN A 171 "
            pdb="HD13 ILE A 333 "
     model   vdw
     1.291 2.270
  nonbonded pdb="HD21 ASN A 171 "
            pdb="HG21 ILE A 333 "
     model   vdw
     1.293 2.270
  nonbonded pdb=" HB3 HIS A  57 "
            pdb="HD21 ASN A 630 "
     model   vdw
     1.554 2.270
  nonbonded pdb=" H   ARG A 258 "
            pdb=" OD2 ASP A 263 "
     model   vdw
     1.613 1.850
  nonbonded pdb=" O   GLY A 419 "
            pdb=" HG  SER A 422 "
     model   vdw
     1.615 1.850
  ... (remaining 136229 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             1.110
  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:             0.150
  Extract box with map and model:          5.940
  Check model and map are aligned:         0.140
  Set scattering table:                    0.090
  Process input model:                     35.160
  Find NCS groups from input model:        0.190
  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:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
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      :  0.002   0.034   5148  Z= 0.124
  Angle     :  0.467   9.658   6989  Z= 0.259
  Chirality :  0.043   0.389    809
  Planarity :  0.003   0.028    873
  Dihedral  :  9.249  54.339   1835
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  3.64 %
    Favored  : 95.45 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.35), residues: 633
  helix:  0.74 (0.31), residues: 297
  sheet:  1.33 (0.64), residues: 71
  loop : -0.19 (0.41), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 264 
 HIS   0.001   0.000   HIS A 469 
 PHE   0.005   0.001   PHE A 520 
 TYR   0.004   0.001   TYR A  56 
 ARG   0.002   0.000   ARG A  34 

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 549 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 140
  time to evaluate  : 0.849 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 SER cc_start: 0.9182 (p) cc_final: 0.8757 (t)
REVERT: A  198 TYR cc_start: 0.7554 (m-80) cc_final: 0.7248 (m-80)
REVERT: A  292 MET cc_start: 0.8132 (tpt) cc_final: 0.7855 (tpp)
REVERT: A  306 LEU cc_start: 0.8622 (tp) cc_final: 0.8383 (mt)
REVERT: A  312 SER cc_start: 0.7470 (p) cc_final: 0.7244 (t)
REVERT: A  617 VAL cc_start: 0.9018 (t) cc_final: 0.8758 (p)
  outliers start: 5
  outliers final: 2
  residues processed: 142
  average time/residue: 0.3896
  time to fit residues: 70.8688
Evaluate side-chains
  99 residues out of total 549 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 379 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.3332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5148  Z= 0.204
  Angle     :  0.605   5.395   6989  Z= 0.330
  Chirality :  0.047   0.405    809
  Planarity :  0.005   0.038    873
  Dihedral  :  4.390  16.491    680
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  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:  0.51 (0.34), residues: 633
  helix:  0.68 (0.28), residues: 313
  sheet:  0.80 (0.63), residues: 67
  loop : -0.06 (0.44), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 264 
 HIS   0.003   0.001   HIS A 260 
 PHE   0.017   0.002   PHE A 248 
 TYR   0.024   0.001   TYR A 588 
 ARG   0.012   0.001   ARG A 258 

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 549 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.810 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLN cc_start: 0.8417 (mt0) cc_final: 0.7984 (tt0)
REVERT: A  198 TYR cc_start: 0.7477 (m-80) cc_final: 0.7229 (m-80)
REVERT: A  312 SER cc_start: 0.7095 (p) cc_final: 0.6768 (t)
REVERT: A  407 MET cc_start: 0.7749 (mmp) cc_final: 0.7208 (mmt)
REVERT: A  581 MET cc_start: 0.8183 (ttm) cc_final: 0.7834 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.3200
  time to fit residues: 45.0028
Evaluate side-chains
  87 residues out of total 549 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 18 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 57 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 379 GLN
A 609 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.3818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5148  Z= 0.181
  Angle     :  0.519   6.168   6989  Z= 0.285
  Chirality :  0.044   0.385    809
  Planarity :  0.004   0.037    873
  Dihedral  :  4.330  15.225    680
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.34), residues: 633
  helix:  0.68 (0.28), residues: 315
  sheet:  0.49 (0.61), residues: 73
  loop : -0.11 (0.44), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 646 
 HIS   0.002   0.001   HIS A 260 
 PHE   0.011   0.001   PHE A  41 
 TYR   0.011   0.001   TYR A  56 
 ARG   0.006   0.000   ARG A 258 

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 549 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.906 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLN cc_start: 0.8325 (mt0) cc_final: 0.7965 (tt0)
REVERT: A  312 SER cc_start: 0.7019 (p) cc_final: 0.6764 (t)
REVERT: A  407 MET cc_start: 0.7675 (mmp) cc_final: 0.7230 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.3314
  time to fit residues: 42.9197
Evaluate side-chains
  86 residues out of total 549 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 39 optimal weight:    0.3980
   chunk 58 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0670
   chunk 51 optimal weight:    8.9990
   overall best weight:    1.4522

-------------------------------------------------------------------------------
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: 0.7682
moved from start:          0.4140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5148  Z= 0.182
  Angle     :  0.503   5.568   6989  Z= 0.274
  Chirality :  0.044   0.382    809
  Planarity :  0.005   0.067    873
  Dihedral  :  4.327  15.162    680
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  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:  0.57 (0.34), residues: 633
  helix:  0.78 (0.28), residues: 316
  sheet:  0.42 (0.61), residues: 73
  loop :  0.01 (0.44), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  77 
 HIS   0.002   0.001   HIS A 260 
 PHE   0.015   0.001   PHE A  41 
 TYR   0.018   0.001   TYR A 588 
 ARG   0.004   0.000   ARG A 258 

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 549 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.808 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLN cc_start: 0.8302 (mt0) cc_final: 0.7975 (tt0)
REVERT: A  198 TYR cc_start: 0.7493 (m-80) cc_final: 0.7184 (m-80)
REVERT: A  312 SER cc_start: 0.7012 (p) cc_final: 0.6694 (t)
REVERT: A  407 MET cc_start: 0.7661 (mmp) cc_final: 0.7226 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.3067
  time to fit residues: 39.6540
Evaluate side-chains
  85 residues out of total 549 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 0 optimal weight:    7.9990
   chunk 46 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 20 optimal weight:    9.9990
   chunk 12 optimal weight:    8.9990
   overall best weight:    2.7588

-------------------------------------------------------------------------------
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: 0.7756
moved from start:          0.4352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5148  Z= 0.246
  Angle     :  0.531   5.105   6989  Z= 0.293
  Chirality :  0.044   0.391    809
  Planarity :  0.004   0.050    873
  Dihedral  :  4.464  16.063    680
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.34), residues: 633
  helix:  0.67 (0.28), residues: 316
  sheet:  0.16 (0.60), residues: 73
  loop : -0.15 (0.44), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 646 
 HIS   0.003   0.001   HIS A 260 
 PHE   0.013   0.001   PHE A 162 
 TYR   0.014   0.001   TYR A 167 
 ARG   0.004   0.000   ARG A 258 

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 549 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.878 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLN cc_start: 0.8253 (mt0) cc_final: 0.7975 (tt0)
REVERT: A  312 SER cc_start: 0.7129 (p) cc_final: 0.6852 (t)
REVERT: A  407 MET cc_start: 0.7598 (mmp) cc_final: 0.7188 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.3102
  time to fit residues: 40.2743
Evaluate side-chains
  82 residues out of total 549 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9990
   chunk 61 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 20 optimal weight:    8.9990
   chunk 32 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.4517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5148  Z= 0.214
  Angle     :  0.524   5.287   6989  Z= 0.286
  Chirality :  0.044   0.392    809
  Planarity :  0.004   0.045    873
  Dihedral  :  4.468  15.985    680
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.34), residues: 633
  helix:  0.76 (0.28), residues: 318
  sheet:  0.20 (0.59), residues: 73
  loop : -0.08 (0.44), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 622 
 HIS   0.009   0.001   HIS A 260 
 PHE   0.015   0.001   PHE A  41 
 TYR   0.023   0.001   TYR A 588 
 ARG   0.004   0.000   ARG A 258 

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 549 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.869 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.7571 (mmp) cc_final: 0.7174 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.3262
  time to fit residues: 42.2095
Evaluate side-chains
  80 residues out of total 549 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 35 optimal weight:    9.9990
   chunk 52 optimal weight:    9.9990
   chunk 34 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 37 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   overall best weight:    2.5186

-------------------------------------------------------------------------------
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: 0.7746
moved from start:          0.4606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5148  Z= 0.233
  Angle     :  0.523   5.164   6989  Z= 0.286
  Chirality :  0.044   0.391    809
  Planarity :  0.004   0.043    873
  Dihedral  :  4.520  16.295    680
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  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:  0.39 (0.34), residues: 633
  helix:  0.69 (0.28), residues: 318
  sheet:  0.17 (0.62), residues: 67
  loop : -0.12 (0.44), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 622 
 HIS   0.006   0.001   HIS A 260 
 PHE   0.015   0.001   PHE A 372 
 TYR   0.030   0.002   TYR A 588 
 ARG   0.003   0.000   ARG A 258 

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 549 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.739 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.7585 (mmp) cc_final: 0.7154 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.3230
  time to fit residues: 39.3378
Evaluate side-chains
  82 residues out of total 549 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 11 optimal weight:    0.3980
   chunk 39 optimal weight:    1.9990
   chunk 42 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    1.6386

-------------------------------------------------------------------------------
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: 0.7713
moved from start:          0.4705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5148  Z= 0.176
  Angle     :  0.494   5.270   6989  Z= 0.266
  Chirality :  0.044   0.389    809
  Planarity :  0.004   0.042    873
  Dihedral  :  4.418  15.673    680
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.34), residues: 633
  helix:  0.87 (0.29), residues: 318
  sheet:  0.28 (0.63), residues: 67
  loop : -0.08 (0.44), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 622 
 HIS   0.006   0.001   HIS A 260 
 PHE   0.013   0.001   PHE A  41 
 TYR   0.012   0.001   TYR A 167 
 ARG   0.002   0.000   ARG A 258 

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 549 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.815 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.7606 (mmp) cc_final: 0.7195 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.3364
  time to fit residues: 42.1363
Evaluate side-chains
  79 residues out of total 549 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 17 optimal weight:    0.5980
   chunk 51 optimal weight:    7.9990
   chunk 54 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 630 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.4846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5148  Z= 0.154
  Angle     :  0.496   5.313   6989  Z= 0.264
  Chirality :  0.043   0.387    809
  Planarity :  0.004   0.038    873
  Dihedral  :  4.313  15.006    680
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  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:  0.76 (0.35), residues: 633
  helix:  1.11 (0.29), residues: 314
  sheet:  0.35 (0.63), residues: 67
  loop : -0.09 (0.44), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 622 
 HIS   0.006   0.001   HIS A 260 
 PHE   0.020   0.001   PHE A 372 
 TYR   0.015   0.001   TYR A 588 
 ARG   0.002   0.000   ARG A  27 

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 549 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.685 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.7576 (mmp) cc_final: 0.7177 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.3165
  time to fit residues: 38.5459
Evaluate side-chains
  79 residues out of total 549 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 39 optimal weight:    7.9990
   chunk 31 optimal weight:    4.9990
   chunk 40 optimal weight:    8.9990
   chunk 54 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 46 optimal weight:    7.9990
   overall best weight:    1.6984

-------------------------------------------------------------------------------
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: 0.7707
moved from start:          0.4887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5148  Z= 0.185
  Angle     :  0.507   5.344   6989  Z= 0.270
  Chirality :  0.044   0.388    809
  Planarity :  0.004   0.037    873
  Dihedral  :  4.326  14.987    680
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  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:  0.72 (0.34), residues: 633
  helix:  1.07 (0.29), residues: 314
  sheet:  0.33 (0.63), residues: 67
  loop : -0.11 (0.43), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 622 
 HIS   0.005   0.001   HIS A 260 
 PHE   0.014   0.001   PHE A 372 
 TYR   0.012   0.001   TYR A  91 
 ARG   0.002   0.000   ARG A 303 

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 549 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.741 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.7591 (mmp) cc_final: 0.7195 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.3252
  time to fit residues: 37.9825
Evaluate side-chains
  78 residues out of total 549 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 14 optimal weight:    6.9990
   chunk 50 optimal weight:    7.9990
   chunk 21 optimal weight:    6.9990
   chunk 52 optimal weight:    0.0980
   chunk 6 optimal weight:    0.9990
   chunk 9 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    2.8188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.119077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.096802 restraints weight = 44110.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.100240 restraints weight = 25346.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.102451 restraints weight = 17783.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.4932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5148  Z= 0.247
  Angle     :  0.526   5.269   6989  Z= 0.290
  Chirality :  0.044   0.393    809
  Planarity :  0.004   0.038    873
  Dihedral  :  4.484  15.583    680
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.34), residues: 633
  helix:  0.81 (0.28), residues: 318
  sheet:  0.27 (0.63), residues: 67
  loop : -0.16 (0.43), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 622 
 HIS   0.006   0.001   HIS A 260 
 PHE   0.027   0.001   PHE A 372 
 TYR   0.016   0.001   TYR A 167 
 ARG   0.002   0.001   ARG A  27 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2779.74 seconds
wall clock time: 49 minutes 25.23 seconds (2965.23 seconds total)