Starting phenix.real_space_refine
on Fri Aug 22 13:22:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v4f_42970/08_2025/8v4f_42970.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v4f_42970/08_2025/8v4f_42970.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v4f_42970/08_2025/8v4f_42970.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v4f_42970/08_2025/8v4f_42970.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v4f_42970/08_2025/8v4f_42970.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v4f_42970/08_2025/8v4f_42970.map"
  }
  resolution = 2.68
  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=   0.008
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    2064      2.51       5
     N     548      2.21       5
     O     611      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3237
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 905
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 905
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 3, 'TRANS': 112}
    Chain: "D"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 802
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98}
    Chain: "A"
      Number of atoms: 1530
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1530
          Classifications: {'peptide': 190}
          Link IDs: {'PTRANS': 11, 'TRANS': 178}
          Chain breaks: 1
  Time building chain proxies: 1.25, per 1000 atoms: 0.39
  Number of scatterers: 3237
  At special positions: 0
  Unit cell: (72.72, 70.7, 85.85, 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     611      8.00
     N     548      7.00
     C    2064      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03

  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: 0.26
  Conformation dependent library (CDL) restraints added in 127.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  748

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 9 sheets defined
      12.1% alpha, 33.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'B' and resid 28 through 32
    Processing helix  chain 'B' and resid 86 through 90
      removed outlier: 3.804A  pdb=" N   THR B  90 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 79 through 83
      removed outlier: 3.639A  pdb=" N   PHE D  83 " --> pdb=" O   PRO D  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 3.751A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 3.843A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 368
      removed outlier: 4.068A  pdb=" N   VAL A 367 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 387
      removed outlier: 3.668A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.521A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 7
    Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 12
      removed outlier: 6.717A  pdb=" N   MET B  34 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   VAL B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 12
      removed outlier: 6.931A  pdb=" N   CYS B  95 " --> pdb=" O   TRP B 107 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   TRP B 107 " --> pdb=" O   CYS B  95 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ARG B  97 " --> pdb=" O   ASP B 105 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 6
      removed outlier: 3.846A  pdb=" N   ASP D  70 " --> pdb=" O   SER D  67 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.485A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   LEU D  33 " --> pdb=" O   PHE D  49 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   PHE D  49 " --> pdb=" O   LEU D  33 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392
    Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474

    110 hydrogen bonds defined for protein.
    261 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: 0.56

  Time building geometry restraints manager: 0.38 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: 1000
        1.34 -     1.46: 779
        1.46 -     1.58: 1528
        1.58 -     1.70: 0
        1.70 -     1.82: 16
  Bond restraints: 3323
  Sorted by residual:
  bond pdb=" N   VAL D   3 "
       pdb=" CA  VAL D   3 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.24e-02 6.50e+03 7.14e+00
  bond pdb=" N   PHE A 347 "
       pdb=" CA  PHE A 347 "
    ideal  model  delta    sigma   weight residual
    1.453  1.485 -0.032 1.22e-02 6.72e+03 6.88e+00
  bond pdb=" N   ILE D   2 "
       pdb=" CA  ILE D   2 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.25e-02 6.40e+03 6.68e+00
  bond pdb=" N   TYR B 106 "
       pdb=" CA  TYR B 106 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.032 1.27e-02 6.20e+03 6.47e+00
  bond pdb=" N   LEU D   4 "
       pdb=" CA  LEU D   4 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.27e-02 6.20e+03 4.69e+00
  ... (remaining 3318 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 4187
        1.71 -     3.43: 256
        3.43 -     5.14: 50
        5.14 -     6.86: 13
        6.86 -     8.57: 5
  Bond angle restraints: 4511
  Sorted by residual:
  angle pdb=" C   GLY D  50 "
        pdb=" N   ALA D  51 "
        pdb=" CA  ALA D  51 "
      ideal   model   delta    sigma   weight residual
     121.54  129.68   -8.14 1.91e+00 2.74e-01 1.82e+01
  angle pdb=" CG  ARG D  61 "
        pdb=" CD  ARG D  61 "
        pdb=" NE  ARG D  61 "
      ideal   model   delta    sigma   weight residual
     112.00  120.29   -8.29 2.20e+00 2.07e-01 1.42e+01
  angle pdb=" CA  TYR D  91 "
        pdb=" CB  TYR D  91 "
        pdb=" CG  TYR D  91 "
      ideal   model   delta    sigma   weight residual
     113.90  119.86   -5.96 1.80e+00 3.09e-01 1.10e+01
  angle pdb=" C   GLU D  17 "
        pdb=" N   ARG D  18 "
        pdb=" CA  ARG D  18 "
      ideal   model   delta    sigma   weight residual
     121.54  127.19   -5.65 1.91e+00 2.74e-01 8.75e+00
  angle pdb=" C   ARG D  18 "
        pdb=" N   ALA D  19 "
        pdb=" CA  ALA D  19 "
      ideal   model   delta    sigma   weight residual
     121.87  128.17   -6.30 2.24e+00 1.99e-01 7.91e+00
  ... (remaining 4506 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.86: 1729
       16.86 -    33.72: 175
       33.72 -    50.58: 35
       50.58 -    67.44: 5
       67.44 -    84.30: 3
  Dihedral angle restraints: 1947
    sinusoidal: 762
      harmonic: 1185
  Sorted by residual:
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  95 "
           pdb=" CB  CYS B  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   58.90   34.10     1      1.00e+01 1.00e-02 1.65e+01
  dihedral pdb=" SG  CYS A 391 "
           pdb=" CB  CYS A 525 "
           pdb=" SG  CYS A 525 "
           pdb=" CA  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00  -13.63  -59.37     1      2.00e+01 2.50e-03 1.18e+01
  dihedral pdb=" CA  ASP D  70 "
           pdb=" CB  ASP D  70 "
           pdb=" CG  ASP D  70 "
           pdb=" OD1 ASP D  70 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.57   56.57     1      2.00e+01 2.50e-03 1.08e+01
  ... (remaining 1944 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 283
       0.046 -    0.093: 120
       0.093 -    0.139: 52
       0.139 -    0.185: 13
       0.185 -    0.231: 6
  Chirality restraints: 474
  Sorted by residual:
  chirality pdb=" CA  TYR D  91 "
            pdb=" N   TYR D  91 "
            pdb=" C   TYR D  91 "
            pdb=" CB  TYR D  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CB  THR B 114 "
            pdb=" CA  THR B 114 "
            pdb=" OG1 THR B 114 "
            pdb=" CG2 THR B 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CB  ILE B  12 "
            pdb=" CA  ILE B  12 "
            pdb=" CG1 ILE B  12 "
            pdb=" CG2 ILE B  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 471 not shown)

  Planarity restraints: 587
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 509 "    0.215 9.50e-02 1.11e+02   9.70e-02 7.24e+00
        pdb=" NE  ARG A 509 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 509 "    0.019 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 509 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 509 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D  79 "   -0.038 5.00e-02 4.00e+02   5.77e-02 5.33e+00
        pdb=" N   PRO D  80 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO D  80 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO D  80 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 468 "   -0.010 2.00e-02 2.50e+03   2.05e-02 4.18e+00
        pdb=" C   ILE A 468 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ILE A 468 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   SER A 469 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 584 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 1163
        2.87 -     3.38: 2685
        3.38 -     3.88: 5539
        3.88 -     4.39: 6229
        4.39 -     4.90: 10738
  Nonbonded interactions: 26354
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  56 "
            pdb=" OD2 ASP A 420 "
     model   vdw
     2.360 3.040
  nonbonded pdb=" OH  TYR B  33 "
            pdb=" O   LEU A 455 "
     model   vdw
     2.366 3.040
  nonbonded pdb=" O   ASP D  82 "
            pdb=" OH  TYR D  86 "
     model   vdw
     2.368 3.040
  nonbonded pdb=" OD1 ASN A 448 "
            pdb=" ND2 ASN A 450 "
     model   vdw
     2.391 3.120
  nonbonded pdb=" O   TYR B  52 "
            pdb=" NH2 ARG B  71 "
     model   vdw
     2.394 3.120
  ... (remaining 26349 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:             6.300
  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:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     5.960
  Find NCS groups from input model:        0.020
  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:11.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
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   0.039   3329  Z= 0.267
  Angle     :  0.993   8.572   4523  Z= 0.540
  Chirality :  0.064   0.231    474
  Planarity :  0.008   0.097    587
  Dihedral  : 13.785  84.298   1181
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -0.42 (0.42), residues: 404
  helix: -1.61 (1.32), residues: 13
  sheet:  0.46 (0.44), residues: 135
  loop : -0.60 (0.40), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.002   ARG A 509 
 TYR   0.027   0.003   TYR B  52 
 PHE   0.024   0.002   PHE A 464 
 TRP   0.010   0.002   TRP B  36 
 HIS   0.003   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 ( 3323)
  covalent geometry    : angle       0.99120 ( 4511)
  SS BOND              : bond        0.00344 (    6)
  SS BOND              : angle       1.57666 (   12)
  hydrogen bonds       : bond        0.16714 (  105)
  hydrogen bonds       : angle       8.37222 (  261)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.141 
Fit side-chains
REVERT: B   18 LEU cc_start: 0.8361 (tp) cc_final: 0.8033 (tp)
REVERT: B   30 SER cc_start: 0.8532 (p) cc_final: 0.8295 (t)
REVERT: B   59 TYR cc_start: 0.8618 (m-80) cc_final: 0.8065 (m-80)
REVERT: B   79 TYR cc_start: 0.8477 (m-80) cc_final: 0.8249 (m-10)
REVERT: B  109 GLN cc_start: 0.7499 (pm20) cc_final: 0.6914 (pm20)
REVERT: B  112 LEU cc_start: 0.8829 (tp) cc_final: 0.8628 (tm)
REVERT: A  342 PHE cc_start: 0.8551 (m-80) cc_final: 0.8331 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.3904
  time to fit residues: 39.2906
Evaluate side-chains
  94 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.1980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0670
   chunk 25 optimal weight:    0.0000
   chunk 19 optimal weight:    0.0670
   chunk 30 optimal weight:    0.1980
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.1060

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

Flipped N/Q/H residues before XYZ refinement:
** D  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.141672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.132433 restraints weight = 4703.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 1.89
r_work: 0.3691 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3564 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.1566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   3329  Z= 0.103
  Angle     :  0.516   4.843   4523  Z= 0.270
  Chirality :  0.043   0.133    474
  Planarity :  0.005   0.051    587
  Dihedral  :  4.281  16.401    462
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 12.07 %
    Favored  : 86.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -0.33 (0.42), residues: 404
  helix: -3.22 (1.02), residues: 14
  sheet:  0.74 (0.44), residues: 134
  loop : -0.56 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D  61 
 TYR   0.012   0.001   TYR B  33 
 PHE   0.008   0.001   PHE A 464 
 TRP   0.007   0.001   TRP B 107 
 HIS   0.002   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 3323)
  covalent geometry    : angle       0.51021 ( 4511)
  SS BOND              : bond        0.00373 (    6)
  SS BOND              : angle       1.60786 (   12)
  hydrogen bonds       : bond        0.03201 (  105)
  hydrogen bonds       : angle       5.82743 (  261)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.094 
Fit side-chains
REVERT: B   18 LEU cc_start: 0.8287 (tp) cc_final: 0.8014 (tt)
REVERT: B   19 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7702 (ttt-90)
REVERT: B   59 TYR cc_start: 0.8578 (m-80) cc_final: 0.7962 (m-80)
REVERT: B   79 TYR cc_start: 0.8488 (m-80) cc_final: 0.8237 (m-80)
REVERT: B  109 GLN cc_start: 0.7354 (pm20) cc_final: 0.6923 (pm20)
REVERT: D   61 ARG cc_start: 0.8120 (mtm110) cc_final: 0.7646 (ptp90)
REVERT: A  409 GLN cc_start: 0.8622 (mt0) cc_final: 0.8400 (mt0)
REVERT: A  424 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8074 (tttm)
  outliers start: 6
  outliers final: 2
  residues processed: 107
  average time/residue: 0.3546
  time to fit residues: 39.3708
Evaluate side-chains
  98 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain D residue   20 SER
Chi-restraints excluded: chain A residue  424 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.2980
   chunk 10 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 24 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 1 optimal weight:    0.1980
   chunk 29 optimal weight:    0.1980
   overall best weight:    0.3380

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

Flipped N/Q/H residues before XYZ refinement:
B  83 ASN
D  89 GLN
A 450 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.136385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.127089 restraints weight = 4714.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 1.88
r_work: 0.3628 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3495 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3329  Z= 0.211
  Angle     :  0.572   6.067   4523  Z= 0.295
  Chirality :  0.045   0.128    474
  Planarity :  0.005   0.055    587
  Dihedral  :  4.717  18.914    462
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 13.79 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -0.38 (0.42), residues: 404
  helix: -3.12 (0.83), residues: 20
  sheet:  0.62 (0.43), residues: 143
  loop : -0.51 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 498 
 TYR   0.015   0.002   TYR A 495 
 PHE   0.017   0.002   PHE A 464 
 TRP   0.011   0.002   TRP B 107 
 HIS   0.002   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 3323)
  covalent geometry    : angle       0.56703 ( 4511)
  SS BOND              : bond        0.00555 (    6)
  SS BOND              : angle       1.61728 (   12)
  hydrogen bonds       : bond        0.03449 (  105)
  hydrogen bonds       : angle       5.83487 (  261)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.113 
Fit side-chains
REVERT: B   19 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7507 (ttt-90)
REVERT: B   66 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8458 (ptm-80)
REVERT: B   79 TYR cc_start: 0.8561 (m-80) cc_final: 0.8345 (m-80)
REVERT: B  109 GLN cc_start: 0.7246 (pm20) cc_final: 0.6855 (pm20)
REVERT: D   61 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7537 (ptp90)
REVERT: D   79 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6566 (mp0)
  outliers start: 13
  outliers final: 8
  residues processed: 97
  average time/residue: 0.3654
  time to fit residues: 36.8059
Evaluate side-chains
  105 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   66 ARG
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain D residue   20 SER
Chi-restraints excluded: chain D residue   22 SER
Chi-restraints excluded: chain D residue   67 SER
Chi-restraints excluded: chain D residue   79 GLU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  458 LYS
Chi-restraints excluded: chain A residue  483 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 33 optimal weight:    0.4980
   chunk 6 optimal weight:    0.8980
   chunk 35 optimal weight:    0.3980
   chunk 25 optimal weight:    0.2980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
D   6 GLN
D  37 GLN
A 409 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.135166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.125801 restraints weight = 4690.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 1.86
r_work: 0.3597 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3465 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.039   3329  Z= 0.296
  Angle     :  0.627   7.302   4523  Z= 0.319
  Chirality :  0.048   0.138    474
  Planarity :  0.005   0.059    587
  Dihedral  :  5.029  20.572    462
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 13.22 %
    Favored  : 80.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -0.18 (0.42), residues: 404
  helix: -1.78 (1.50), residues: 12
  sheet:  0.57 (0.43), residues: 146
  loop : -0.42 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 498 
 TYR   0.015   0.002   TYR A 495 
 PHE   0.020   0.002   PHE A 464 
 TRP   0.012   0.002   TRP B 107 
 HIS   0.002   0.001   HIS B   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00660 ( 3323)
  covalent geometry    : angle       0.62271 ( 4511)
  SS BOND              : bond        0.00684 (    6)
  SS BOND              : angle       1.55776 (   12)
  hydrogen bonds       : bond        0.03553 (  105)
  hydrogen bonds       : angle       5.72992 (  261)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.098 
Fit side-chains
REVERT: B   19 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7489 (ttt-90)
REVERT: B   66 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8485 (ptm-80)
REVERT: B   71 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7388 (ptm160)
REVERT: B  109 GLN cc_start: 0.7333 (pm20) cc_final: 0.6931 (pm20)
REVERT: D   61 ARG cc_start: 0.8067 (mtm110) cc_final: 0.7770 (ptp90)
REVERT: D   79 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6160 (mp0)
REVERT: A  357 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8073 (ttt-90)
REVERT: A  377 PHE cc_start: 0.7897 (t80) cc_final: 0.7697 (t80)
  outliers start: 21
  outliers final: 10
  residues processed: 107
  average time/residue: 0.3279
  time to fit residues: 36.5123
Evaluate side-chains
  113 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   66 ARG
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain D residue   20 SER
Chi-restraints excluded: chain D residue   22 SER
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain D residue   67 SER
Chi-restraints excluded: chain D residue   79 GLU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  357 ARG
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.4980
   chunk 22 optimal weight:    0.3980
   chunk 39 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0970
   chunk 25 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 38 optimal weight:    0.2980
   chunk 23 optimal weight:    0.0970
   chunk 32 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0670
   overall best weight:    0.1914

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

Flipped N/Q/H residues before XYZ refinement:
D   6 GLN
D  37 GLN
A 409 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.137703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.128386 restraints weight = 4588.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 1.85
r_work: 0.3648 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3518 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3329  Z= 0.134
  Angle     :  0.516   6.707   4523  Z= 0.264
  Chirality :  0.044   0.138    474
  Planarity :  0.004   0.053    587
  Dihedral  :  4.515  20.092    462
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.95 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -0.14 (0.42), residues: 404
  helix: -1.63 (1.55), residues: 12
  sheet:  0.46 (0.43), residues: 145
  loop : -0.30 (0.41), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 498 
 TYR   0.012   0.001   TYR B  33 
 PHE   0.011   0.001   PHE A 377 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.001   0.000   HIS B   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 3323)
  covalent geometry    : angle       0.51323 ( 4511)
  SS BOND              : bond        0.00519 (    6)
  SS BOND              : angle       1.16477 (   12)
  hydrogen bonds       : bond        0.02946 (  105)
  hydrogen bonds       : angle       5.43884 (  261)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.130 
Fit side-chains
REVERT: B   19 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7737 (ttt-90)
REVERT: B  109 GLN cc_start: 0.7337 (pm20) cc_final: 0.6945 (pm20)
REVERT: D   61 ARG cc_start: 0.7996 (mtm110) cc_final: 0.7678 (ptp90)
REVERT: A  421 TYR cc_start: 0.8667 (m-80) cc_final: 0.8392 (m-80)
  outliers start: 11
  outliers final: 6
  residues processed: 106
  average time/residue: 0.2914
  time to fit residues: 32.3249
Evaluate side-chains
  106 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain D residue   20 SER
Chi-restraints excluded: chain D residue   22 SER
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0870
   chunk 37 optimal weight:    0.1980
   chunk 20 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 10 optimal weight:    0.2980
   overall best weight:    0.3558

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

Flipped N/Q/H residues before XYZ refinement:
B  83 ASN
D  37 GLN
A 409 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.136398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.127029 restraints weight = 4642.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 1.85
r_work: 0.3616 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3486 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   3329  Z= 0.219
  Angle     :  0.576   6.745   4523  Z= 0.292
  Chirality :  0.045   0.133    474
  Planarity :  0.005   0.056    587
  Dihedral  :  4.791  21.837    462
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 18.68 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -0.17 (0.42), residues: 404
  helix: -1.34 (1.67), residues: 12
  sheet:  0.46 (0.44), residues: 143
  loop : -0.35 (0.40), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 457 
 TYR   0.013   0.002   TYR A 351 
 PHE   0.021   0.002   PHE A 377 
 TRP   0.011   0.001   TRP B 107 
 HIS   0.002   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 ( 3323)
  covalent geometry    : angle       0.57240 ( 4511)
  SS BOND              : bond        0.00595 (    6)
  SS BOND              : angle       1.44928 (   12)
  hydrogen bonds       : bond        0.03233 (  105)
  hydrogen bonds       : angle       5.58384 (  261)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.079 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7432 (ttt-90)
REVERT: B  109 GLN cc_start: 0.7357 (pm20) cc_final: 0.6951 (pm20)
REVERT: D   61 ARG cc_start: 0.8016 (mtm110) cc_final: 0.7704 (ptp90)
REVERT: D   79 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6211 (mp0)
  outliers start: 16
  outliers final: 11
  residues processed: 101
  average time/residue: 0.2872
  time to fit residues: 30.2522
Evaluate side-chains
  105 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain D residue   20 SER
Chi-restraints excluded: chain D residue   22 SER
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain D residue   79 GLU
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 21 optimal weight:    0.3980
   chunk 23 optimal weight:    0.1980
   chunk 10 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0040
   chunk 9 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 28 optimal weight:    0.4980
   chunk 7 optimal weight:    0.0370
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.2270

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

Flipped N/Q/H residues before XYZ refinement:
B  83 ASN
D  37 GLN
A 409 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.137739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.128374 restraints weight = 4679.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3724 rms_B_bonded: 1.85
r_work: 0.3634 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3504 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3329  Z= 0.152
  Angle     :  0.529   6.715   4523  Z= 0.269
  Chirality :  0.044   0.132    474
  Planarity :  0.004   0.052    587
  Dihedral  :  4.568  21.915    462
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 17.82 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -0.10 (0.43), residues: 404
  helix: -1.29 (1.66), residues: 12
  sheet:  0.43 (0.44), residues: 145
  loop : -0.26 (0.41), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 357 
 TYR   0.013   0.001   TYR A 351 
 PHE   0.013   0.001   PHE A 377 
 TRP   0.008   0.001   TRP B 107 
 HIS   0.001   0.000   HIS B   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 3323)
  covalent geometry    : angle       0.52609 ( 4511)
  SS BOND              : bond        0.00486 (    6)
  SS BOND              : angle       1.25774 (   12)
  hydrogen bonds       : bond        0.02909 (  105)
  hydrogen bonds       : angle       5.47464 (  261)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7720 (ttt-90)
REVERT: B   80 LEU cc_start: 0.8894 (tp) cc_final: 0.8577 (tp)
REVERT: B  109 GLN cc_start: 0.7317 (pm20) cc_final: 0.6920 (pm20)
REVERT: D   79 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6048 (mp0)
REVERT: A  351 TYR cc_start: 0.8473 (p90) cc_final: 0.8221 (p90)
REVERT: A  357 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7991 (tpt-90)
REVERT: A  409 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8395 (mt0)
  outliers start: 16
  outliers final: 8
  residues processed: 107
  average time/residue: 0.2625
  time to fit residues: 29.5624
Evaluate side-chains
  113 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain D residue   20 SER
Chi-restraints excluded: chain D residue   22 SER
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain D residue   79 GLU
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain A residue  357 ARG
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  409 GLN
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    0.3980
   chunk 20 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 34 optimal weight:    0.4980
   chunk 21 optimal weight:    0.0010
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 29 optimal weight:    0.2980
   chunk 23 optimal weight:    0.3980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.3186

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

Flipped N/Q/H residues before XYZ refinement:
B  83 ASN
D  37 GLN
A 409 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.136819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.127256 restraints weight = 4748.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3710 rms_B_bonded: 1.90
r_work: 0.3616 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3482 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.2962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   3329  Z= 0.201
  Angle     :  0.562   6.814   4523  Z= 0.285
  Chirality :  0.045   0.130    474
  Planarity :  0.005   0.054    587
  Dihedral  :  4.738  22.817    462
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 18.68 %
    Favored  : 77.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -0.14 (0.42), residues: 404
  helix: -1.18 (1.69), residues: 12
  sheet:  0.38 (0.44), residues: 145
  loop : -0.28 (0.41), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  61 
 TYR   0.014   0.002   TYR D  36 
 PHE   0.023   0.002   PHE A 377 
 TRP   0.010   0.001   TRP B 107 
 HIS   0.001   0.000   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 3323)
  covalent geometry    : angle       0.55774 ( 4511)
  SS BOND              : bond        0.00557 (    6)
  SS BOND              : angle       1.42250 (   12)
  hydrogen bonds       : bond        0.03129 (  105)
  hydrogen bonds       : angle       5.51305 (  261)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7396 (ttt-90)
REVERT: B  109 GLN cc_start: 0.7334 (pm20) cc_final: 0.6924 (pm20)
REVERT: D   79 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6103 (mp0)
REVERT: A  357 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8073 (tpt-90)
REVERT: A  409 GLN cc_start: 0.8661 (mt0) cc_final: 0.8371 (mt0)
  outliers start: 15
  outliers final: 9
  residues processed: 106
  average time/residue: 0.2254
  time to fit residues: 25.1816
Evaluate side-chains
  111 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain D residue   20 SER
Chi-restraints excluded: chain D residue   22 SER
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain D residue   79 GLU
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain A residue  357 ARG
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0050
   chunk 32 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 35 optimal weight:    0.5980
   chunk 39 optimal weight:    0.0170
   chunk 14 optimal weight:    0.0970
   overall best weight:    0.2630

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

Flipped N/Q/H residues before XYZ refinement:
B  83 ASN
D  37 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.137378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.127843 restraints weight = 4716.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3720 rms_B_bonded: 1.88
r_work: 0.3629 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3496 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.3024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3329  Z= 0.171
  Angle     :  0.548   6.730   4523  Z= 0.279
  Chirality :  0.045   0.129    474
  Planarity :  0.004   0.052    587
  Dihedral  :  4.691  24.636    462
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 19.25 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole: -0.11 (0.43), residues: 404
  helix: -1.09 (1.73), residues: 12
  sheet:  0.37 (0.44), residues: 145
  loop : -0.24 (0.41), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  61 
 TYR   0.019   0.002   TYR A 351 
 PHE   0.015   0.001   PHE A 377 
 TRP   0.009   0.001   TRP B 107 
 HIS   0.001   0.000   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 3323)
  covalent geometry    : angle       0.54349 ( 4511)
  SS BOND              : bond        0.00522 (    6)
  SS BOND              : angle       1.44657 (   12)
  hydrogen bonds       : bond        0.03006 (  105)
  hydrogen bonds       : angle       5.48822 (  261)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7746 (ttt-90)
REVERT: B   80 LEU cc_start: 0.8897 (tp) cc_final: 0.8568 (tp)
REVERT: B  109 GLN cc_start: 0.7324 (pm20) cc_final: 0.6907 (pm20)
REVERT: D   79 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6138 (mp0)
REVERT: A  357 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7986 (tpt-90)
  outliers start: 14
  outliers final: 9
  residues processed: 103
  average time/residue: 0.2295
  time to fit residues: 24.9558
Evaluate side-chains
  112 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain D residue   20 SER
Chi-restraints excluded: chain D residue   22 SER
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain D residue   79 GLU
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain A residue  357 ARG
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0870
   chunk 18 optimal weight:    0.1980
   chunk 34 optimal weight:    0.0980
   chunk 33 optimal weight:    0.3980
   chunk 7 optimal weight:    0.0870
   chunk 21 optimal weight:    0.0570
   overall best weight:    0.1054

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

Flipped N/Q/H residues before XYZ refinement:
B  83 ASN
A 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.139901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.130415 restraints weight = 4685.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 1.88
r_work: 0.3667 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3535 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.3078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   3329  Z= 0.097
  Angle     :  0.492   6.169   4523  Z= 0.252
  Chirality :  0.043   0.130    474
  Planarity :  0.004   0.050    587
  Dihedral  :  4.286  21.940    462
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 20.98 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole:  0.05 (0.43), residues: 404
  helix: -1.21 (1.69), residues: 12
  sheet:  0.57 (0.45), residues: 134
  loop : -0.15 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 357 
 TYR   0.015   0.001   TYR D  36 
 PHE   0.021   0.001   PHE A 377 
 TRP   0.010   0.001   TRP A 436 
 HIS   0.001   0.000   HIS B   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 3323)
  covalent geometry    : angle       0.48973 ( 4511)
  SS BOND              : bond        0.00381 (    6)
  SS BOND              : angle       1.08006 (   12)
  hydrogen bonds       : bond        0.02626 (  105)
  hydrogen bonds       : angle       5.28648 (  261)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: B  109 GLN cc_start: 0.7346 (pm20) cc_final: 0.6922 (pm20)
REVERT: A  335 LEU cc_start: 0.7262 (mm) cc_final: 0.6548 (mm)
REVERT: A  409 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8423 (mt0)
REVERT: A  424 LYS cc_start: 0.8368 (ttmm) cc_final: 0.8151 (tttp)
  outliers start: 10
  outliers final: 7
  residues processed: 101
  average time/residue: 0.2215
  time to fit residues: 23.6015
Evaluate side-chains
  102 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   71 ARG
Chi-restraints excluded: chain D residue   20 SER
Chi-restraints excluded: chain D residue   22 SER
Chi-restraints excluded: chain D residue   26 SER
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  409 GLN
Chi-restraints excluded: chain A residue  512 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    0.0980
   chunk 21 optimal weight:    0.0770
   chunk 20 optimal weight:    0.4980
   chunk 19 optimal weight:    0.3980
   chunk 29 optimal weight:    0.0770
   chunk 16 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0980
   chunk 23 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 26 optimal weight:    0.4980
   chunk 33 optimal weight:    0.4980
   overall best weight:    0.1496

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

Flipped N/Q/H residues before XYZ refinement:
B  83 ASN
D  37 GLN
A 343 ASN
A 409 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.139393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.129753 restraints weight = 4711.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 1.89
r_work: 0.3653 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3519 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3329  Z= 0.115
  Angle     :  0.505   7.392   4523  Z= 0.257
  Chirality :  0.043   0.130    474
  Planarity :  0.004   0.051    587
  Dihedral  :  4.275  21.762    462
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 21.55 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 aren not related in a simple way.
  whole:  0.08 (0.43), residues: 404
  helix: -1.15 (1.72), residues: 12
  sheet:  0.63 (0.46), residues: 132
  loop : -0.15 (0.40), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 357 
 TYR   0.014   0.001   TYR D  36 
 PHE   0.012   0.001   PHE A 377 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.001   0.000   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 3323)
  covalent geometry    : angle       0.50176 ( 4511)
  SS BOND              : bond        0.00404 (    6)
  SS BOND              : angle       1.15195 (   12)
  hydrogen bonds       : bond        0.02723 (  105)
  hydrogen bonds       : angle       5.27584 (  261)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1494.04 seconds
wall clock time: 26 minutes 12.28 seconds (1572.28 seconds total)