Starting phenix.real_space_refine
on Wed Jun  3 10:14:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9z1n_73750/06_2026/9z1n_73750.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9z1n_73750/06_2026/9z1n_73750.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.44
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9z1n_73750/06_2026/9z1n_73750.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9z1n_73750/06_2026/9z1n_73750.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9z1n_73750/06_2026/9z1n_73750.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9z1n_73750/06_2026/9z1n_73750.cif"
  }
  resolution = 3.44
  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=  -0.000 sd=   0.009
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      14      5.16       5
     C    1966      2.51       5
     N     524      2.21       5
     O     593      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3097
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 2145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 269, 2145
          Classifications: {'peptide': 269}
          Link IDs: {'PTRANS': 18, 'TRANS': 250}
    Chain: "E"
      Number of atoms: 952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 952
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 3, 'TRANS': 122}
  Time building chain proxies: 1.00, per 1000 atoms: 0.32
  Number of scatterers: 3097
  At special positions: 0
  Unit cell: (61.088, 92.0746, 104.469, 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      14     16.00
     O     593      8.00
     N     524      7.00
     C    1966      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 333 " - pdb=" SG  CYS B 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 376 " - pdb=" SG  CYS B 429 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 388 " - pdb=" SG  CYS B 521 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 477 " - pdb=" SG  CYS B 484 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  50 " - pdb=" SG  CYS E 104 " 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: 0.25
  Conformation dependent library (CDL) restraints added in 81.9 milliseconds
  

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  724

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 7 sheets defined
      8.1% alpha, 23.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'B' and resid 364 through 368
      removed outlier: 3.545A  pdb=" N   PHE B 368 " --> pdb=" O   LEU B 365 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 384
      removed outlier: 4.219A  pdb=" N   LEU B 384 " --> pdb=" O   PRO B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 404
      No H-bonds generated for 'chain 'B' and resid 402 through 404'
    Processing helix  chain 'B' and resid 414 through 419
      removed outlier: 3.817A  pdb=" N   TYR B 418 " --> pdb=" O   ASN B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 498 through 501
    Processing helix  chain 'E' and resid 62 through 65
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.612A  pdb=" N   THR E  91 " --> pdb=" O   LEU E  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 321 through 322
      removed outlier: 6.783A  pdb=" N   GLU B 321 " --> pdb=" O   ASN B 536 " (cutoff:3.500A)
      removed outlier: 8.267A  pdb=" N   ASN B 538 " --> pdb=" O   GLU B 321 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   PHE B 539 " --> pdb=" O   LEU B 542 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 351 through 355
      removed outlier: 4.221A  pdb=" N   VAL B 392 " --> pdb=" O   ILE B 355 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 449 through 451
    Processing sheet with id=AA4, first strand: chain 'B' and resid 470 through 471
      removed outlier: 3.736A  pdb=" N   TYR B 485 " --> pdb=" O   TYR B 470 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 561 through 563
      removed outlier: 4.262A  pdb=" N   ALA B 571 " --> pdb=" O   GLY B 562 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 6 through 7
      removed outlier: 3.823A  pdb=" N   SER E  21 " --> pdb=" O   SER E   7 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.996A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 126 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   THR E  34 " --> pdb=" O   CYS E  50 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   CYS E  50 " --> pdb=" O   THR E  34 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)

    64 hydrogen bonds defined for protein.
    153 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: 0.27

  Time building geometry restraints manager: 0.34 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 994
        1.35 -     1.47: 850
        1.47 -     1.60: 1319
        1.60 -     1.72: 0
        1.72 -     1.84: 15
  Bond restraints: 3178
  Sorted by residual:
  bond pdb=" N   CYS E 104 "
       pdb=" CA  CYS E 104 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.19e-02 7.06e+03 6.12e+00
  bond pdb=" N   ILE E  51 "
       pdb=" CA  ILE E  51 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.24e-02 6.50e+03 5.94e+00
  bond pdb=" N   VAL E 103 "
       pdb=" CA  VAL E 103 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.029 1.19e-02 7.06e+03 5.78e+00
  bond pdb=" C   LYS B 459 "
       pdb=" N   PRO B 460 "
    ideal  model  delta    sigma   weight residual
    1.330  1.355 -0.025 1.19e-02 7.06e+03 4.39e+00
  bond pdb=" CB  PRO B 482 "
       pdb=" CG  PRO B 482 "
    ideal  model  delta    sigma   weight residual
    1.492  1.593 -0.101 5.00e-02 4.00e+02 4.08e+00
  ... (remaining 3173 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 4129
        2.00 -     4.00: 153
        4.00 -     5.99: 28
        5.99 -     7.99: 6
        7.99 -     9.99: 1
  Bond angle restraints: 4317
  Sorted by residual:
  angle pdb=" CA  PRO B 482 "
        pdb=" N   PRO B 482 "
        pdb=" CD  PRO B 482 "
      ideal   model   delta    sigma   weight residual
     112.00  102.01    9.99 1.40e+00 5.10e-01 5.09e+01
  angle pdb=" CA  GLN E  82 "
        pdb=" CB  GLN E  82 "
        pdb=" CG  GLN E  82 "
      ideal   model   delta    sigma   weight residual
     114.10  121.29   -7.19 2.00e+00 2.50e-01 1.29e+01
  angle pdb=" C   LYS E  76 "
        pdb=" N   ASN E  77 "
        pdb=" CA  ASN E  77 "
      ideal   model   delta    sigma   weight residual
     121.54  128.15   -6.61 1.91e+00 2.74e-01 1.20e+01
  angle pdb=" N   ILE E  51 "
        pdb=" CA  ILE E  51 "
        pdb=" C   ILE E  51 "
      ideal   model   delta    sigma   weight residual
     108.58  103.69    4.89 1.44e+00 4.82e-01 1.15e+01
  angle pdb=" O   SER E  49 "
        pdb=" C   SER E  49 "
        pdb=" N   CYS E  50 "
      ideal   model   delta    sigma   weight residual
     123.42  119.81    3.61 1.07e+00 8.73e-01 1.14e+01
  ... (remaining 4312 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.02: 1647
       16.02 -    32.05: 175
       32.05 -    48.07: 47
       48.07 -    64.09: 7
       64.09 -    80.12: 6
  Dihedral angle restraints: 1882
    sinusoidal: 740
      harmonic: 1142
  Sorted by residual:
  dihedral pdb=" CB  CYS B 477 "
           pdb=" SG  CYS B 477 "
           pdb=" SG  CYS B 484 "
           pdb=" CB  CYS B 484 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -146.64   60.64     1      1.00e+01 1.00e-02 4.89e+01
  dihedral pdb=" CB  CYS B 388 "
           pdb=" SG  CYS B 388 "
           pdb=" SG  CYS B 521 "
           pdb=" CB  CYS B 521 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   53.87   39.13     1      1.00e+01 1.00e-02 2.15e+01
  dihedral pdb=" CB  CYS E  22 "
           pdb=" SG  CYS E  22 "
           pdb=" SG  CYS E  96 "
           pdb=" CB  CYS E  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   57.53   35.47     1      1.00e+01 1.00e-02 1.78e+01
  ... (remaining 1879 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 296
       0.042 -    0.084: 117
       0.084 -    0.126: 38
       0.126 -    0.167: 7
       0.167 -    0.209: 3
  Chirality restraints: 461
  Sorted by residual:
  chirality pdb=" CB  ILE B 323 "
            pdb=" CA  ILE B 323 "
            pdb=" CG1 ILE B 323 "
            pdb=" CG2 ILE B 323 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CA  VAL E 103 "
            pdb=" N   VAL E 103 "
            pdb=" C   VAL E 103 "
            pdb=" CB  VAL E 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  ILE E  51 "
            pdb=" N   ILE E  51 "
            pdb=" C   ILE E  51 "
            pdb=" CB  ILE E  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.70e-01
  ... (remaining 458 not shown)

  Planarity restraints: 564
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 481 "    0.094 5.00e-02 4.00e+02   1.36e-01 2.96e+01
        pdb=" N   PRO B 482 "   -0.235 5.00e-02 4.00e+02
        pdb=" CA  PRO B 482 "    0.068 5.00e-02 4.00e+02
        pdb=" CD  PRO B 482 "    0.072 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 459 "   -0.035 5.00e-02 4.00e+02   5.27e-02 4.44e+00
        pdb=" N   PRO B 460 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO B 460 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 460 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER E  49 "    0.009 2.00e-02 2.50e+03   1.76e-02 3.10e+00
        pdb=" C   SER E  49 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   SER E  49 "    0.011 2.00e-02 2.50e+03
        pdb=" N   CYS E  50 "    0.010 2.00e-02 2.50e+03
  ... (remaining 561 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 102
        2.70 -     3.25: 2813
        3.25 -     3.80: 4384
        3.80 -     4.35: 5741
        4.35 -     4.90: 10061
  Nonbonded interactions: 23101
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 320 "
            pdb=" OE1 GLU B 321 "
     model   vdw
     2.154 3.040
  nonbonded pdb=" NH2 ARG B 451 "
            pdb=" O   SER B 466 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" N   LYS E  87 "
            pdb=" OD2 ASP E  90 "
     model   vdw
     2.388 3.120
  nonbonded pdb=" O   ASN E  84 "
            pdb=" OG  SER E  85 "
     model   vdw
     2.389 3.040
  nonbonded pdb=" NH1 ARG B 494 "
            pdb=" OH  TYR B 497 "
     model   vdw
     2.394 3.120
  ... (remaining 23096 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:             6.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     4.360
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  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:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
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   0.101   3184  Z= 0.251
  Angle     :  0.933   9.988   4329  Z= 0.515
  Chirality :  0.052   0.209    461
  Planarity :  0.009   0.136    564
  Dihedral  : 14.660  80.117   1140
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 2.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.46 (0.39), residues: 391
  helix: -3.81 (1.25), residues: 13
  sheet: -0.73 (0.44), residues: 108
  loop : -2.04 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 573 
 TYR   0.014   0.002   TYR E 110 
 PHE   0.017   0.002   PHE B 326 
 TRP   0.013   0.002   TRP B 350 
 HIS   0.013   0.002   HIS E  30 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00544 /  0.25 ( 3178)
  covalent geometry    : angle       0.92626 /  0.51 ( 4317)
  SS BOND              : bond        0.00782 /  0.30 (    6)
  SS BOND              : angle       2.37746 /  1.42 (   12)
  hydrogen bonds       : bond        0.17594 / 11.73 (   64)
  hydrogen bonds       : angle       8.67115 /  5.75 (  153)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: E   73 ASP cc_start: 0.8287 (t0) cc_final: 0.8026 (t0)
REVERT: E   99 ASP cc_start: 0.8506 (t0) cc_final: 0.8217 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.0702
  time to fit residues: 7.1619
Evaluate side-chains
  58 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    0.0170
   chunk 26 optimal weight:    0.1980
   chunk 2 optimal weight:    0.1980
   chunk 16 optimal weight:    0.1980
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.2618

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

Flipped N/Q/H residues before XYZ refinement:
B 414 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.080945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.065736 restraints weight = 8531.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 4.21
r_work: 0.2842 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3184  Z= 0.112
  Angle     :  0.572   5.061   4329  Z= 0.302
  Chirality :  0.044   0.169    461
  Planarity :  0.006   0.067    564
  Dihedral  :  4.562  16.092    435
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  7.94 %
    Favored  : 90.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.05 (0.41), residues: 391
  helix: -5.57 (0.26), residues: 7
  sheet: -0.12 (0.46), residues: 107
  loop : -1.90 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 494 
 TYR   0.012   0.001   TYR E  60 
 PHE   0.013   0.001   PHE B 344 
 TRP   0.007   0.001   TRP B 350 
 HIS   0.009   0.001   HIS E  30 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.11 ( 3178)
  covalent geometry    : angle       0.57057 /  0.30 ( 4317)
  SS BOND              : bond        0.00388 /  0.15 (    6)
  SS BOND              : angle       1.04809 /  0.52 (   12)
  hydrogen bonds       : bond        0.02988 /  2.02 (   64)
  hydrogen bonds       : angle       6.80213 /  4.45 (  153)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 62
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
REVERT: B  371 PHE cc_start: 0.9063 (m-10) cc_final: 0.8850 (m-10)
REVERT: B  462 GLU cc_start: 0.9057 (tt0) cc_final: 0.8559 (tt0)
REVERT: B  489 GLU cc_start: 0.8860 (tp30) cc_final: 0.8461 (tp30)
REVERT: E   73 ASP cc_start: 0.8390 (t0) cc_final: 0.7866 (t0)
REVERT: E   99 ASP cc_start: 0.8758 (t0) cc_final: 0.8375 (t0)
REVERT: E  115 ASP cc_start: 0.7923 (t0) cc_final: 0.7610 (t0)
  outliers start: 4
  outliers final: 3
  residues processed: 65
  average time/residue: 0.0616
  time to fit residues: 4.9473
Evaluate side-chains
  62 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue  103 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 19 optimal weight:    0.0970
   chunk 26 optimal weight:    0.0570
   chunk 25 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.0100

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

Flipped N/Q/H residues before XYZ refinement:
** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.076787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.061490 restraints weight = 8520.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.2895 rms_B_bonded: 3.94
r_work: 0.2765 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8739
moved from start:          0.3195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3184  Z= 0.183
  Angle     :  0.585   6.514   4329  Z= 0.311
  Chirality :  0.045   0.195    461
  Planarity :  0.005   0.049    564
  Dihedral  :  4.462  19.452    435
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 10.59 %
    Favored  : 87.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.72 (0.42), residues: 391
  helix: -4.86 (0.45), residues: 13
  sheet: -0.12 (0.50), residues: 106
  loop : -1.46 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 454 
 TYR   0.013   0.001   TYR E  60 
 PHE   0.018   0.002   PHE B 344 
 TRP   0.009   0.001   TRP B 350 
 HIS   0.008   0.002   HIS E  30 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00422 /  0.18 ( 3178)
  covalent geometry    : angle       0.58104 /  0.31 ( 4317)
  SS BOND              : bond        0.00502 /  0.21 (    6)
  SS BOND              : angle       1.39739 /  0.73 (   12)
  hydrogen bonds       : bond        0.03316 /  2.30 (   64)
  hydrogen bonds       : angle       6.13694 /  4.02 (  153)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: B  337 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8165 (tm-30)
REVERT: B  579 GLU cc_start: 0.8442 (pp20) cc_final: 0.8095 (pp20)
REVERT: E   73 ASP cc_start: 0.8852 (t0) cc_final: 0.8449 (t0)
REVERT: E   87 LYS cc_start: 0.7960 (ptmm) cc_final: 0.7064 (ptmm)
REVERT: E   99 ASP cc_start: 0.9115 (t0) cc_final: 0.8692 (t0)
REVERT: E  115 ASP cc_start: 0.8164 (t0) cc_final: 0.7800 (t0)
  outliers start: 7
  outliers final: 6
  residues processed: 58
  average time/residue: 0.0591
  time to fit residues: 4.2945
Evaluate side-chains
  58 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  543 THR
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue  103 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.075208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.059848 restraints weight = 8517.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 3.97
r_work: 0.2722 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8782
moved from start:          0.3644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3184  Z= 0.206
  Angle     :  0.578   6.778   4329  Z= 0.307
  Chirality :  0.045   0.191    461
  Planarity :  0.004   0.040    564
  Dihedral  :  4.503  19.831    435
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 13.24 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.71 (0.42), residues: 391
  helix: -4.70 (0.57), residues: 13
  sheet: -0.12 (0.46), residues: 114
  loop : -1.50 (0.39), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 463 
 TYR   0.011   0.001   TYR E  60 
 PHE   0.013   0.001   PHE B 344 
 TRP   0.010   0.001   TRP B 350 
 HIS   0.003   0.001   HIS E 105 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00473 /  0.21 ( 3178)
  covalent geometry    : angle       0.57377 /  0.30 ( 4317)
  SS BOND              : bond        0.00496 /  0.21 (    6)
  SS BOND              : angle       1.50849 /  0.78 (   12)
  hydrogen bonds       : bond        0.03233 /  2.26 (   64)
  hydrogen bonds       : angle       5.81216 /  3.84 (  153)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: B  337 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8122 (tm-30)
REVERT: B  579 GLU cc_start: 0.8460 (pp20) cc_final: 0.8161 (pp20)
REVERT: E   73 ASP cc_start: 0.8928 (t0) cc_final: 0.8544 (t0)
REVERT: E   82 GLN cc_start: 0.9026 (tp40) cc_final: 0.8631 (tp-100)
REVERT: E   83 MET cc_start: 0.9167 (mtp) cc_final: 0.8811 (mtp)
REVERT: E   99 ASP cc_start: 0.9209 (t0) cc_final: 0.8845 (t0)
REVERT: E  115 ASP cc_start: 0.8209 (t0) cc_final: 0.7802 (t0)
  outliers start: 9
  outliers final: 8
  residues processed: 60
  average time/residue: 0.0568
  time to fit residues: 4.1853
Evaluate side-chains
  59 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  543 THR
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue  103 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 8 optimal weight:    0.0970
   chunk 5 optimal weight:    0.0370
   chunk 33 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.4256

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.077341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.062234 restraints weight = 8440.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 3.92
r_work: 0.2776 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8737
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3184  Z= 0.110
  Angle     :  0.532   5.568   4329  Z= 0.279
  Chirality :  0.044   0.186    461
  Planarity :  0.004   0.035    564
  Dihedral  :  4.143  19.507    435
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 12.94 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.48 (0.42), residues: 391
  helix: -4.68 (0.56), residues: 13
  sheet:  0.32 (0.50), residues: 99
  loop : -1.38 (0.38), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 454 
 TYR   0.010   0.001   TYR E  60 
 PHE   0.010   0.001   PHE B 389 
 TRP   0.007   0.001   TRP B 350 
 HIS   0.001   0.000   HIS E 105 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.11 ( 3178)
  covalent geometry    : angle       0.52890 /  0.28 ( 4317)
  SS BOND              : bond        0.00451 /  0.18 (    6)
  SS BOND              : angle       1.20026 /  0.59 (   12)
  hydrogen bonds       : bond        0.02727 /  1.90 (   64)
  hydrogen bonds       : angle       5.38537 /  3.52 (  153)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
REVERT: B  337 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8083 (tm-30)
REVERT: B  403 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8822 (mt-10)
REVERT: B  579 GLU cc_start: 0.8415 (pp20) cc_final: 0.8144 (pp20)
REVERT: E   73 ASP cc_start: 0.8819 (t0) cc_final: 0.8373 (t0)
REVERT: E   82 GLN cc_start: 0.8952 (tp40) cc_final: 0.8618 (tp-100)
REVERT: E   99 ASP cc_start: 0.9142 (t0) cc_final: 0.8728 (t0)
REVERT: E  115 ASP cc_start: 0.8021 (t0) cc_final: 0.7635 (t0)
  outliers start: 9
  outliers final: 6
  residues processed: 61
  average time/residue: 0.0799
  time to fit residues: 5.8325
Evaluate side-chains
  59 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  491 TYR
Chi-restraints excluded: chain B residue  543 THR
Chi-restraints excluded: chain E residue   48 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 12 optimal weight:    0.1980
   chunk 15 optimal weight:    0.0980
   chunk 6 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.4580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.077075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.061977 restraints weight = 8484.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 3.96
r_work: 0.2774 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8742
moved from start:          0.3919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3184  Z= 0.115
  Angle     :  0.538   5.529   4329  Z= 0.281
  Chirality :  0.043   0.172    461
  Planarity :  0.004   0.032    564
  Dihedral  :  4.004  19.475    435
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 14.41 %
    Favored  : 83.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.26 (0.42), residues: 391
  helix: -3.71 (1.24), residues: 6
  sheet:  0.55 (0.51), residues: 98
  loop : -1.38 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 454 
 TYR   0.010   0.001   TYR E  60 
 PHE   0.009   0.001   PHE B 389 
 TRP   0.007   0.001   TRP B 350 
 HIS   0.001   0.000   HIS E 105 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.12 ( 3178)
  covalent geometry    : angle       0.53482 /  0.28 ( 4317)
  SS BOND              : bond        0.00427 /  0.17 (    6)
  SS BOND              : angle       1.18792 /  0.58 (   12)
  hydrogen bonds       : bond        0.02615 /  1.82 (   64)
  hydrogen bonds       : angle       5.18846 /  3.36 (  153)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: B  337 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8066 (tm-30)
REVERT: B  403 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8839 (mt-10)
REVERT: B  579 GLU cc_start: 0.8414 (pp20) cc_final: 0.8163 (pp20)
REVERT: E   46 GLU cc_start: 0.8853 (pt0) cc_final: 0.8610 (pm20)
REVERT: E   73 ASP cc_start: 0.8790 (t0) cc_final: 0.8346 (t0)
REVERT: E   82 GLN cc_start: 0.8923 (tp40) cc_final: 0.8546 (tp-100)
REVERT: E   83 MET cc_start: 0.9085 (mtp) cc_final: 0.8750 (mtp)
REVERT: E   99 ASP cc_start: 0.9161 (t0) cc_final: 0.8757 (t0)
REVERT: E  115 ASP cc_start: 0.8047 (t0) cc_final: 0.7597 (t0)
  outliers start: 6
  outliers final: 6
  residues processed: 60
  average time/residue: 0.0716
  time to fit residues: 5.2646
Evaluate side-chains
  60 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  491 TYR
Chi-restraints excluded: chain B residue  543 THR
Chi-restraints excluded: chain E residue   48 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 36 optimal weight:    0.1980
   chunk 7 optimal weight:    0.4980
   overall best weight:    0.5180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.077144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.062032 restraints weight = 8511.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 3.95
r_work: 0.2771 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8731
moved from start:          0.4004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3184  Z= 0.123
  Angle     :  0.561   5.612   4329  Z= 0.293
  Chirality :  0.043   0.182    461
  Planarity :  0.004   0.032    564
  Dihedral  :  3.945  19.212    435
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 16.18 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.17 (0.42), residues: 391
  helix: -3.68 (1.27), residues: 6
  sheet:  0.59 (0.50), residues: 98
  loop : -1.31 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 463 
 TYR   0.008   0.001   TYR E  60 
 PHE   0.009   0.001   PHE B 389 
 TRP   0.007   0.001   TRP B 350 
 HIS   0.001   0.000   HIS E 105 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.12 ( 3178)
  covalent geometry    : angle       0.55768 /  0.29 ( 4317)
  SS BOND              : bond        0.00429 /  0.17 (    6)
  SS BOND              : angle       1.20290 /  0.60 (   12)
  hydrogen bonds       : bond        0.02590 /  1.79 (   64)
  hydrogen bonds       : angle       5.09382 /  3.31 (  153)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
REVERT: B  337 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8079 (tm-30)
REVERT: B  403 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8857 (mt-10)
REVERT: B  462 GLU cc_start: 0.8825 (tt0) cc_final: 0.8465 (tt0)
REVERT: B  579 GLU cc_start: 0.8381 (pp20) cc_final: 0.8160 (pp20)
REVERT: E   57 THR cc_start: 0.9114 (p) cc_final: 0.8735 (p)
REVERT: E   73 ASP cc_start: 0.8780 (t0) cc_final: 0.8331 (t0)
REVERT: E   82 GLN cc_start: 0.8939 (tp40) cc_final: 0.8597 (tp-100)
REVERT: E   83 MET cc_start: 0.9107 (mtp) cc_final: 0.8742 (mtp)
REVERT: E   99 ASP cc_start: 0.9206 (t0) cc_final: 0.8790 (t0)
REVERT: E  115 ASP cc_start: 0.8067 (t0) cc_final: 0.7629 (t0)
  outliers start: 8
  outliers final: 8
  residues processed: 60
  average time/residue: 0.0686
  time to fit residues: 5.0397
Evaluate side-chains
  63 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  491 TYR
Chi-restraints excluded: chain B residue  520 VAL
Chi-restraints excluded: chain B residue  543 THR
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   48 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 5 optimal weight:    0.4980
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.075763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.060479 restraints weight = 8749.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 4.03
r_work: 0.2736 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8769
moved from start:          0.4135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3184  Z= 0.155
  Angle     :  0.573   5.675   4329  Z= 0.300
  Chirality :  0.044   0.188    461
  Planarity :  0.004   0.032    564
  Dihedral  :  4.037  19.827    435
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.88 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.19 (0.42), residues: 391
  helix: -3.48 (0.95), residues: 13
  sheet:  0.57 (0.50), residues: 98
  loop : -1.24 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 454 
 TYR   0.009   0.001   TYR B 491 
 PHE   0.009   0.001   PHE B 389 
 TRP   0.008   0.001   TRP B 350 
 HIS   0.002   0.000   HIS E 105 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.15 ( 3178)
  covalent geometry    : angle       0.56960 /  0.30 ( 4317)
  SS BOND              : bond        0.00461 /  0.18 (    6)
  SS BOND              : angle       1.33415 /  0.69 (   12)
  hydrogen bonds       : bond        0.02744 /  1.90 (   64)
  hydrogen bonds       : angle       5.17550 /  3.36 (  153)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  337 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8087 (tm-30)
REVERT: B  403 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8875 (mt-10)
REVERT: B  462 GLU cc_start: 0.8782 (tt0) cc_final: 0.8424 (tt0)
REVERT: B  579 GLU cc_start: 0.8392 (pp20) cc_final: 0.8167 (pp20)
REVERT: E   46 GLU cc_start: 0.8392 (pm20) cc_final: 0.7927 (pm20)
REVERT: E   57 THR cc_start: 0.9155 (p) cc_final: 0.8788 (p)
REVERT: E   73 ASP cc_start: 0.8814 (t0) cc_final: 0.8384 (t0)
REVERT: E   82 GLN cc_start: 0.8996 (tp40) cc_final: 0.8601 (tp-100)
REVERT: E   83 MET cc_start: 0.9172 (mtp) cc_final: 0.8874 (mtp)
REVERT: E   99 ASP cc_start: 0.9254 (t0) cc_final: 0.8896 (t0)
REVERT: E  115 ASP cc_start: 0.8136 (t0) cc_final: 0.7715 (t0)
  outliers start: 8
  outliers final: 8
  residues processed: 63
  average time/residue: 0.0732
  time to fit residues: 5.5722
Evaluate side-chains
  65 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  491 TYR
Chi-restraints excluded: chain B residue  520 VAL
Chi-restraints excluded: chain B residue  543 THR
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   48 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 28 optimal weight:    0.0670
   chunk 32 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0870
   chunk 22 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.4896

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.076184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.061180 restraints weight = 8674.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 4.00
r_work: 0.2749 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8726
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      :  0.003   0.038   3184  Z= 0.121
  Angle     :  0.570   6.589   4329  Z= 0.299
  Chirality :  0.043   0.189    461
  Planarity :  0.004   0.031    564
  Dihedral  :  3.927  19.354    435
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 16.47 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.16 (0.42), residues: 391
  helix: -3.43 (1.53), residues: 6
  sheet:  0.54 (0.50), residues: 100
  loop : -1.29 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 463 
 TYR   0.010   0.001   TYR E  60 
 PHE   0.009   0.001   PHE B 389 
 TRP   0.007   0.001   TRP B 350 
 HIS   0.001   0.000   HIS E 105 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.12 ( 3178)
  covalent geometry    : angle       0.56711 /  0.30 ( 4317)
  SS BOND              : bond        0.00439 /  0.17 (    6)
  SS BOND              : angle       1.20604 /  0.60 (   12)
  hydrogen bonds       : bond        0.02549 /  1.76 (   64)
  hydrogen bonds       : angle       5.03214 /  3.27 (  153)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  403 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8904 (mt-10)
REVERT: B  462 GLU cc_start: 0.8858 (tt0) cc_final: 0.8493 (tt0)
REVERT: E   46 GLU cc_start: 0.8462 (pm20) cc_final: 0.7978 (pm20)
REVERT: E   57 THR cc_start: 0.9080 (p) cc_final: 0.8710 (p)
REVERT: E   73 ASP cc_start: 0.8766 (t0) cc_final: 0.8320 (t0)
REVERT: E   82 GLN cc_start: 0.8966 (tp40) cc_final: 0.8630 (tp-100)
REVERT: E   83 MET cc_start: 0.9152 (mtp) cc_final: 0.8753 (mtp)
REVERT: E   99 ASP cc_start: 0.9242 (t0) cc_final: 0.8867 (t0)
REVERT: E  115 ASP cc_start: 0.8144 (t0) cc_final: 0.7708 (t0)
  outliers start: 8
  outliers final: 7
  residues processed: 60
  average time/residue: 0.0674
  time to fit residues: 4.9666
Evaluate side-chains
  62 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  491 TYR
Chi-restraints excluded: chain B residue  520 VAL
Chi-restraints excluded: chain B residue  543 THR
Chi-restraints excluded: chain E residue   48 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 6 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.074585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.059426 restraints weight = 8550.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 4.01
r_work: 0.2711 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8759
moved from start:          0.4294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3184  Z= 0.180
  Angle     :  0.614   6.327   4329  Z= 0.321
  Chirality :  0.045   0.201    461
  Planarity :  0.004   0.032    564
  Dihedral  :  4.141  20.336    435
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 17.06 %
    Favored  : 80.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.12 (0.42), residues: 391
  helix: -2.67 (1.21), residues: 13
  sheet:  0.61 (0.50), residues: 98
  loop : -1.24 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 463 
 TYR   0.010   0.001   TYR B 491 
 PHE   0.010   0.001   PHE B 389 
 TRP   0.009   0.001   TRP B 350 
 HIS   0.002   0.000   HIS E 105 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00421 /  0.18 ( 3178)
  covalent geometry    : angle       0.60986 /  0.32 ( 4317)
  SS BOND              : bond        0.00483 /  0.19 (    6)
  SS BOND              : angle       1.43938 /  0.75 (   12)
  hydrogen bonds       : bond        0.02909 /  2.02 (   64)
  hydrogen bonds       : angle       5.14723 /  3.36 (  153)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  337 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8136 (tm-30)
REVERT: B  403 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8887 (mt-10)
REVERT: B  462 GLU cc_start: 0.8851 (tt0) cc_final: 0.8430 (tt0)
REVERT: E   46 GLU cc_start: 0.8576 (pm20) cc_final: 0.8110 (pm20)
REVERT: E   57 THR cc_start: 0.9132 (p) cc_final: 0.8777 (p)
REVERT: E   73 ASP cc_start: 0.8813 (t0) cc_final: 0.8399 (t0)
REVERT: E   82 GLN cc_start: 0.8992 (tp40) cc_final: 0.8607 (tp-100)
REVERT: E   99 ASP cc_start: 0.9320 (t0) cc_final: 0.8988 (t0)
REVERT: E  115 ASP cc_start: 0.8307 (t0) cc_final: 0.7863 (t0)
  outliers start: 7
  outliers final: 6
  residues processed: 58
  average time/residue: 0.0674
  time to fit residues: 4.8043
Evaluate side-chains
  58 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  392 VAL
Chi-restraints excluded: chain B residue  491 TYR
Chi-restraints excluded: chain B residue  520 VAL
Chi-restraints excluded: chain B residue  543 THR
Chi-restraints excluded: chain E residue   48 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0670
   chunk 27 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   chunk 34 optimal weight:    0.4980
   chunk 11 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.4718

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.076114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.061140 restraints weight = 8558.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 3.99
r_work: 0.2751 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8730
moved from start:          0.4310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3184  Z= 0.123
  Angle     :  0.597   7.334   4329  Z= 0.310
  Chirality :  0.044   0.185    461
  Planarity :  0.004   0.033    564
  Dihedral  :  3.986  19.319    435
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 16.18 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.90 (0.43), residues: 391
  helix: -1.59 (1.96), residues: 7
  sheet:  0.67 (0.49), residues: 100
  loop : -1.12 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 119 
 TYR   0.008   0.001   TYR E  60 
 PHE   0.008   0.001   PHE B 537 
 TRP   0.007   0.001   TRP B 350 
 HIS   0.002   0.000   HIS E 105 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.12 ( 3178)
  covalent geometry    : angle       0.59451 /  0.31 ( 4317)
  SS BOND              : bond        0.00452 /  0.18 (    6)
  SS BOND              : angle       1.27755 /  0.60 (   12)
  hydrogen bonds       : bond        0.02600 /  1.78 (   64)
  hydrogen bonds       : angle       5.02646 /  3.28 (  153)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1112.11 seconds
wall clock time: 19 minutes 48.72 seconds (1188.72 seconds total)