Starting phenix.real_space_refine
on Sun May 18 00:16:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8avb_15677/05_2025/8avb_15677.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8avb_15677/05_2025/8avb_15677.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8avb_15677/05_2025/8avb_15677.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8avb_15677/05_2025/8avb_15677.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8avb_15677/05_2025/8avb_15677.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8avb_15677/05_2025/8avb_15677.cif"
  }
  resolution = 4.43
  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=   0.048
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6823 atoms to isotropic.
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      51      5.16       5
     C    6790      2.51       5
     N    1778      2.21       5
     O    1972      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 10591
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1077
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 133}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 593, 4757
          Classifications: {'peptide': 593}
          Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 555}
    Chain: "F"
      Number of atoms: 4757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 593, 4757
          Classifications: {'peptide': 593}
          Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 555}
  Time building chain proxies: 6.65, per 1000 atoms: 0.63
  Number of scatterers: 10591
  At special positions: 0
  Unit cell: (99.66, 137.41, 175.16, 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      51     16.00
     O    1972      8.00
     N    1778      7.00
     C    6790      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=13, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 117 " - pdb=" SG  CYS A 167 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 350 " - pdb=" SG  CYS B 410 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 411 " - pdb=" SG  CYS B 416 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 434 " - pdb=" SG  CYS B 445 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 471 " - pdb=" SG  CYS B 526 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 486 " - pdb=" SG  CYS B 496 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 602 " - pdb=" SG  CYS B 672 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 350 " - pdb=" SG  CYS F 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 411 " - pdb=" SG  CYS F 416 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F 434 " - pdb=" SG  CYS F 445 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 471 " - pdb=" SG  CYS F 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 486 " - pdb=" SG  CYS F 496 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 602 " - pdb=" SG  CYS F 672 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.71
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2538

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 29 sheets defined
      10.0% alpha, 37.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 44
    Processing helix  chain 'A' and resid 45 through 49
      removed outlier: 3.564A  pdb=" N   GLN A  49 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 89
      removed outlier: 3.853A  pdb=" N   SER A  88 " --> pdb=" O   GLN A  84 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU A  89 " --> pdb=" O   VAL A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 116
    Processing helix  chain 'A' and resid 130 through 138
      removed outlier: 3.677A  pdb=" N   VAL A 134 " --> pdb=" O   SER A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 160
    Processing helix  chain 'B' and resid 528 through 533
      removed outlier: 3.855A  pdb=" N   VAL B 533 " --> pdb=" O   ASP B 530 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 732 through 736
      removed outlier: 3.942A  pdb=" N   LYS B 735 " --> pdb=" O   PRO B 732 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 360 through 362
      No H-bonds generated for 'chain 'F' and resid 360 through 362'
    Processing helix  chain 'F' and resid 375 through 377
      No H-bonds generated for 'chain 'F' and resid 375 through 377'
    Processing helix  chain 'F' and resid 528 through 533
      removed outlier: 3.821A  pdb=" N   VAL F 533 " --> pdb=" O   ASP F 530 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 731 through 735
    Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58
    Processing sheet with id=AA2, first strand: chain 'B' and resid 240 through 246
      removed outlier: 5.590A  pdb=" N   GLY B 241 " --> pdb=" O   ASP B 257 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ASP B 257 " --> pdb=" O   GLY B 241 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 279 through 286
    Processing sheet with id=AA4, first strand: chain 'B' and resid 332 through 334
    Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 340
    Processing sheet with id=AA6, first strand: chain 'B' and resid 353 through 354
    Processing sheet with id=AA7, first strand: chain 'B' and resid 432 through 436
      removed outlier: 3.694A  pdb=" N   VAL B 487 " --> pdb=" O   GLU B 495 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 482 through 484
      removed outlier: 4.578A  pdb=" N   LEU B 462 " --> pdb=" O   LYS B 484 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 482 through 484
      removed outlier: 4.578A  pdb=" N   LEU B 462 " --> pdb=" O   LYS B 484 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 539 through 545
      removed outlier: 6.016A  pdb=" N   ASN B 540 " --> pdb=" O   GLU B 557 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   GLU B 557 " --> pdb=" O   ASN B 540 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 582 through 586
    Processing sheet with id=AB3, first strand: chain 'B' and resid 643 through 648
    Processing sheet with id=AB4, first strand: chain 'B' and resid 687 through 694
      removed outlier: 6.094A  pdb=" N   TYR B 677 " --> pdb=" O   VAL B 693 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 739 through 745
    Processing sheet with id=AB6, first strand: chain 'B' and resid 782 through 787
    Processing sheet with id=AB7, first strand: chain 'F' and resid 240 through 246
      removed outlier: 5.214A  pdb=" N   GLY F 241 " --> pdb=" O   ASP F 257 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 279 through 286
    Processing sheet with id=AB9, first strand: chain 'F' and resid 331 through 333
    Processing sheet with id=AC1, first strand: chain 'F' and resid 331 through 333
    Processing sheet with id=AC2, first strand: chain 'F' and resid 337 through 339
      removed outlier: 6.596A  pdb=" N   ILE F 338 " --> pdb=" O   TYR F 424 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 433 through 436
    Processing sheet with id=AC4, first strand: chain 'F' and resid 482 through 484
      removed outlier: 4.031A  pdb=" N   LEU F 462 " --> pdb=" O   LYS F 484 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'F' and resid 482 through 484
      removed outlier: 4.031A  pdb=" N   LEU F 462 " --> pdb=" O   LYS F 484 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'F' and resid 539 through 545
      removed outlier: 3.816A  pdb=" N   VAL F 541 " --> pdb=" O   SER F 555 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   SER F 555 " --> pdb=" O   VAL F 541 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   ALA F 543 " --> pdb=" O   LYS F 553 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   LYS F 553 " --> pdb=" O   ALA F 543 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'F' and resid 582 through 586
    Processing sheet with id=AC8, first strand: chain 'F' and resid 643 through 648
    Processing sheet with id=AC9, first strand: chain 'F' and resid 690 through 694
      removed outlier: 5.576A  pdb=" N   TYR F 677 " --> pdb=" O   VAL F 693 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'F' and resid 739 through 746
    Processing sheet with id=AD2, first strand: chain 'F' and resid 782 through 787
      removed outlier: 3.839A  pdb=" N   TYR F 767 " --> pdb=" O   VAL F 812 " (cutoff:3.500A)

    440 hydrogen bonds defined for protein.
    1140 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.70

  Time building geometry restraints manager: 3.14 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1808
        1.32 -     1.46: 3328
        1.46 -     1.59: 5659
        1.59 -     1.72: 1
        1.72 -     1.85: 72
  Bond restraints: 10868
  Sorted by residual:
  bond pdb=" CG  PRO F 801 "
       pdb=" CD  PRO F 801 "
    ideal  model  delta    sigma   weight residual
    1.503  1.191  0.312 3.40e-02 8.65e+02 8.41e+01
  bond pdb=" N   PRO F 801 "
       pdb=" CD  PRO F 801 "
    ideal  model  delta    sigma   weight residual
    1.473  1.536 -0.063 1.40e-02 5.10e+03 2.03e+01
  bond pdb=" CB  PRO F 801 "
       pdb=" CG  PRO F 801 "
    ideal  model  delta    sigma   weight residual
    1.492  1.680 -0.188 5.00e-02 4.00e+02 1.41e+01
  bond pdb=" CB  ASN A 103 "
       pdb=" CG  ASN A 103 "
    ideal  model  delta    sigma   weight residual
    1.516  1.564 -0.048 2.50e-02 1.60e+03 3.66e+00
  bond pdb=" N   PRO F 801 "
       pdb=" CA  PRO F 801 "
    ideal  model  delta    sigma   weight residual
    1.472  1.446  0.025 1.34e-02 5.57e+03 3.61e+00
  ... (remaining 10863 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.77: 14774
        4.77 -     9.54: 33
        9.54 -    14.31: 5
       14.31 -    19.07: 2
       19.07 -    23.84: 1
  Bond angle restraints: 14815
  Sorted by residual:
  angle pdb=" N   PRO F 801 "
        pdb=" CD  PRO F 801 "
        pdb=" CG  PRO F 801 "
      ideal   model   delta    sigma   weight residual
     103.20   86.46   16.74 1.50e+00 4.44e-01 1.25e+02
  angle pdb=" CA  PRO F 801 "
        pdb=" N   PRO F 801 "
        pdb=" CD  PRO F 801 "
      ideal   model   delta    sigma   weight residual
     112.00   97.20   14.80 1.40e+00 5.10e-01 1.12e+02
  angle pdb=" CB  ARG A  41 "
        pdb=" CG  ARG A  41 "
        pdb=" CD  ARG A  41 "
      ideal   model   delta    sigma   weight residual
     111.30  135.14  -23.84 2.30e+00 1.89e-01 1.07e+02
  angle pdb=" CA  PRO F 801 "
        pdb=" CB  PRO F 801 "
        pdb=" CG  PRO F 801 "
      ideal   model   delta    sigma   weight residual
     104.50   93.66   10.84 1.90e+00 2.77e-01 3.26e+01
  angle pdb=" N   SER A  46 "
        pdb=" CA  SER A  46 "
        pdb=" C   SER A  46 "
      ideal   model   delta    sigma   weight residual
     110.80  121.38  -10.58 2.13e+00 2.20e-01 2.47e+01
  ... (remaining 14810 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 6133
       17.93 -    35.87: 350
       35.87 -    53.80: 57
       53.80 -    71.73: 7
       71.73 -    89.66: 6
  Dihedral angle restraints: 6553
    sinusoidal: 2639
      harmonic: 3914
  Sorted by residual:
  dihedral pdb=" CB  CYS F 411 "
           pdb=" SG  CYS F 411 "
           pdb=" SG  CYS F 416 "
           pdb=" CB  CYS F 416 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   42.00   51.00     1      1.00e+01 1.00e-02 3.56e+01
  dihedral pdb=" CA  PHE B 502 "
           pdb=" C   PHE B 502 "
           pdb=" N   LEU B 503 "
           pdb=" CA  LEU B 503 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.29  -27.71     0      5.00e+00 4.00e-02 3.07e+01
  dihedral pdb=" CB  CYS B 486 "
           pdb=" SG  CYS B 486 "
           pdb=" SG  CYS B 496 "
           pdb=" CB  CYS B 496 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.96   43.04     1      1.00e+01 1.00e-02 2.58e+01
  ... (remaining 6550 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 1444
       0.075 -    0.149: 223
       0.149 -    0.224: 8
       0.224 -    0.298: 1
       0.298 -    0.373: 1
  Chirality restraints: 1677
  Sorted by residual:
  chirality pdb=" CA  GLN A  96 "
            pdb=" N   GLN A  96 "
            pdb=" C   GLN A  96 "
            pdb=" CB  GLN A  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.47e+00
  chirality pdb=" CB  ILE F 753 "
            pdb=" CA  ILE F 753 "
            pdb=" CG1 ILE F 753 "
            pdb=" CG2 ILE F 753 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CA  PRO A  90 "
            pdb=" N   PRO A  90 "
            pdb=" C   PRO A  90 "
            pdb=" CB  PRO A  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 9.79e-01
  ... (remaining 1674 not shown)

  Planarity restraints: 1863
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE F 800 "   -0.106 5.00e-02 4.00e+02   1.46e-01 3.42e+01
        pdb=" N   PRO F 801 "    0.252 5.00e-02 4.00e+02
        pdb=" CA  PRO F 801 "   -0.073 5.00e-02 4.00e+02
        pdb=" CD  PRO F 801 "   -0.073 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 558 "    0.050 5.00e-02 4.00e+02   7.71e-02 9.51e+00
        pdb=" N   PRO B 559 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO B 559 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 559 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A  24 "   -0.015 2.00e-02 2.50e+03   3.03e-02 9.20e+00
        pdb=" C   ILE A  24 "    0.052 2.00e-02 2.50e+03
        pdb=" O   ILE A  24 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   GLN A  25 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1860 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 320
        2.69 -     3.25: 10270
        3.25 -     3.80: 17396
        3.80 -     4.35: 22860
        4.35 -     4.90: 36161
  Nonbonded interactions: 87007
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 103 "
            pdb=" OG  SER B 505 "
     model   vdw
     2.142 3.040
  nonbonded pdb=" OG1 THR F 397 "
            pdb=" O   VAL F 425 "
     model   vdw
     2.142 3.040
  nonbonded pdb=" NE2 GLN A  96 "
            pdb=" N   ILE B 501 "
     model   vdw
     2.178 3.200
  nonbonded pdb=" NE1 TRP B 644 "
            pdb=" OE2 GLU B 771 "
     model   vdw
     2.182 3.120
  nonbonded pdb=" NH1 ARG F 368 "
            pdb=" OD2 ASP F 406 "
     model   vdw
     2.206 3.120
  ... (remaining 87002 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.110
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     26.790
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.040
  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:2.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6340
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      :  0.005   0.312  10881  Z= 0.196
  Angle     :  0.811  23.843  14841  Z= 0.456
  Chirality :  0.050   0.373   1677
  Planarity :  0.006   0.146   1863
  Dihedral  : 11.641  89.664   3976
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 17.52
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.40 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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 (0.23), residues: 1318
  helix: -0.94 (0.42), residues: 107
  sheet: -0.07 (0.21), residues: 574
  loop : -0.27 (0.27), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP F 366 
 HIS   0.013   0.001   HIS F 418 
 PHE   0.016   0.001   PHE B 334 
 TYR   0.033   0.002   TYR A 140 
 ARG   0.024   0.001   ARG A  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11505 (  414)
  hydrogen bonds       : angle       7.59479 ( 1140)
  SS BOND              : bond        0.00560 (   13)
  SS BOND              : angle       1.34556 (   26)
  covalent geometry    : bond        0.00480 (10868)
  covalent geometry    : angle       0.81023 (14815)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 1.187 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.8697 (m-10) cc_final: 0.8208 (m-10)
REVERT: A  149 ARG cc_start: 0.8007 (mtt180) cc_final: 0.7247 (mtp180)
REVERT: A  155 GLN cc_start: 0.8374 (tp-100) cc_final: 0.7905 (tp-100)
REVERT: B  509 MET cc_start: 0.8881 (pmm) cc_final: 0.8623 (pmm)
REVERT: B  638 MET cc_start: 0.9329 (mmp) cc_final: 0.9112 (mmm)
REVERT: F  397 THR cc_start: 0.6489 (p) cc_final: 0.6239 (p)
REVERT: F  403 PHE cc_start: 0.7248 (m-10) cc_final: 0.6842 (m-80)
REVERT: F  638 MET cc_start: 0.9243 (mpp) cc_final: 0.8956 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.2074
  time to fit residues: 29.0834
Evaluate side-chains
  60 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 1.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:   20.0000
   chunk 100 optimal weight:   20.0000
   chunk 55 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 67 optimal weight:    7.9990
   chunk 53 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 77 optimal weight:    0.0570
   chunk 119 optimal weight:    6.9990
   overall best weight:    1.4104

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

Flipped N/Q/H residues before XYZ refinement:
A  47 HIS
A 103 ASN
B 267 GLN
** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 685 HIS
** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 461 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.106352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.079560 restraints weight = 107210.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.079666 restraints weight = 95744.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.080889 restraints weight = 72874.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6525
moved from start:          0.0987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10881  Z= 0.131
  Angle     :  0.585   7.300  14841  Z= 0.308
  Chirality :  0.046   0.202   1677
  Planarity :  0.005   0.053   1863
  Dihedral  :  5.407  62.485   1433
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.44 %
    Favored  : 96.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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: -0.28 (0.24), residues: 1318
  helix:  0.83 (0.50), residues: 108
  sheet: -0.07 (0.21), residues: 576
  loop : -0.36 (0.26), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP F 447 
 HIS   0.009   0.001   HIS A  47 
 PHE   0.013   0.001   PHE F 493 
 TYR   0.019   0.001   TYR F 494 
 ARG   0.008   0.001   ARG F 368 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04011 (  414)
  hydrogen bonds       : angle       6.72639 ( 1140)
  SS BOND              : bond        0.00329 (   13)
  SS BOND              : angle       0.90372 (   26)
  covalent geometry    : bond        0.00281 (10868)
  covalent geometry    : angle       0.58428 (14815)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 86
  time to evaluate  : 1.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.8190 (m-10) cc_final: 0.7679 (m-10)
REVERT: A  155 GLN cc_start: 0.8412 (tp-100) cc_final: 0.7917 (tp-100)
REVERT: B  244 MET cc_start: 0.6383 (tmm) cc_final: 0.5553 (tpp)
REVERT: B  447 TRP cc_start: 0.8980 (p-90) cc_final: 0.8764 (p-90)
REVERT: B  547 VAL cc_start: 0.9015 (t) cc_final: 0.8775 (t)
REVERT: B  638 MET cc_start: 0.9230 (mmp) cc_final: 0.8934 (mmm)
REVERT: F  397 THR cc_start: 0.6780 (p) cc_final: 0.6507 (p)
REVERT: F  403 PHE cc_start: 0.7768 (m-10) cc_final: 0.7542 (m-80)
REVERT: F  478 HIS cc_start: 0.8727 (m-70) cc_final: 0.8520 (m-70)
REVERT: F  638 MET cc_start: 0.9218 (mpp) cc_final: 0.8840 (mpp)
REVERT: F  733 MET cc_start: 0.9103 (mpp) cc_final: 0.8602 (tpp)
  outliers start: 2
  outliers final: 1
  residues processed: 88
  average time/residue: 0.2036
  time to fit residues: 27.2153
Evaluate side-chains
  61 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 122 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 130 optimal weight:    6.9990
   chunk 118 optimal weight:   40.0000
   chunk 57 optimal weight:    0.8980
   chunk 50 optimal weight:   20.0000
   chunk 71 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 15 optimal weight:   20.0000
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  96 GLN
A 103 ASN
B 369 ASN
** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 685 HIS
F 259 GLN
** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.108083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.089024 restraints weight = 108125.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.088483 restraints weight = 86201.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.088453 restraints weight = 76930.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.4078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6375
moved from start:          0.1307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10881  Z= 0.116
  Angle     :  0.552   6.960  14841  Z= 0.291
  Chirality :  0.045   0.186   1677
  Planarity :  0.004   0.043   1863
  Dihedral  :  5.238  58.958   1433
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.54 %
    Favored  : 97.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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: -0.28 (0.24), residues: 1318
  helix:  0.84 (0.51), residues: 114
  sheet: -0.06 (0.21), residues: 573
  loop : -0.37 (0.26), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP F 447 
 HIS   0.004   0.001   HIS F 417 
 PHE   0.011   0.001   PHE B 334 
 TYR   0.013   0.001   TYR F 409 
 ARG   0.013   0.000   ARG F 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03664 (  414)
  hydrogen bonds       : angle       6.46101 ( 1140)
  SS BOND              : bond        0.00441 (   13)
  SS BOND              : angle       1.07389 (   26)
  covalent geometry    : bond        0.00245 (10868)
  covalent geometry    : angle       0.55091 (14815)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 1.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 TYR cc_start: 0.8184 (m-80) cc_final: 0.7977 (m-80)
REVERT: A   96 GLN cc_start: 0.8462 (mp10) cc_final: 0.7889 (pp30)
REVERT: A  155 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8217 (tp-100)
REVERT: B  244 MET cc_start: 0.6213 (tmm) cc_final: 0.5919 (tmm)
REVERT: B  443 MET cc_start: 0.2992 (tpt) cc_final: 0.2768 (tpt)
REVERT: B  509 MET cc_start: 0.8975 (pmm) cc_final: 0.8726 (pmm)
REVERT: B  638 MET cc_start: 0.9269 (mmp) cc_final: 0.9009 (mmm)
REVERT: B  647 MET cc_start: 0.6884 (mmp) cc_final: 0.6663 (mmm)
REVERT: F  397 THR cc_start: 0.6340 (p) cc_final: 0.6083 (p)
REVERT: F  403 PHE cc_start: 0.7977 (m-10) cc_final: 0.7711 (m-80)
REVERT: F  478 HIS cc_start: 0.8654 (m-70) cc_final: 0.8427 (m-70)
REVERT: F  638 MET cc_start: 0.9211 (mpp) cc_final: 0.8854 (mpp)
REVERT: F  647 MET cc_start: 0.8794 (mmp) cc_final: 0.7806 (tpp)
REVERT: F  733 MET cc_start: 0.9062 (mpp) cc_final: 0.8594 (tpp)
  outliers start: 1
  outliers final: 1
  residues processed: 86
  average time/residue: 0.2072
  time to fit residues: 26.3650
Evaluate side-chains
  60 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 59 optimal weight:    0.0970
   chunk 56 optimal weight:    2.9990
   chunk 89 optimal weight:    0.0370
   chunk 90 optimal weight:    0.3980
   chunk 22 optimal weight:   20.0000
   chunk 52 optimal weight:    4.9990
   chunk 107 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 104 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 75 optimal weight:    9.9990
   overall best weight:    1.5060

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

Flipped N/Q/H residues before XYZ refinement:
A  49 GLN
B 267 GLN
** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 685 HIS
** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.104792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.079030 restraints weight = 107542.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.078965 restraints weight = 81372.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.079814 restraints weight = 71434.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.4022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6579
moved from start:          0.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10881  Z= 0.129
  Angle     :  0.554   6.592  14841  Z= 0.292
  Chirality :  0.046   0.181   1677
  Planarity :  0.004   0.047   1863
  Dihedral  :  5.189  55.096   1433
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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: -0.34 (0.23), residues: 1318
  helix:  0.76 (0.49), residues: 114
  sheet: -0.09 (0.21), residues: 579
  loop : -0.41 (0.26), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP F 447 
 HIS   0.006   0.001   HIS A  47 
 PHE   0.013   0.001   PHE F 498 
 TYR   0.015   0.001   TYR F 409 
 ARG   0.010   0.000   ARG A  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03492 (  414)
  hydrogen bonds       : angle       6.40066 ( 1140)
  SS BOND              : bond        0.00365 (   13)
  SS BOND              : angle       0.92712 (   26)
  covalent geometry    : bond        0.00267 (10868)
  covalent geometry    : angle       0.55358 (14815)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLN cc_start: 0.7954 (mp10) cc_final: 0.7700 (tm-30)
REVERT: A  140 TYR cc_start: 0.8071 (m-80) cc_final: 0.7776 (m-10)
REVERT: A  149 ARG cc_start: 0.8002 (mtt180) cc_final: 0.7791 (mtp180)
REVERT: A  155 GLN cc_start: 0.8351 (tp-100) cc_final: 0.7839 (tp-100)
REVERT: B  244 MET cc_start: 0.6331 (tmm) cc_final: 0.5876 (tmm)
REVERT: B  447 TRP cc_start: 0.9008 (p-90) cc_final: 0.8741 (p-90)
REVERT: B  632 MET cc_start: 0.8354 (mmp) cc_final: 0.8108 (pmm)
REVERT: B  638 MET cc_start: 0.9143 (mmp) cc_final: 0.8857 (mmm)
REVERT: B  647 MET cc_start: 0.6819 (mmp) cc_final: 0.6581 (mmm)
REVERT: F  397 THR cc_start: 0.6835 (p) cc_final: 0.6586 (p)
REVERT: F  478 HIS cc_start: 0.8536 (m-70) cc_final: 0.8283 (m-70)
REVERT: F  638 MET cc_start: 0.9215 (mpp) cc_final: 0.8822 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1999
  time to fit residues: 26.2687
Evaluate side-chains
  62 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   chunk 16 optimal weight:    9.9990
   chunk 71 optimal weight:    5.9990
   chunk 131 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0980
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 92 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 267 GLN
** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 685 HIS
** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.105648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.073982 restraints weight = 106650.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.075898 restraints weight = 79412.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.076817 restraints weight = 64801.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.4013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6612
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10881  Z= 0.102
  Angle     :  0.530   7.439  14841  Z= 0.277
  Chirality :  0.045   0.161   1677
  Planarity :  0.004   0.058   1863
  Dihedral  :  5.033  51.034   1433
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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: -0.24 (0.24), residues: 1318
  helix:  0.94 (0.50), residues: 114
  sheet: -0.04 (0.21), residues: 574
  loop : -0.36 (0.26), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP F 447 
 HIS   0.006   0.001   HIS A  47 
 PHE   0.016   0.001   PHE F 403 
 TYR   0.011   0.001   TYR A  82 
 ARG   0.003   0.000   ARG F 656 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03251 (  414)
  hydrogen bonds       : angle       6.17590 ( 1140)
  SS BOND              : bond        0.00365 (   13)
  SS BOND              : angle       0.98731 (   26)
  covalent geometry    : bond        0.00219 (10868)
  covalent geometry    : angle       0.52876 (14815)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ARG cc_start: 0.8218 (mtt180) cc_final: 0.8000 (mtp180)
REVERT: A  155 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7663 (tp-100)
REVERT: B  447 TRP cc_start: 0.8982 (p-90) cc_final: 0.8693 (p-90)
REVERT: B  632 MET cc_start: 0.8351 (mmp) cc_final: 0.8031 (pmm)
REVERT: B  638 MET cc_start: 0.9246 (mmp) cc_final: 0.8971 (mmm)
REVERT: F  397 THR cc_start: 0.6777 (p) cc_final: 0.6531 (p)
REVERT: F  403 PHE cc_start: 0.7338 (m-80) cc_final: 0.7096 (m-80)
REVERT: F  478 HIS cc_start: 0.8312 (m-70) cc_final: 0.8109 (m-70)
REVERT: F  638 MET cc_start: 0.9198 (mpp) cc_final: 0.8811 (mpp)
REVERT: F  647 MET cc_start: 0.8763 (mmp) cc_final: 0.7718 (tpp)
REVERT: F  733 MET cc_start: 0.8903 (mpp) cc_final: 0.8269 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.2130
  time to fit residues: 28.8000
Evaluate side-chains
  64 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 72 optimal weight:   20.0000
   chunk 102 optimal weight:    5.9990
   chunk 131 optimal weight:   20.0000
   chunk 66 optimal weight:    7.9990
   chunk 54 optimal weight:    0.2980
   chunk 128 optimal weight:   20.0000
   chunk 91 optimal weight:    8.9990
   chunk 62 optimal weight:    9.9990
   chunk 104 optimal weight:    7.9990
   chunk 85 optimal weight:    0.8980
   overall best weight:    3.8386

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
A 103 ASN
** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 608 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.099830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.079545 restraints weight = 110278.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.078789 restraints weight = 91933.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.078928 restraints weight = 84114.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6751
moved from start:          0.2972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.087  10881  Z= 0.248
  Angle     :  0.731  10.621  14841  Z= 0.385
  Chirality :  0.050   0.190   1677
  Planarity :  0.007   0.115   1863
  Dihedral  :  5.713  51.334   1433
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 25.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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: -0.85 (0.23), residues: 1318
  helix: -0.88 (0.45), residues: 114
  sheet: -0.34 (0.22), residues: 558
  loop : -0.57 (0.25), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP F 447 
 HIS   0.007   0.002   HIS F 417 
 PHE   0.022   0.002   PHE B 498 
 TYR   0.024   0.002   TYR B 439 
 ARG   0.014   0.001   ARG B 446 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04524 (  414)
  hydrogen bonds       : angle       7.24820 ( 1140)
  SS BOND              : bond        0.00629 (   13)
  SS BOND              : angle       1.23410 (   26)
  covalent geometry    : bond        0.00525 (10868)
  covalent geometry    : angle       0.72969 (14815)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 1.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.9084 (m-10) cc_final: 0.8598 (m-10)
REVERT: A  149 ARG cc_start: 0.8367 (mtt180) cc_final: 0.8093 (mtp180)
REVERT: A  155 GLN cc_start: 0.8593 (tp-100) cc_final: 0.8156 (tp-100)
REVERT: B  443 MET cc_start: 0.5611 (mmm) cc_final: 0.5066 (tpt)
REVERT: B  447 TRP cc_start: 0.8947 (p-90) cc_final: 0.8614 (p-90)
REVERT: B  509 MET cc_start: 0.9227 (pmm) cc_final: 0.8993 (pmm)
REVERT: B  632 MET cc_start: 0.7895 (mmp) cc_final: 0.7360 (pmm)
REVERT: B  638 MET cc_start: 0.9225 (mmp) cc_final: 0.8934 (mmm)
REVERT: B  647 MET cc_start: 0.6553 (mmp) cc_final: 0.6212 (mmm)
REVERT: F  478 HIS cc_start: 0.8511 (m-70) cc_final: 0.8305 (m-70)
REVERT: F  638 MET cc_start: 0.9230 (mpp) cc_final: 0.8751 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.2299
  time to fit residues: 27.3362
Evaluate side-chains
  61 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 102 optimal weight:    0.2980
   chunk 48 optimal weight:    0.0050
   chunk 57 optimal weight:    6.9990
   chunk 40 optimal weight:    0.5980
   chunk 130 optimal weight:    6.9990
   chunk 9 optimal weight:   20.0000
   chunk 54 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0370
   chunk 88 optimal weight:    0.9990
   chunk 72 optimal weight:    8.9990
   overall best weight:    0.3874

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

Flipped N/Q/H residues before XYZ refinement:
B 685 HIS
** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.104188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.086038 restraints weight = 110657.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.084622 restraints weight = 84270.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.084595 restraints weight = 83754.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.4011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6503
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10881  Z= 0.116
  Angle     :  0.573   7.677  14841  Z= 0.302
  Chirality :  0.046   0.170   1677
  Planarity :  0.005   0.079   1863
  Dihedral  :  5.300  45.675   1433
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 15.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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: -0.53 (0.24), residues: 1318
  helix:  0.27 (0.49), residues: 114
  sheet: -0.31 (0.21), residues: 566
  loop : -0.35 (0.26), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP F 366 
 HIS   0.008   0.001   HIS F 349 
 PHE   0.018   0.001   PHE F 334 
 TYR   0.018   0.001   TYR B 605 
 ARG   0.004   0.000   ARG B 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03284 (  414)
  hydrogen bonds       : angle       6.54894 ( 1140)
  SS BOND              : bond        0.00756 (   13)
  SS BOND              : angle       0.89646 (   26)
  covalent geometry    : bond        0.00246 (10868)
  covalent geometry    : angle       0.57213 (14815)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 1.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ARG cc_start: 0.8322 (mtt180) cc_final: 0.7687 (mtp180)
REVERT: A  155 GLN cc_start: 0.8672 (tp-100) cc_final: 0.8260 (tp-100)
REVERT: B  443 MET cc_start: 0.5107 (mmm) cc_final: 0.4541 (mmm)
REVERT: B  447 TRP cc_start: 0.8973 (p-90) cc_final: 0.8764 (p-90)
REVERT: B  509 MET cc_start: 0.9028 (pmm) cc_final: 0.8802 (pmm)
REVERT: B  632 MET cc_start: 0.8625 (mmp) cc_final: 0.7857 (pmm)
REVERT: B  638 MET cc_start: 0.9323 (mmp) cc_final: 0.9074 (mmm)
REVERT: B  647 MET cc_start: 0.6778 (mmp) cc_final: 0.6509 (mmm)
REVERT: F  478 HIS cc_start: 0.8431 (m-70) cc_final: 0.8218 (m-70)
REVERT: F  638 MET cc_start: 0.9200 (mpp) cc_final: 0.8803 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.2020
  time to fit residues: 26.1797
Evaluate side-chains
  65 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 26 optimal weight:   20.0000
   chunk 60 optimal weight:   20.0000
   chunk 92 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 128 optimal weight:    9.9990
   chunk 74 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 87 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 151 GLN
B 349 HIS
** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 369 ASN
** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.098717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.078123 restraints weight = 109428.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.078156 restraints weight = 83773.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.077887 restraints weight = 80746.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6771
moved from start:          0.3593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  10881  Z= 0.229
  Angle     :  0.696   9.257  14841  Z= 0.372
  Chirality :  0.049   0.222   1677
  Planarity :  0.006   0.083   1863
  Dihedral  :  5.670  43.546   1433
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 25.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.23), residues: 1318
  helix: -0.66 (0.45), residues: 114
  sheet: -0.44 (0.22), residues: 537
  loop : -0.62 (0.25), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP F 366 
 HIS   0.005   0.001   HIS B 349 
 PHE   0.022   0.002   PHE F 403 
 TYR   0.022   0.002   TYR B 507 
 ARG   0.008   0.001   ARG A  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04302 (  414)
  hydrogen bonds       : angle       7.34346 ( 1140)
  SS BOND              : bond        0.00561 (   13)
  SS BOND              : angle       1.09669 (   26)
  covalent geometry    : bond        0.00475 (10868)
  covalent geometry    : angle       0.69494 (14815)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.9192 (m-80) cc_final: 0.8905 (m-10)
REVERT: A  155 GLN cc_start: 0.8877 (tp-100) cc_final: 0.8480 (tp-100)
REVERT: B  244 MET cc_start: 0.7064 (tmm) cc_final: 0.6526 (tpp)
REVERT: B  443 MET cc_start: 0.5788 (mmm) cc_final: 0.5508 (tpt)
REVERT: B  447 TRP cc_start: 0.9028 (p-90) cc_final: 0.8803 (p-90)
REVERT: B  509 MET cc_start: 0.9155 (pmm) cc_final: 0.8916 (pmm)
REVERT: B  638 MET cc_start: 0.9206 (mmp) cc_final: 0.8971 (mmm)
REVERT: F  638 MET cc_start: 0.9194 (mpp) cc_final: 0.8831 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.2240
  time to fit residues: 25.9675
Evaluate side-chains
  57 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 33 optimal weight:    8.9990
   chunk 67 optimal weight:    0.9990
   chunk 18 optimal weight:   20.0000
   chunk 127 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 21 optimal weight:   40.0000
   chunk 7 optimal weight:    0.6980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 151 GLN
B 685 HIS
** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.101652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.082619 restraints weight = 110932.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.081118 restraints weight = 93950.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.081669 restraints weight = 84874.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6610
moved from start:          0.3580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10881  Z= 0.134
  Angle     :  0.605   7.200  14841  Z= 0.321
  Chirality :  0.047   0.159   1677
  Planarity :  0.005   0.072   1863
  Dihedral  :  5.457  37.440   1433
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 18.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.82 (0.24), residues: 1318
  helix: -0.20 (0.49), residues: 114
  sheet: -0.49 (0.22), residues: 540
  loop : -0.51 (0.26), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP F 366 
 HIS   0.008   0.001   HIS F 465 
 PHE   0.015   0.002   PHE F 334 
 TYR   0.013   0.001   TYR F 424 
 ARG   0.003   0.000   ARG A 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03489 (  414)
  hydrogen bonds       : angle       6.88932 ( 1140)
  SS BOND              : bond        0.00398 (   13)
  SS BOND              : angle       1.05177 (   26)
  covalent geometry    : bond        0.00287 (10868)
  covalent geometry    : angle       0.60364 (14815)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 1.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 TYR cc_start: 0.8616 (m-80) cc_final: 0.8349 (m-80)
REVERT: A  140 TYR cc_start: 0.8935 (m-80) cc_final: 0.8541 (m-10)
REVERT: A  149 ARG cc_start: 0.8509 (mtt180) cc_final: 0.7978 (mtp180)
REVERT: A  155 GLN cc_start: 0.8719 (tp-100) cc_final: 0.8291 (tp-100)
REVERT: B  244 MET cc_start: 0.6182 (tmm) cc_final: 0.5705 (tmm)
REVERT: B  443 MET cc_start: 0.5483 (mmm) cc_final: 0.5236 (tpt)
REVERT: B  447 TRP cc_start: 0.8926 (p-90) cc_final: 0.8707 (p-90)
REVERT: B  509 MET cc_start: 0.9064 (pmm) cc_final: 0.8719 (pmm)
REVERT: B  534 LYS cc_start: 0.7721 (ptpt) cc_final: 0.7491 (tptp)
REVERT: B  632 MET cc_start: 0.8985 (mmm) cc_final: 0.8088 (pmm)
REVERT: B  638 MET cc_start: 0.9183 (mmp) cc_final: 0.8930 (mmm)
REVERT: F  478 HIS cc_start: 0.8132 (m-70) cc_final: 0.7910 (m90)
REVERT: F  638 MET cc_start: 0.9197 (mpp) cc_final: 0.8796 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.2079
  time to fit residues: 26.7818
Evaluate side-chains
  66 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 93 optimal weight:    0.7980
   chunk 27 optimal weight:    8.9990
   chunk 7 optimal weight:    5.9990
   chunk 127 optimal weight:    9.9990
   chunk 3 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 44 optimal weight:    6.9990
   chunk 115 optimal weight:   20.0000
   chunk 125 optimal weight:    0.0050
   chunk 90 optimal weight:    4.9990
   chunk 120 optimal weight:    5.9990
   overall best weight:    3.1600

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 251 ASN
B 363 GLN
** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 540 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.098438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.079411 restraints weight = 110322.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.077875 restraints weight = 80196.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.077958 restraints weight = 83237.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6748
moved from start:          0.4169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  10881  Z= 0.201
  Angle     :  0.677   7.450  14841  Z= 0.360
  Chirality :  0.049   0.179   1677
  Planarity :  0.006   0.077   1863
  Dihedral  :  5.701  31.201   1433
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 25.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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: -1.17 (0.23), residues: 1318
  helix: -0.94 (0.45), residues: 120
  sheet: -0.65 (0.22), residues: 532
  loop : -0.73 (0.25), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP F 366 
 HIS   0.008   0.002   HIS B 515 
 PHE   0.019   0.002   PHE F 403 
 TYR   0.024   0.002   TYR B 507 
 ARG   0.011   0.001   ARG B 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04176 (  414)
  hydrogen bonds       : angle       7.34748 ( 1140)
  SS BOND              : bond        0.00506 (   13)
  SS BOND              : angle       1.11054 (   26)
  covalent geometry    : bond        0.00422 (10868)
  covalent geometry    : angle       0.67617 (14815)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 1.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.8933 (m-80) cc_final: 0.8478 (m-10)
REVERT: A  155 GLN cc_start: 0.8674 (tp-100) cc_final: 0.8123 (tp-100)
REVERT: B  244 MET cc_start: 0.6310 (tmm) cc_final: 0.6062 (tmm)
REVERT: B  443 MET cc_start: 0.5500 (mmm) cc_final: 0.5097 (tpt)
REVERT: B  447 TRP cc_start: 0.8931 (p-90) cc_final: 0.8636 (p-90)
REVERT: B  509 MET cc_start: 0.9129 (pmm) cc_final: 0.8887 (pmm)
REVERT: B  609 VAL cc_start: 0.9311 (t) cc_final: 0.9007 (m)
REVERT: B  638 MET cc_start: 0.9213 (mmp) cc_final: 0.8947 (mmm)
REVERT: F  261 MET cc_start: -0.0468 (pmm) cc_final: -0.0709 (pmm)
REVERT: F  478 HIS cc_start: 0.8467 (m-70) cc_final: 0.8189 (m90)
REVERT: F  638 MET cc_start: 0.9228 (mpp) cc_final: 0.8700 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.2040
  time to fit residues: 25.2447
Evaluate side-chains
  62 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 1.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 16 optimal weight:    0.4980
   chunk 4 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 20 optimal weight:    9.9990
   chunk 122 optimal weight:    8.9990
   chunk 28 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 112 optimal weight:   10.0000
   chunk 64 optimal weight:    7.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 267 GLN
F 369 ASN
** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 540 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.101768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.083606 restraints weight = 108755.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.082053 restraints weight = 92828.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.082347 restraints weight = 83530.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6578
moved from start:          0.4101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10881  Z= 0.119
  Angle     :  0.595   7.431  14841  Z= 0.317
  Chirality :  0.047   0.190   1677
  Planarity :  0.005   0.071   1863
  Dihedral  :  5.342  29.041   1433
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 17.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.50 %
    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: -0.93 (0.23), residues: 1318
  helix: -0.43 (0.46), residues: 120
  sheet: -0.52 (0.22), residues: 535
  loop : -0.60 (0.25), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP F 366 
 HIS   0.011   0.001   HIS A  47 
 PHE   0.015   0.001   PHE F 334 
 TYR   0.017   0.001   TYR A  82 
 ARG   0.003   0.000   ARG F 398 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03461 (  414)
  hydrogen bonds       : angle       6.77828 ( 1140)
  SS BOND              : bond        0.00361 (   13)
  SS BOND              : angle       1.00489 (   26)
  covalent geometry    : bond        0.00258 (10868)
  covalent geometry    : angle       0.59449 (14815)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4330.03 seconds
wall clock time: 76 minutes 10.54 seconds (4570.54 seconds total)