Starting phenix.real_space_refine
on Wed Feb  4 00:10:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9neb_49304/02_2026/9neb_49304_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9neb_49304/02_2026/9neb_49304.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9neb_49304/02_2026/9neb_49304_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9neb_49304/02_2026/9neb_49304_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9neb_49304/02_2026/9neb_49304.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9neb_49304/02_2026/9neb_49304.map"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    5034      2.51       5
     N    1406      2.21       5
     O    1362      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7830
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 2410
          Classifications: {'peptide': 312}
          Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 285}
          Chain breaks: 11
    Chain: "C"
      Number of atoms: 5420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 717, 5420
          Classifications: {'peptide': 717}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 5, 'PTRANS': 51, 'TRANS': 660}
          Chain breaks: 4
  Time building chain proxies: 1.85, per 1000 atoms: 0.24
  Number of scatterers: 7830
  At special positions: 0
  Unit cell: (94.77, 95.499, 144.342, 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      28     16.00
     O    1362      8.00
     N    1406      7.00
     C    5034      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 241.0 milliseconds
  

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1900

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 10 sheets defined
      45.3% alpha, 16.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 409 through 418
    Processing helix  chain 'A' and resid 427 through 438
    Processing helix  chain 'A' and resid 440 through 445
      removed outlier: 3.893A  pdb=" N   LEU A 444 " --> pdb=" O   ALA A 440 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   THR A 445 " --> pdb=" O   PRO A 441 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 440 through 445'
    Processing helix  chain 'A' and resid 457 through 471
    Processing helix  chain 'A' and resid 505 through 510
    Processing helix  chain 'A' and resid 554 through 560
      removed outlier: 3.646A  pdb=" N   ILE A 558 " --> pdb=" O   ASP A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 563
      No H-bonds generated for 'chain 'A' and resid 561 through 563'
    Processing helix  chain 'A' and resid 578 through 590
    Processing helix  chain 'A' and resid 603 through 611
    Processing helix  chain 'A' and resid 638 through 661
    Processing helix  chain 'A' and resid 776 through 793
    Processing helix  chain 'A' and resid 854 through 860
    Processing helix  chain 'A' and resid 861 through 866
      removed outlier: 6.120A  pdb=" N   ARG A 864 " --> pdb=" O   ALA A 861 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 57 through 65
    Processing helix  chain 'C' and resid 73 through 83
    Processing helix  chain 'C' and resid 89 through 93
    Processing helix  chain 'C' and resid 94 through 113
    Processing helix  chain 'C' and resid 161 through 172
      removed outlier: 3.540A  pdb=" N   LEU C 165 " --> pdb=" O   ASP C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 188
    Processing helix  chain 'C' and resid 189 through 194
      removed outlier: 3.732A  pdb=" N   SER C 193 " --> pdb=" O   PRO C 189 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 267 through 283
      removed outlier: 3.555A  pdb=" N   LEU C 271 " --> pdb=" O   SER C 267 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 297 through 301
      removed outlier: 3.615A  pdb=" N   GLU C 301 " --> pdb=" O   PRO C 298 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 334 through 344
    Processing helix  chain 'C' and resid 351 through 356
      removed outlier: 3.697A  pdb=" N   ARG C 354 " --> pdb=" O   VAL C 351 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 358 through 360
      No H-bonds generated for 'chain 'C' and resid 358 through 360'
    Processing helix  chain 'C' and resid 361 through 372
      removed outlier: 3.570A  pdb=" N   VAL C 365 " --> pdb=" O   ALA C 361 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 374 through 384
    Processing helix  chain 'C' and resid 412 through 425
    Processing helix  chain 'C' and resid 435 through 448
    Processing helix  chain 'C' and resid 451 through 469
      removed outlier: 3.956A  pdb=" N   GLY C 455 " --> pdb=" O   GLU C 451 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ARG C 460 " --> pdb=" O   ALA C 456 " (cutoff:3.500A)
      Proline residue:  C 463  - end of helix
    Processing helix  chain 'C' and resid 469 through 494
      removed outlier: 3.811A  pdb=" N   ARG C 473 " --> pdb=" O   CYS C 469 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   SER C 493 " --> pdb=" O   GLU C 489 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 516 through 542
    Processing helix  chain 'C' and resid 588 through 608
    Processing helix  chain 'C' and resid 618 through 638
    Processing helix  chain 'C' and resid 642 through 647
    Processing helix  chain 'C' and resid 662 through 672
      removed outlier: 4.947A  pdb=" N   GLY C 667 " --> pdb=" O   PHE C 664 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ALA C 668 " --> pdb=" O   ARG C 665 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   LEU C 669 " --> pdb=" O   GLY C 666 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 693 through 697
      removed outlier: 3.694A  pdb=" N   TYR C 697 " --> pdb=" O   VAL C 694 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 707 through 731
    Processing sheet with id=AA1, first strand: chain 'A' and resid 419 through 425
      removed outlier: 5.082A  pdb=" N   THR A 419 " --> pdb=" O   LEU A 887 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   LEU A 887 " --> pdb=" O   THR A 419 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   ARG A 421 " --> pdb=" O   HIS A 885 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   VAL A 773 " --> pdb=" O   LEU A 884 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   SER A 886 " --> pdb=" O   VAL A 773 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 456
      removed outlier: 5.363A  pdb=" N   VAL A 535 " --> pdb=" O   ILE A 615 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 624 through 630
      removed outlier: 4.136A  pdb=" N   PHE A 675 " --> pdb=" O   VAL A 843 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 56
      removed outlier: 6.084A  pdb=" N   TYR C  36 " --> pdb=" O   LEU C  18 " (cutoff:3.500A)
      removed outlier: 5.214A  pdb=" N   LEU C  18 " --> pdb=" O   TYR C  36 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   VAL C  38 " --> pdb=" O   ILE C  16 " (cutoff:3.500A)
      removed outlier: 5.633A  pdb=" N   ILE C  16 " --> pdb=" O   VAL C  38 " (cutoff:3.500A)
      removed outlier: 8.268A  pdb=" N   ARG C  40 " --> pdb=" O   SER C  14 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   SER C  14 " --> pdb=" O   ARG C  40 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 221 through 223
    Processing sheet with id=AA6, first strand: chain 'C' and resid 232 through 237
    Processing sheet with id=AA7, first strand: chain 'C' and resid 293 through 296
    Processing sheet with id=AA8, first strand: chain 'C' and resid 398 through 400
    Processing sheet with id=AA9, first strand: chain 'C' and resid 496 through 501
      removed outlier: 5.560A  pdb=" N   VAL C 498 " --> pdb=" O   VAL C 509 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   VAL C 509 " --> pdb=" O   VAL C 498 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLY C 556 " --> pdb=" O   ARG C 407 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   CYS C 409 " --> pdb=" O   LEU C 554 " (cutoff:3.500A)
      removed outlier: 5.466A  pdb=" N   LEU C 554 " --> pdb=" O   CYS C 409 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 648 through 650

    418 hydrogen bonds defined for protein.
    1164 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.24

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2586
        1.34 -     1.45: 1370
        1.45 -     1.57: 4038
        1.57 -     1.69: 0
        1.69 -     1.81: 38
  Bond restraints: 8032
  Sorted by residual:
  bond pdb=" CA  ARG C 303 "
       pdb=" C   ARG C 303 "
    ideal  model  delta    sigma   weight residual
    1.523  1.435  0.088 1.41e-02 5.03e+03 3.86e+01
  bond pdb=" C   VAL A 773 "
       pdb=" N   VAL A 774 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.038 1.26e-02 6.30e+03 8.87e+00
  bond pdb=" CB  VAL C 680 "
       pdb=" CG1 VAL C 680 "
    ideal  model  delta    sigma   weight residual
    1.521  1.456  0.065 3.30e-02 9.18e+02 3.87e+00
  bond pdb=" CB  VAL A 791 "
       pdb=" CG1 VAL A 791 "
    ideal  model  delta    sigma   weight residual
    1.521  1.462  0.059 3.30e-02 9.18e+02 3.24e+00
  bond pdb=" CB  THR A 438 "
       pdb=" CG2 THR A 438 "
    ideal  model  delta    sigma   weight residual
    1.521  1.462  0.059 3.30e-02 9.18e+02 3.19e+00
  ... (remaining 8027 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 10545
        2.01 -     4.01: 370
        4.01 -     6.02: 43
        6.02 -     8.02: 9
        8.02 -    10.03: 4
  Bond angle restraints: 10971
  Sorted by residual:
  angle pdb=" CB  ARG C  79 "
        pdb=" CG  ARG C  79 "
        pdb=" CD  ARG C  79 "
      ideal   model   delta    sigma   weight residual
     111.30  120.17   -8.87 2.30e+00 1.89e-01 1.49e+01
  angle pdb=" C   ARG C 254 "
        pdb=" N   ASP C 255 "
        pdb=" CA  ASP C 255 "
      ideal   model   delta    sigma   weight residual
     121.54  127.92   -6.38 1.91e+00 2.74e-01 1.11e+01
  angle pdb=" N   PRO A 672 "
        pdb=" CA  PRO A 672 "
        pdb=" C   PRO A 672 "
      ideal   model   delta    sigma   weight residual
     111.03  115.78   -4.75 1.54e+00 4.22e-01 9.49e+00
  angle pdb=" N   THR C 559 "
        pdb=" CA  THR C 559 "
        pdb=" C   THR C 559 "
      ideal   model   delta    sigma   weight residual
     114.04  110.27    3.77 1.24e+00 6.50e-01 9.26e+00
  angle pdb=" N   GLY A 514 "
        pdb=" CA  GLY A 514 "
        pdb=" C   GLY A 514 "
      ideal   model   delta    sigma   weight residual
     112.34  118.38   -6.04 2.04e+00 2.40e-01 8.77e+00
  ... (remaining 10966 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.09: 4232
       15.09 -    30.18: 417
       30.18 -    45.27: 78
       45.27 -    60.36: 13
       60.36 -    75.46: 6
  Dihedral angle restraints: 4746
    sinusoidal: 1807
      harmonic: 2939
  Sorted by residual:
  dihedral pdb=" CA  TYR C 309 "
           pdb=" C   TYR C 309 "
           pdb=" N   PHE C 310 "
           pdb=" CA  PHE C 310 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.22   27.78     0      5.00e+00 4.00e-02 3.09e+01
  dihedral pdb=" CA  GLY A 514 "
           pdb=" C   GLY A 514 "
           pdb=" N   PRO A 515 "
           pdb=" CA  PRO A 515 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.32   25.68     0      5.00e+00 4.00e-02 2.64e+01
  dihedral pdb=" CA  TYR A 772 "
           pdb=" C   TYR A 772 "
           pdb=" N   VAL A 773 "
           pdb=" CA  VAL A 773 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.33   25.67     0      5.00e+00 4.00e-02 2.64e+01
  ... (remaining 4743 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 863
       0.050 -    0.101: 285
       0.101 -    0.151: 86
       0.151 -    0.202: 6
       0.202 -    0.252: 1
  Chirality restraints: 1241
  Sorted by residual:
  chirality pdb=" CB  VAL C 494 "
            pdb=" CA  VAL C 494 "
            pdb=" CG1 VAL C 494 "
            pdb=" CG2 VAL C 494 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CA  ARG C  79 "
            pdb=" N   ARG C  79 "
            pdb=" C   ARG C  79 "
            pdb=" CB  ARG C  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.04e-01
  chirality pdb=" CB  THR C 320 "
            pdb=" CA  THR C 320 "
            pdb=" OG1 THR C 320 "
            pdb=" CG2 THR C 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.19 2.00e-01 2.50e+01 8.71e-01
  ... (remaining 1238 not shown)

  Planarity restraints: 1427
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 797 "    0.034 2.00e-02 2.50e+03   2.81e-02 1.38e+01
        pdb=" CG  PHE A 797 "   -0.063 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 797 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 797 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 797 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 797 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 797 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C  83 "    0.050 5.00e-02 4.00e+02   7.52e-02 9.04e+00
        pdb=" N   PRO C  84 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO C  84 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO C  84 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  87 "    0.046 5.00e-02 4.00e+02   6.98e-02 7.79e+00
        pdb=" N   PRO C  88 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO C  88 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO C  88 "    0.039 5.00e-02 4.00e+02
  ... (remaining 1424 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 86
        2.63 -     3.20: 6945
        3.20 -     3.77: 12153
        3.77 -     4.33: 16692
        4.33 -     4.90: 27782
  Nonbonded interactions: 63658
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C 205 "
            pdb=" OD2 ASP C 255 "
     model   vdw
     2.067 3.040
  nonbonded pdb=" O   ALA A 521 "
            pdb=" N   LEU A 523 "
     model   vdw
     2.092 3.120
  nonbonded pdb=" OG  SER C 450 "
            pdb=" OE1 GLU C 451 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" OH  TYR A 671 "
            pdb=" O   PRO A 767 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" OD1 ASP A 553 "
            pdb=" OH  TYR A 609 "
     model   vdw
     2.206 3.040
  ... (remaining 63653 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
========== 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.540
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:6.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.100   8032  Z= 0.338
  Angle     :  0.856  10.025  10971  Z= 0.453
  Chirality :  0.054   0.252   1241
  Planarity :  0.010   0.093   1427
  Dihedral  : 12.599  75.455   2846
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.73 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.25), residues: 995
  helix:  0.20 (0.24), residues: 423
  sheet: -0.12 (0.37), residues: 167
  loop : -1.76 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C  79 
 TYR   0.028   0.003   TYR A 772 
 PHE   0.063   0.004   PHE A 797 
 TRP   0.017   0.002   TRP A 552 
 HIS   0.012   0.002   HIS C 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00778 ( 8032)
  covalent geometry    : angle       0.85646 (10971)
  hydrogen bonds       : bond        0.13308 (  418)
  hydrogen bonds       : angle       6.24343 ( 1164)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
REVERT: A  537 ARG cc_start: 0.6958 (ttp80) cc_final: 0.6570 (ttp80)
REVERT: C   10 GLU cc_start: 0.7095 (tp30) cc_final: 0.6031 (tm-30)
REVERT: C  673 GLU cc_start: 0.7159 (tt0) cc_final: 0.6716 (tt0)
REVERT: C  675 TYR cc_start: 0.7732 (t80) cc_final: 0.6909 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 201
  average time/residue: 0.5060
  time to fit residues: 108.2223
Evaluate side-chains
  185 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0870
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    0.1980
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.3758

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

Flipped N/Q/H residues before XYZ refinement:
** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 820 HIS
** C  94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 486 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 = 0.3684 r_free = 0.3684 target = 0.122883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.113845 restraints weight = 11317.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 1.72
r_work: 0.3456 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8032  Z= 0.173
  Angle     :  0.702   9.770  10971  Z= 0.353
  Chirality :  0.046   0.174   1241
  Planarity :  0.008   0.077   1427
  Dihedral  :  5.262  25.115   1126
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 11.54 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.26), residues: 995
  helix:  1.02 (0.25), residues: 421
  sheet: -0.08 (0.37), residues: 171
  loop : -1.46 (0.29), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C 383 
 TYR   0.019   0.002   TYR A 772 
 PHE   0.020   0.002   PHE A 797 
 TRP   0.018   0.001   TRP C  98 
 HIS   0.005   0.001   HIS C 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 8032)
  covalent geometry    : angle       0.70189 (10971)
  hydrogen bonds       : bond        0.04868 (  418)
  hydrogen bonds       : angle       5.15783 ( 1164)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 195
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  868 PHE cc_start: 0.8455 (m-80) cc_final: 0.8153 (m-80)
REVERT: C   10 GLU cc_start: 0.7065 (tp30) cc_final: 0.5009 (mm-30)
REVERT: C   37 PHE cc_start: 0.7201 (m-10) cc_final: 0.6962 (m-80)
REVERT: C  299 GLU cc_start: 0.8058 (mp0) cc_final: 0.7735 (mp0)
REVERT: C  421 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7932 (mp)
REVERT: C  516 ASP cc_start: 0.7297 (m-30) cc_final: 0.7050 (m-30)
REVERT: C  525 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7135 (mm-30)
REVERT: C  673 GLU cc_start: 0.7694 (tt0) cc_final: 0.7135 (tt0)
  outliers start: 19
  outliers final: 10
  residues processed: 202
  average time/residue: 0.5015
  time to fit residues: 107.7367
Evaluate side-chains
  194 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 183
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  608 MET
Chi-restraints excluded: chain C residue  161 ASP
Chi-restraints excluded: chain C residue  292 VAL
Chi-restraints excluded: chain C residue  333 LEU
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  421 LEU
Chi-restraints excluded: chain C residue  587 ARG
Chi-restraints excluded: chain C residue  632 LEU
Chi-restraints excluded: chain C residue  651 SER
Chi-restraints excluded: chain C residue  694 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 98 optimal weight:    0.4980
   chunk 64 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 88 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C 172 HIS
** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 486 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 = 0.3658 r_free = 0.3658 target = 0.121058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.112253 restraints weight = 11250.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 1.69
r_work: 0.3427 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3287 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.079   8032  Z= 0.246
  Angle     :  0.699  11.263  10971  Z= 0.354
  Chirality :  0.048   0.240   1241
  Planarity :  0.008   0.076   1427
  Dihedral  :  5.220  25.006   1126
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 14.23 %
    Favored  : 82.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.26), residues: 995
  helix:  1.16 (0.25), residues: 421
  sheet: -0.06 (0.37), residues: 181
  loop : -1.43 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 537 
 TYR   0.025   0.002   TYR A 772 
 PHE   0.020   0.002   PHE C 310 
 TRP   0.015   0.001   TRP C  98 
 HIS   0.006   0.002   HIS C 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00583 ( 8032)
  covalent geometry    : angle       0.69916 (10971)
  hydrogen bonds       : bond        0.05145 (  418)
  hydrogen bonds       : angle       5.07303 ( 1164)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 190
  time to evaluate  : 0.426 
Fit side-chains
REVERT: A  797 PHE cc_start: 0.5580 (OUTLIER) cc_final: 0.4957 (m-10)
REVERT: A  868 PHE cc_start: 0.8446 (m-80) cc_final: 0.8194 (m-80)
REVERT: C   10 GLU cc_start: 0.7291 (tp30) cc_final: 0.5640 (tm-30)
REVERT: C  220 ILE cc_start: 0.8547 (mp) cc_final: 0.8330 (pp)
REVERT: C  231 GLU cc_start: 0.7739 (tt0) cc_final: 0.7537 (tt0)
REVERT: C  299 GLU cc_start: 0.8149 (mp0) cc_final: 0.7554 (mp0)
REVERT: C  421 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7944 (mp)
REVERT: C  460 ARG cc_start: 0.7328 (tpp80) cc_final: 0.7102 (mmp80)
REVERT: C  516 ASP cc_start: 0.7316 (m-30) cc_final: 0.7055 (m-30)
REVERT: C  525 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7125 (mm-30)
REVERT: C  673 GLU cc_start: 0.7772 (tt0) cc_final: 0.7516 (tt0)
REVERT: C  695 ASP cc_start: 0.7612 (m-30) cc_final: 0.7393 (m-30)
  outliers start: 28
  outliers final: 14
  residues processed: 201
  average time/residue: 0.4807
  time to fit residues: 103.0813
Evaluate side-chains
  201 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 185
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  608 MET
Chi-restraints excluded: chain A residue  797 PHE
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  292 VAL
Chi-restraints excluded: chain C residue  320 THR
Chi-restraints excluded: chain C residue  333 LEU
Chi-restraints excluded: chain C residue  421 LEU
Chi-restraints excluded: chain C residue  587 ARG
Chi-restraints excluded: chain C residue  632 LEU
Chi-restraints excluded: chain C residue  651 SER
Chi-restraints excluded: chain C residue  694 VAL
Chi-restraints excluded: chain C residue  721 LEU
Chi-restraints excluded: chain C residue  738 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 67 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0970
   chunk 62 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 83 optimal weight:    0.0010
   chunk 60 optimal weight:    0.0060
   chunk 31 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 96 optimal weight:    0.0170
   overall best weight:    0.1438

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

Flipped N/Q/H residues before XYZ refinement:
** A 860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 HIS
** C 242 HIS ** 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 = 0.3707 r_free = 0.3707 target = 0.124397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.115386 restraints weight = 11492.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 1.75
r_work: 0.3479 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3339 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8032  Z= 0.124
  Angle     :  0.608   7.691  10971  Z= 0.306
  Chirality :  0.043   0.159   1241
  Planarity :  0.007   0.073   1427
  Dihedral  :  4.703  23.376   1126
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.79 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.27), residues: 995
  helix:  1.62 (0.26), residues: 414
  sheet:  0.05 (0.37), residues: 182
  loop : -1.19 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 537 
 TYR   0.017   0.001   TYR A 772 
 PHE   0.012   0.001   PHE A 856 
 TRP   0.015   0.001   TRP C  98 
 HIS   0.004   0.001   HIS C 548 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8032)
  covalent geometry    : angle       0.60762 (10971)
  hydrogen bonds       : bond        0.03981 (  418)
  hydrogen bonds       : angle       4.66431 ( 1164)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 193
  time to evaluate  : 0.338 
Fit side-chains
REVERT: A  868 PHE cc_start: 0.8396 (m-80) cc_final: 0.8104 (m-80)
REVERT: C   10 GLU cc_start: 0.7015 (tp30) cc_final: 0.5643 (tm-30)
REVERT: C   37 PHE cc_start: 0.7146 (m-10) cc_final: 0.6913 (m-80)
REVERT: C  220 ILE cc_start: 0.8557 (mp) cc_final: 0.8318 (pp)
REVERT: C  421 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7909 (mp)
REVERT: C  460 ARG cc_start: 0.7290 (tpp80) cc_final: 0.7049 (mmp80)
REVERT: C  516 ASP cc_start: 0.7310 (m-30) cc_final: 0.7025 (m-30)
REVERT: C  525 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7075 (mm-30)
REVERT: C  540 ARG cc_start: 0.7648 (ttm110) cc_final: 0.7356 (ttm170)
REVERT: C  673 GLU cc_start: 0.7641 (tt0) cc_final: 0.7142 (tt0)
  outliers start: 24
  outliers final: 10
  residues processed: 205
  average time/residue: 0.4570
  time to fit residues: 99.8286
Evaluate side-chains
  194 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 183
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain C residue  138 ARG
Chi-restraints excluded: chain C residue  161 ASP
Chi-restraints excluded: chain C residue  196 SER
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  320 THR
Chi-restraints excluded: chain C residue  421 LEU
Chi-restraints excluded: chain C residue  632 LEU
Chi-restraints excluded: chain C residue  694 VAL
Chi-restraints excluded: chain C residue  743 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 96 optimal weight:    0.0870
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
A 860 HIS
C 172 HIS
** C 242 HIS ** 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 = 0.3665 r_free = 0.3665 target = 0.121274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.112325 restraints weight = 11361.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 1.72
r_work: 0.3433 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.086   8032  Z= 0.223
  Angle     :  0.674   8.449  10971  Z= 0.340
  Chirality :  0.047   0.273   1241
  Planarity :  0.007   0.070   1427
  Dihedral  :  4.919  23.841   1126
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 17.95 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.26), residues: 995
  helix:  1.49 (0.26), residues: 420
  sheet:  0.01 (0.37), residues: 187
  loop : -1.36 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  61 
 TYR   0.022   0.002   TYR A 772 
 PHE   0.018   0.002   PHE C 119 
 TRP   0.012   0.001   TRP C  98 
 HIS   0.006   0.001   HIS C 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00528 ( 8032)
  covalent geometry    : angle       0.67442 (10971)
  hydrogen bonds       : bond        0.04730 (  418)
  hydrogen bonds       : angle       4.81913 ( 1164)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 191
  time to evaluate  : 0.310 
Fit side-chains
REVERT: A  797 PHE cc_start: 0.5688 (OUTLIER) cc_final: 0.5080 (m-10)
REVERT: A  826 TYR cc_start: 0.8473 (m-80) cc_final: 0.8194 (m-80)
REVERT: A  868 PHE cc_start: 0.8448 (m-80) cc_final: 0.8216 (m-80)
REVERT: C   10 GLU cc_start: 0.7275 (tp30) cc_final: 0.6186 (tm-30)
REVERT: C   37 PHE cc_start: 0.7205 (m-10) cc_final: 0.6951 (m-80)
REVERT: C  220 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8215 (mt)
REVERT: C  421 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7856 (mp)
REVERT: C  516 ASP cc_start: 0.7250 (m-30) cc_final: 0.6983 (m-30)
REVERT: C  525 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7118 (mm-30)
REVERT: C  540 ARG cc_start: 0.7617 (ttm110) cc_final: 0.7327 (ttm170)
REVERT: C  673 GLU cc_start: 0.7763 (tt0) cc_final: 0.7244 (tt0)
  outliers start: 26
  outliers final: 15
  residues processed: 202
  average time/residue: 0.4216
  time to fit residues: 90.7675
Evaluate side-chains
  204 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 186
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  797 PHE
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  196 SER
Chi-restraints excluded: chain C residue  220 ILE
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  292 VAL
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  320 THR
Chi-restraints excluded: chain C residue  421 LEU
Chi-restraints excluded: chain C residue  512 VAL
Chi-restraints excluded: chain C residue  587 ARG
Chi-restraints excluded: chain C residue  632 LEU
Chi-restraints excluded: chain C residue  694 VAL
Chi-restraints excluded: chain C residue  743 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 88 optimal weight:    0.5980
   chunk 76 optimal weight:    0.4980
   chunk 79 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   chunk 59 optimal weight:    0.5980
   chunk 101 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
C 112 GLN
C 172 HIS
** C 242 HIS ** 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 = 0.3671 r_free = 0.3671 target = 0.121738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.112727 restraints weight = 11340.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 1.72
r_work: 0.3440 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3297 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071   8032  Z= 0.194
  Angle     :  0.637   7.414  10971  Z= 0.323
  Chirality :  0.046   0.168   1241
  Planarity :  0.007   0.068   1427
  Dihedral  :  4.835  23.783   1126
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 18.21 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.29 (0.26), residues: 995
  helix:  1.66 (0.26), residues: 413
  sheet:  0.03 (0.37), residues: 186
  loop : -1.34 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  61 
 TYR   0.017   0.002   TYR A 772 
 PHE   0.020   0.002   PHE C 119 
 TRP   0.015   0.001   TRP C  98 
 HIS   0.005   0.001   HIS C 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 8032)
  covalent geometry    : angle       0.63743 (10971)
  hydrogen bonds       : bond        0.04522 (  418)
  hydrogen bonds       : angle       4.80639 ( 1164)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 193
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  797 PHE cc_start: 0.5700 (OUTLIER) cc_final: 0.5183 (m-80)
REVERT: A  868 PHE cc_start: 0.8457 (m-80) cc_final: 0.8209 (m-80)
REVERT: C   10 GLU cc_start: 0.7279 (tp30) cc_final: 0.5953 (tm-30)
REVERT: C   37 PHE cc_start: 0.7207 (m-10) cc_final: 0.6945 (m-80)
REVERT: C   79 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.7095 (tpp-160)
REVERT: C  220 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8191 (mt)
REVERT: C  310 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7294 (p90)
REVERT: C  421 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7880 (mp)
REVERT: C  516 ASP cc_start: 0.7234 (m-30) cc_final: 0.6976 (m-30)
REVERT: C  525 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7094 (mm-30)
REVERT: C  540 ARG cc_start: 0.7637 (ttm110) cc_final: 0.7334 (ttm170)
REVERT: C  673 GLU cc_start: 0.7753 (tt0) cc_final: 0.7288 (tt0)
  outliers start: 29
  outliers final: 15
  residues processed: 205
  average time/residue: 0.4328
  time to fit residues: 94.7277
Evaluate side-chains
  205 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 185
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  797 PHE
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  126 SER
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  161 ASP
Chi-restraints excluded: chain C residue  196 SER
Chi-restraints excluded: chain C residue  220 ILE
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  292 VAL
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  310 PHE
Chi-restraints excluded: chain C residue  421 LEU
Chi-restraints excluded: chain C residue  587 ARG
Chi-restraints excluded: chain C residue  632 LEU
Chi-restraints excluded: chain C residue  706 VAL
Chi-restraints excluded: chain C residue  743 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 96 optimal weight:    0.5980
   chunk 91 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 72 optimal weight:    0.0570
   chunk 66 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 28 optimal weight:    0.4980
   chunk 44 optimal weight:    3.9990
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
C 112 GLN
C 172 HIS
** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 486 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 = 0.3664 r_free = 0.3664 target = 0.121292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.112250 restraints weight = 11387.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 1.73
r_work: 0.3432 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3290 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075   8032  Z= 0.214
  Angle     :  0.658   7.481  10971  Z= 0.333
  Chirality :  0.048   0.330   1241
  Planarity :  0.007   0.069   1427
  Dihedral  :  4.892  23.889   1126
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 18.85 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.27), residues: 995
  helix:  1.62 (0.26), residues: 413
  sheet: -0.04 (0.37), residues: 192
  loop : -1.36 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  61 
 TYR   0.014   0.002   TYR C 256 
 PHE   0.022   0.002   PHE C 119 
 TRP   0.014   0.001   TRP C  98 
 HIS   0.006   0.001   HIS C 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 ( 8032)
  covalent geometry    : angle       0.65758 (10971)
  hydrogen bonds       : bond        0.04669 (  418)
  hydrogen bonds       : angle       4.85741 ( 1164)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 191
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  797 PHE cc_start: 0.5783 (OUTLIER) cc_final: 0.5241 (m-80)
REVERT: A  868 PHE cc_start: 0.8459 (m-80) cc_final: 0.8198 (m-80)
REVERT: C   10 GLU cc_start: 0.7234 (tp30) cc_final: 0.6018 (tm-30)
REVERT: C   79 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.7100 (tpp-160)
REVERT: C  220 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8157 (mt)
REVERT: C  231 GLU cc_start: 0.7741 (tt0) cc_final: 0.7484 (tt0)
REVERT: C  310 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7213 (p90)
REVERT: C  421 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7876 (mp)
REVERT: C  525 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7109 (mm-30)
REVERT: C  540 ARG cc_start: 0.7640 (ttm110) cc_final: 0.7343 (ttm170)
REVERT: C  673 GLU cc_start: 0.7764 (tt0) cc_final: 0.7286 (tt0)
  outliers start: 31
  outliers final: 20
  residues processed: 204
  average time/residue: 0.4468
  time to fit residues: 97.3073
Evaluate side-chains
  211 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 186
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  797 PHE
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain C residue   45 GLU
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  161 ASP
Chi-restraints excluded: chain C residue  187 ASP
Chi-restraints excluded: chain C residue  196 SER
Chi-restraints excluded: chain C residue  220 ILE
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  292 VAL
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  310 PHE
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  355 VAL
Chi-restraints excluded: chain C residue  421 LEU
Chi-restraints excluded: chain C residue  512 VAL
Chi-restraints excluded: chain C residue  587 ARG
Chi-restraints excluded: chain C residue  632 LEU
Chi-restraints excluded: chain C residue  706 VAL
Chi-restraints excluded: chain C residue  743 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 75 optimal weight:    0.0970
   chunk 55 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 100 optimal weight:    0.5980
   chunk 88 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 79 optimal weight:    0.2980
   chunk 32 optimal weight:    1.9990
   chunk 67 optimal weight:    0.3980
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
C 172 HIS
** C 242 HIS ** 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 = 0.3680 r_free = 0.3680 target = 0.122293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.113270 restraints weight = 11406.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.74
r_work: 0.3449 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3306 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   8032  Z= 0.171
  Angle     :  0.634   7.386  10971  Z= 0.321
  Chirality :  0.045   0.166   1241
  Planarity :  0.007   0.068   1427
  Dihedral  :  4.769  23.177   1126
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 19.62 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.27), residues: 995
  helix:  1.73 (0.26), residues: 413
  sheet:  0.02 (0.37), residues: 187
  loop : -1.27 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  61 
 TYR   0.013   0.002   TYR C 256 
 PHE   0.021   0.002   PHE C 119 
 TRP   0.017   0.001   TRP C  98 
 HIS   0.005   0.001   HIS C 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 8032)
  covalent geometry    : angle       0.63411 (10971)
  hydrogen bonds       : bond        0.04394 (  418)
  hydrogen bonds       : angle       4.75592 ( 1164)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 191
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A  792 LEU cc_start: 0.8121 (mt) cc_final: 0.7917 (mm)
REVERT: A  797 PHE cc_start: 0.5767 (OUTLIER) cc_final: 0.5151 (m-80)
REVERT: A  868 PHE cc_start: 0.8444 (m-80) cc_final: 0.8185 (m-80)
REVERT: C   10 GLU cc_start: 0.7173 (tp30) cc_final: 0.5979 (tm-30)
REVERT: C   79 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7097 (tpp-160)
REVERT: C  220 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8252 (pp)
REVERT: C  231 GLU cc_start: 0.7762 (tt0) cc_final: 0.7493 (tt0)
REVERT: C  310 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.7217 (p90)
REVERT: C  516 ASP cc_start: 0.7250 (m-30) cc_final: 0.6989 (m-30)
REVERT: C  525 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7128 (mm-30)
REVERT: C  540 ARG cc_start: 0.7633 (ttm110) cc_final: 0.7348 (ttm170)
REVERT: C  673 GLU cc_start: 0.7756 (tt0) cc_final: 0.7295 (tt0)
  outliers start: 28
  outliers final: 18
  residues processed: 202
  average time/residue: 0.4614
  time to fit residues: 99.2280
Evaluate side-chains
  207 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 185
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  797 PHE
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  161 ASP
Chi-restraints excluded: chain C residue  187 ASP
Chi-restraints excluded: chain C residue  196 SER
Chi-restraints excluded: chain C residue  220 ILE
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  292 VAL
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  310 PHE
Chi-restraints excluded: chain C residue  355 VAL
Chi-restraints excluded: chain C residue  409 CYS
Chi-restraints excluded: chain C residue  421 LEU
Chi-restraints excluded: chain C residue  460 ARG
Chi-restraints excluded: chain C residue  512 VAL
Chi-restraints excluded: chain C residue  587 ARG
Chi-restraints excluded: chain C residue  632 LEU
Chi-restraints excluded: chain C residue  706 VAL
Chi-restraints excluded: chain C residue  743 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 29 optimal weight:    0.2980
   chunk 30 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   chunk 91 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0060
   chunk 92 optimal weight:    0.7980
   chunk 100 optimal weight:    0.4980
   overall best weight:    0.4196

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

Flipped N/Q/H residues before XYZ refinement:
C 112 GLN
C 172 HIS
** C 242 HIS ** 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 = 0.3690 r_free = 0.3690 target = 0.122892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.113649 restraints weight = 11274.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 1.73
r_work: 0.3447 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8032  Z= 0.167
  Angle     :  0.637   7.460  10971  Z= 0.322
  Chirality :  0.046   0.374   1241
  Planarity :  0.007   0.068   1427
  Dihedral  :  4.695  23.084   1126
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 20.77 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.44 (0.27), residues: 995
  helix:  1.79 (0.26), residues: 413
  sheet:  0.08 (0.37), residues: 191
  loop : -1.24 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  61 
 TYR   0.013   0.002   TYR C 212 
 PHE   0.021   0.002   PHE C 119 
 TRP   0.015   0.001   TRP C  98 
 HIS   0.005   0.001   HIS C 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 8032)
  covalent geometry    : angle       0.63685 (10971)
  hydrogen bonds       : bond        0.04319 (  418)
  hydrogen bonds       : angle       4.74579 ( 1164)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 190
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: A  792 LEU cc_start: 0.8107 (mt) cc_final: 0.7906 (mm)
REVERT: A  797 PHE cc_start: 0.5817 (OUTLIER) cc_final: 0.5268 (m-80)
REVERT: A  826 TYR cc_start: 0.8428 (m-80) cc_final: 0.8175 (m-80)
REVERT: A  868 PHE cc_start: 0.8427 (m-80) cc_final: 0.8147 (m-80)
REVERT: C   10 GLU cc_start: 0.7188 (tp30) cc_final: 0.5980 (tm-30)
REVERT: C   79 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.7082 (tpp-160)
REVERT: C  220 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8288 (pp)
REVERT: C  231 GLU cc_start: 0.7787 (tt0) cc_final: 0.7537 (tt0)
REVERT: C  310 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7228 (p90)
REVERT: C  379 GLU cc_start: 0.7636 (tt0) cc_final: 0.7202 (tm-30)
REVERT: C  516 ASP cc_start: 0.7247 (m-30) cc_final: 0.6987 (m-30)
REVERT: C  525 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7105 (mm-30)
REVERT: C  540 ARG cc_start: 0.7630 (ttm110) cc_final: 0.7364 (ttm170)
REVERT: C  673 GLU cc_start: 0.7750 (tt0) cc_final: 0.7203 (tt0)
  outliers start: 25
  outliers final: 18
  residues processed: 202
  average time/residue: 0.4763
  time to fit residues: 102.3097
Evaluate side-chains
  209 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 187
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  797 PHE
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  161 ASP
Chi-restraints excluded: chain C residue  187 ASP
Chi-restraints excluded: chain C residue  220 ILE
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  292 VAL
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  310 PHE
Chi-restraints excluded: chain C residue  355 VAL
Chi-restraints excluded: chain C residue  409 CYS
Chi-restraints excluded: chain C residue  421 LEU
Chi-restraints excluded: chain C residue  460 ARG
Chi-restraints excluded: chain C residue  512 VAL
Chi-restraints excluded: chain C residue  587 ARG
Chi-restraints excluded: chain C residue  632 LEU
Chi-restraints excluded: chain C residue  743 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0470
   chunk 72 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 87 optimal weight:    0.6980
   chunk 59 optimal weight:    0.4980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
C 112 GLN
C 172 HIS
** C 242 HIS ** 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 = 0.3684 r_free = 0.3684 target = 0.122498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.113304 restraints weight = 11074.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 1.71
r_work: 0.3440 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   8032  Z= 0.194
  Angle     :  0.652   7.515  10971  Z= 0.328
  Chirality :  0.046   0.167   1241
  Planarity :  0.007   0.068   1427
  Dihedral  :  4.773  23.468   1126
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 21.03 %
    Favored  : 75.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.27), residues: 995
  helix:  1.77 (0.26), residues: 413
  sheet:  0.01 (0.37), residues: 193
  loop : -1.28 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  61 
 TYR   0.013   0.002   TYR C  64 
 PHE   0.022   0.002   PHE C 119 
 TRP   0.014   0.001   TRP C  98 
 HIS   0.005   0.001   HIS C 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 8032)
  covalent geometry    : angle       0.65155 (10971)
  hydrogen bonds       : bond        0.04486 (  418)
  hydrogen bonds       : angle       4.77687 ( 1164)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 188
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
REVERT: A  797 PHE cc_start: 0.5903 (OUTLIER) cc_final: 0.5419 (m-80)
REVERT: A  868 PHE cc_start: 0.8431 (m-80) cc_final: 0.8181 (m-80)
REVERT: C   10 GLU cc_start: 0.7228 (tp30) cc_final: 0.6034 (tm-30)
REVERT: C   79 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.7076 (tpp-160)
REVERT: C  220 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8281 (pp)
REVERT: C  231 GLU cc_start: 0.7792 (tt0) cc_final: 0.7543 (tt0)
REVERT: C  310 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7279 (p90)
REVERT: C  516 ASP cc_start: 0.7240 (m-30) cc_final: 0.6987 (m-30)
REVERT: C  525 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7111 (mm-30)
REVERT: C  673 GLU cc_start: 0.7733 (tt0) cc_final: 0.7248 (tt0)
  outliers start: 25
  outliers final: 19
  residues processed: 198
  average time/residue: 0.4915
  time to fit residues: 103.5861
Evaluate side-chains
  210 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 187
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  797 PHE
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain C residue   79 ARG
Chi-restraints excluded: chain C residue  126 SER
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  161 ASP
Chi-restraints excluded: chain C residue  187 ASP
Chi-restraints excluded: chain C residue  220 ILE
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  292 VAL
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  310 PHE
Chi-restraints excluded: chain C residue  355 VAL
Chi-restraints excluded: chain C residue  409 CYS
Chi-restraints excluded: chain C residue  421 LEU
Chi-restraints excluded: chain C residue  460 ARG
Chi-restraints excluded: chain C residue  512 VAL
Chi-restraints excluded: chain C residue  587 ARG
Chi-restraints excluded: chain C residue  632 LEU
Chi-restraints excluded: chain C residue  706 VAL
Chi-restraints excluded: chain C residue  743 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 80 optimal weight:    0.0270
   chunk 43 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 101 optimal weight:    0.3980
   chunk 79 optimal weight:    0.6980
   chunk 90 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
C 112 GLN
C 172 HIS
** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 486 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 = 0.3675 r_free = 0.3675 target = 0.121984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.113105 restraints weight = 11280.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 1.67
r_work: 0.3448 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   8032  Z= 0.176
  Angle     :  0.653   7.590  10971  Z= 0.331
  Chirality :  0.046   0.165   1241
  Planarity :  0.007   0.068   1427
  Dihedral  :  4.711  23.142   1126
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 21.67 %
    Favored  : 75.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.27), residues: 995
  helix:  1.79 (0.26), residues: 413
  sheet: -0.02 (0.37), residues: 192
  loop : -1.26 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 473 
 TYR   0.013   0.002   TYR C 212 
 PHE   0.021   0.002   PHE C 119 
 TRP   0.015   0.001   TRP C  98 
 HIS   0.005   0.001   HIS C 710 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 8032)
  covalent geometry    : angle       0.65291 (10971)
  hydrogen bonds       : bond        0.04393 (  418)
  hydrogen bonds       : angle       4.75165 ( 1164)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3044.06 seconds
wall clock time: 52 minutes 25.34 seconds (3145.34 seconds total)