Starting phenix.real_space_refine
on Fri Aug 22 14:41:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jgg_22326/08_2025/7jgg_22326.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jgg_22326/08_2025/7jgg_22326.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jgg_22326/08_2025/7jgg_22326.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jgg_22326/08_2025/7jgg_22326.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jgg_22326/08_2025/7jgg_22326.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jgg_22326/08_2025/7jgg_22326.cif"
  }
  resolution = 4.88
  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=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    2643      2.51       5
     N     713      2.21       5
     O     799      1.98       5
     H      28      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 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: 4210
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4210
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 4210
          Classifications: {'peptide': 506}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 14, 'TRANS': 491}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 1.02, per 1000 atoms: 0.24
  Number of scatterers: 4210
  At special positions: 0
  Unit cell: (75.118, 131.192, 93.104, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     O     799      8.00
     N     713      7.00
     C    2643      6.00
     H      28      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A2202 " - pdb=" SG  CYS A2218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2334 " - pdb=" SG  CYS A2480 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2520 " - pdb=" SG  CYS A2604 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2534 " - pdb=" SG  CYS A2551 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2598 " - pdb=" SG  CYS A2602 " 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: 0.31
  Conformation dependent library (CDL) restraints added in 119.6 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  962

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 0 sheets defined
      70.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2017 through 2026
      Proline residue:  A2024  - end of helix
    Processing helix  chain 'A' and resid 2034 through 2039
      removed outlier: 3.937A  pdb=" N   GLN A2039 " --> pdb=" O   PRO A2035 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2054 through 2081
    Processing helix  chain 'A' and resid 2084 through 2102
    Processing helix  chain 'A' and resid 2113 through 2125
      removed outlier: 3.708A  pdb=" N   LYS A2125 " --> pdb=" O   ARG A2121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2129 through 2147
      removed outlier: 4.073A  pdb=" N   VAL A2133 " --> pdb=" O   ASN A2129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2174 through 2201
      removed outlier: 3.585A  pdb=" N   LYS A2201 " --> pdb=" O   TYR A2197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2211 through 2214
    Processing helix  chain 'A' and resid 2215 through 2247
      removed outlier: 3.821A  pdb=" N   THR A2219 " --> pdb=" O   SER A2215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2298 through 2303
      removed outlier: 3.647A  pdb=" N   LYS A2302 " --> pdb=" O   ASN A2298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2305 through 2309
    Processing helix  chain 'A' and resid 2332 through 2334
      No H-bonds generated for 'chain 'A' and resid 2332 through 2334'
    Processing helix  chain 'A' and resid 2335 through 2340
    Processing helix  chain 'A' and resid 2369 through 2374
      removed outlier: 4.100A  pdb=" N   ASN A2374 " --> pdb=" O   PRO A2370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2380 through 2382
      No H-bonds generated for 'chain 'A' and resid 2380 through 2382'
    Processing helix  chain 'A' and resid 2383 through 2390
      removed outlier: 3.621A  pdb=" N   LYS A2388 " --> pdb=" O   ILE A2384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2390 through 2414
      removed outlier: 3.746A  pdb=" N   PHE A2394 " --> pdb=" O   ASP A2390 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLY A2414 " --> pdb=" O   LYS A2410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2416 through 2436
    Processing helix  chain 'A' and resid 2442 through 2453
      removed outlier: 3.750A  pdb=" N   SER A2446 " --> pdb=" O   GLU A2442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2460 through 2486
    Processing helix  chain 'A' and resid 2506 through 2535
      removed outlier: 3.537A  pdb=" N   PHE A2512 " --> pdb=" O   PHE A2508 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   CYS A2534 " --> pdb=" O   MET A2530 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ASN A2535 " --> pdb=" O   VAL A2531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2549 through 2552
    Processing helix  chain 'A' and resid 2553 through 2581
      removed outlier: 3.883A  pdb=" N   ASN A2557 " --> pdb=" O   GLU A2553 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   TYR A2558 " --> pdb=" O   ALA A2554 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LYS A2581 " --> pdb=" O   ASP A2577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2589 through 2597

    243 hydrogen bonds defined for protein.
    717 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: 0.53

  Time building geometry restraints manager: 0.42 seconds

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

  Histogram of bond lengths:
        0.86 -     1.05: 28
        1.05 -     1.24: 543
        1.24 -     1.43: 1258
        1.43 -     1.62: 2425
        1.62 -     1.81: 38
  Bond restraints: 4292
  Sorted by residual:
  bond pdb=" CB  PRO A2391 "
       pdb=" CG  PRO A2391 "
    ideal  model  delta    sigma   weight residual
    1.492  1.594 -0.102 5.00e-02 4.00e+02 4.20e+00
  bond pdb=" CB  LEU A2040 "
       pdb=" CG  LEU A2040 "
    ideal  model  delta    sigma   weight residual
    1.530  1.552 -0.022 2.00e-02 2.50e+03 1.20e+00
  bond pdb=" CA  PRO A2391 "
       pdb=" CB  PRO A2391 "
    ideal  model  delta    sigma   weight residual
    1.533  1.543 -0.010 1.42e-02 4.96e+03 5.25e-01
  bond pdb=" N   PRO A2391 "
       pdb=" CD  PRO A2391 "
    ideal  model  delta    sigma   weight residual
    1.473  1.463  0.010 1.40e-02 5.10e+03 4.93e-01
  bond pdb=" N   PRO A2034 "
       pdb=" CA  PRO A2034 "
    ideal  model  delta    sigma   weight residual
    1.459  1.469 -0.009 1.40e-02 5.10e+03 4.36e-01
  ... (remaining 4287 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 5720
        2.07 -     4.15: 35
        4.15 -     6.22: 5
        6.22 -     8.29: 0
        8.29 -    10.36: 1
  Bond angle restraints: 5761
  Sorted by residual:
  angle pdb=" CA  PRO A2391 "
        pdb=" N   PRO A2391 "
        pdb=" CD  PRO A2391 "
      ideal   model   delta    sigma   weight residual
     112.00  106.54    5.46 1.40e+00 5.10e-01 1.52e+01
  angle pdb=" CB  LEU A2040 "
        pdb=" CG  LEU A2040 "
        pdb=" CD1 LEU A2040 "
      ideal   model   delta    sigma   weight residual
     110.70  121.06  -10.36 3.00e+00 1.11e-01 1.19e+01
  angle pdb=" C   GLN A2039 "
        pdb=" N   LEU A2040 "
        pdb=" CA  LEU A2040 "
      ideal   model   delta    sigma   weight residual
     121.54  127.66   -6.12 1.91e+00 2.74e-01 1.03e+01
  angle pdb=" N   PRO A2391 "
        pdb=" CD  PRO A2391 "
        pdb=" CG  PRO A2391 "
      ideal   model   delta    sigma   weight residual
     103.20   99.07    4.13 1.50e+00 4.44e-01 7.59e+00
  angle pdb=" C   ARG A2038 "
        pdb=" N   GLN A2039 "
        pdb=" CA  GLN A2039 "
      ideal   model   delta    sigma   weight residual
     121.54  116.46    5.08 1.91e+00 2.74e-01 7.07e+00
  ... (remaining 5756 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 2380
       17.95 -    35.90: 220
       35.90 -    53.84: 30
       53.84 -    71.79: 4
       71.79 -    89.74: 4
  Dihedral angle restraints: 2638
    sinusoidal: 1151
      harmonic: 1487
  Sorted by residual:
  dihedral pdb=" CB  CYS A2334 "
           pdb=" SG  CYS A2334 "
           pdb=" SG  CYS A2480 "
           pdb=" CB  CYS A2480 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -162.76   76.76     1      1.00e+01 1.00e-02 7.40e+01
  dihedral pdb=" CB  CYS A2202 "
           pdb=" SG  CYS A2202 "
           pdb=" SG  CYS A2218 "
           pdb=" CB  CYS A2218 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -17.19  -68.81     1      1.00e+01 1.00e-02 6.13e+01
  dihedral pdb=" CA  GLN A2039 "
           pdb=" C   GLN A2039 "
           pdb=" N   LEU A2040 "
           pdb=" CA  LEU A2040 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.28   32.72     0      5.00e+00 4.00e-02 4.28e+01
  ... (remaining 2635 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 537
       0.060 -    0.120: 41
       0.120 -    0.180: 2
       0.180 -    0.240: 0
       0.240 -    0.300: 1
  Chirality restraints: 581
  Sorted by residual:
  chirality pdb=" CG  LEU A2040 "
            pdb=" CB  LEU A2040 "
            pdb=" CD1 LEU A2040 "
            pdb=" CD2 LEU A2040 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.29   -0.30 2.00e-01 2.50e+01 2.25e+00
  chirality pdb=" CA  LEU A2040 "
            pdb=" N   LEU A2040 "
            pdb=" C   LEU A2040 "
            pdb=" CB  LEU A2040 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.46e-01
  chirality pdb=" CA  ILE A2499 "
            pdb=" N   ILE A2499 "
            pdb=" C   ILE A2499 "
            pdb=" CB  ILE A2499 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.03e-01
  ... (remaining 578 not shown)

  Planarity restraints: 728
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A2390 "    0.056 5.00e-02 4.00e+02   8.30e-02 1.10e+01
        pdb=" N   PRO A2391 "   -0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO A2391 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A2391 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A2039 "    0.011 2.00e-02 2.50e+03   2.28e-02 5.19e+00
        pdb=" C   GLN A2039 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   GLN A2039 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LEU A2040 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A2515 "    0.016 2.00e-02 2.50e+03   1.03e-02 2.64e+00
        pdb=" CG  TRP A2515 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD1 TRP A2515 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TRP A2515 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A2515 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A2515 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A2515 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A2515 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A2515 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A2515 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 725 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.51: 56
        2.51 -     3.03: 3194
        3.03 -     3.56: 5619
        3.56 -     4.08: 6954
        4.08 -     4.60: 10945
  Nonbonded interactions: 26768
  Sorted by model distance:
  nonbonded pdb=" O   LYS A2199 "
            pdb=" OG  SER A2203 "
     model   vdw
     1.988 2.800
  nonbonded pdb=" OE2 GLU A2415 "
            pdb=" OH  TYR A2486 "
     model   vdw
     2.077 2.800
  nonbonded pdb=" OG1 THR A2521 "
            pdb=" NZ  LYS A2522 "
     model   vdw
     2.204 2.950
  nonbonded pdb=" O   ILE A2100 "
            pdb=" NZ  LYS A2113 "
     model   vdw
     2.209 2.950
  nonbonded pdb=" O   LYS A2216 "
            pdb=" OG1 THR A2219 "
     model   vdw
     2.221 2.800
  ... (remaining 26763 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.75 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.550
  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:             0.030
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.950
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6428
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.102   4269  Z= 0.096
  Angle     :  0.465  10.363   5720  Z= 0.284
  Chirality :  0.034   0.300    581
  Planarity :  0.004   0.083    728
  Dihedral  : 13.224  89.738   1650
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 54.61
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.27 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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:  1.67 (0.39), residues: 490
  helix:  2.22 (0.31), residues: 302
  sheet:  None (None), residues: 0
  loop : -0.78 (0.44), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A2178 
 TYR   0.007   0.000   TYR A2593 
 PHE   0.017   0.001   PHE A2094 
 TRP   0.027   0.001   TRP A2515 
 HIS   0.000   0.000   HIS A2506 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 4264)
  covalent geometry    : angle       0.46415 ( 5710)
  SS BOND              : bond        0.00069 (    5)
  SS BOND              : angle       0.70345 (   10)
  hydrogen bonds       : bond        0.16238 (  243)
  hydrogen bonds       : angle       5.54474 (  717)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2060 GLU cc_start: 0.7934 (tp30) cc_final: 0.7689 (mm-30)
REVERT: A 2576 TYR cc_start: 0.7797 (t80) cc_final: 0.7540 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0613
  time to fit residues: 2.7871
Evaluate side-chains
  28 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 48 optimal weight:    0.5980
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    0.0050
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    7.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    1.0596

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

Flipped N/Q/H residues before XYZ refinement:
** A2140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2459 GLN
** A2506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.067909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.057279 restraints weight = 60152.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.056847 restraints weight = 59687.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.057037 restraints weight = 63057.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.057184 restraints weight = 59098.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.057294 restraints weight = 57084.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3555
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3555 r_free = 0.3555    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3555 r_free = 0.3555    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3555
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6692
moved from start:          0.0909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   4269  Z= 0.100
  Angle     :  0.393   5.125   5720  Z= 0.220
  Chirality :  0.034   0.240    581
  Planarity :  0.003   0.042    728
  Dihedral  :  3.389  29.132    544
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 53.04
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.88 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  3.47 %
    Favored  : 96.10 %
  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 aren not related in a simple way.
  whole:  2.50 (0.40), residues: 490
  helix:  2.96 (0.29), residues: 309
  sheet:  None (None), residues: 0
  loop : -0.76 (0.47), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2053 
 TYR   0.005   0.001   TYR A2095 
 PHE   0.015   0.001   PHE A2072 
 TRP   0.016   0.001   TRP A2511 
 HIS   0.002   0.000   HIS A2506 

Details of bonding type rmsd
  covalent geometry    : bond        0.00198 ( 4264)
  covalent geometry    : angle       0.39236 ( 5710)
  SS BOND              : bond        0.00128 (    5)
  SS BOND              : angle       0.62771 (   10)
  hydrogen bonds       : bond        0.04581 (  243)
  hydrogen bonds       : angle       4.01387 (  717)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2060 GLU cc_start: 0.7734 (tp30) cc_final: 0.7269 (mm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0601
  time to fit residues: 2.9404
Evaluate side-chains
  28 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0870
   chunk 45 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0670
   chunk 46 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 6 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.6300

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

Flipped N/Q/H residues before XYZ refinement:
** A2140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2506 HIS ** 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 = 0.3808 r_free = 0.3808 target = 0.068044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.057244 restraints weight = 60047.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.057030 restraints weight = 62896.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.057200 restraints weight = 64647.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.057423 restraints weight = 59857.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.057515 restraints weight = 57668.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3571
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3571
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6682
moved from start:          0.1194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.023   4269  Z= 0.080
  Angle     :  0.367   4.979   5720  Z= 0.207
  Chirality :  0.032   0.125    581
  Planarity :  0.003   0.052    728
  Dihedral  :  3.379  27.615    544
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 52.31
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.27 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  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 aren not related in a simple way.
  whole:  2.61 (0.40), residues: 490
  helix:  3.02 (0.29), residues: 309
  sheet:  None (None), residues: 0
  loop : -0.67 (0.48), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2038 
 TYR   0.007   0.001   TYR A2580 
 PHE   0.011   0.001   PHE A2072 
 TRP   0.013   0.001   TRP A2511 
 HIS   0.001   0.000   HIS A2506 

Details of bonding type rmsd
  covalent geometry    : bond        0.00149 ( 4264)
  covalent geometry    : angle       0.36557 ( 5710)
  SS BOND              : bond        0.00190 (    5)
  SS BOND              : angle       0.93664 (   10)
  hydrogen bonds       : bond        0.03734 (  243)
  hydrogen bonds       : angle       3.82962 (  717)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2060 GLU cc_start: 0.7763 (tp30) cc_final: 0.7287 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0642
  time to fit residues: 2.9689
Evaluate side-chains
  27 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0770
   chunk 20 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 8 optimal weight:    9.9990
   chunk 47 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 19 optimal weight:   20.0000
   chunk 37 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    2.2144

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

Flipped N/Q/H residues before XYZ refinement:
** A2129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2175 GLN
** A2211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2557 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.063515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.054388 restraints weight = 61507.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.054332 restraints weight = 63907.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.054520 restraints weight = 64594.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.054862 restraints weight = 58756.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.054961 restraints weight = 54907.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3526
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3526 r_free = 0.3526    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3526 r_free = 0.3526    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3526
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6761
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4269  Z= 0.146
  Angle     :  0.472   4.789   5720  Z= 0.269
  Chirality :  0.034   0.126    581
  Planarity :  0.003   0.028    728
  Dihedral  :  3.661  29.739    544
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 70.07
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.29 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  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 aren not related in a simple way.
  whole:  2.14 (0.38), residues: 490
  helix:  2.59 (0.28), residues: 316
  sheet:  None (None), residues: 0
  loop : -0.87 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A2038 
 TYR   0.017   0.001   TYR A2197 
 PHE   0.017   0.003   PHE A2176 
 TRP   0.013   0.001   TRP A2511 
 HIS   0.002   0.001   HIS A2506 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4264)
  covalent geometry    : angle       0.47022 ( 5710)
  SS BOND              : bond        0.00242 (    5)
  SS BOND              : angle       1.05246 (   10)
  hydrogen bonds       : bond        0.03944 (  243)
  hydrogen bonds       : angle       3.97600 (  717)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0530
  time to fit residues: 2.4443
Evaluate side-chains
  28 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 24 optimal weight:    9.9990
   chunk 40 optimal weight:    8.9990
   chunk 47 optimal weight:    2.9990
   chunk 22 optimal weight:    8.9990
   chunk 33 optimal weight:    8.9990
   chunk 31 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 2 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A2140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2473 HIS
** A2506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.063063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.054102 restraints weight = 62548.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.054020 restraints weight = 63332.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.054178 restraints weight = 64990.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.054590 restraints weight = 59261.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.054640 restraints weight = 55246.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3519
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3519 r_free = 0.3519    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3519 r_free = 0.3519    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3519
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6787
moved from start:          0.3011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4269  Z= 0.114
  Angle     :  0.426   4.615   5720  Z= 0.242
  Chirality :  0.034   0.151    581
  Planarity :  0.003   0.029    728
  Dihedral  :  3.741  29.448    544
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 67.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  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 aren not related in a simple way.
  whole:  1.98 (0.38), residues: 490
  helix:  2.55 (0.28), residues: 312
  sheet:  None (None), residues: 0
  loop : -1.04 (0.45), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A2038 
 TYR   0.020   0.001   TYR A2197 
 PHE   0.014   0.002   PHE A2176 
 TRP   0.008   0.001   TRP A2511 
 HIS   0.002   0.001   HIS A2473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 4264)
  covalent geometry    : angle       0.42426 ( 5710)
  SS BOND              : bond        0.00556 (    5)
  SS BOND              : angle       1.06634 (   10)
  hydrogen bonds       : bond        0.03713 (  243)
  hydrogen bonds       : angle       3.79410 (  717)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2060 GLU cc_start: 0.8061 (tp30) cc_final: 0.7680 (mm-30)
REVERT: A 2426 TYR cc_start: 0.7398 (t80) cc_final: 0.7025 (t80)
REVERT: A 2430 ASP cc_start: 0.9033 (t0) cc_final: 0.8657 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0683
  time to fit residues: 3.2139
Evaluate side-chains
  28 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 38 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9980
   chunk 11 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 46 optimal weight:    9.9990
   overall best weight:    2.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A2140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2529 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 = 0.3590 r_free = 0.3590 target = 0.059039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.050214 restraints weight = 65057.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.050445 restraints weight = 61440.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.050445 restraints weight = 58520.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.050445 restraints weight = 58520.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.050445 restraints weight = 58520.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3386
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3386 r_free = 0.3386    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3386 r_free = 0.3386    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3386
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6989
moved from start:          0.4532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4269  Z= 0.183
  Angle     :  0.572   4.886   5720  Z= 0.322
  Chirality :  0.037   0.126    581
  Planarity :  0.004   0.035    728
  Dihedral  :  4.305  31.654    544
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 94.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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:  1.08 (0.37), residues: 490
  helix:  1.76 (0.28), residues: 322
  sheet:  None (None), residues: 0
  loop : -1.40 (0.46), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A2038 
 TYR   0.017   0.002   TYR A2197 
 PHE   0.033   0.004   PHE A2094 
 TRP   0.013   0.001   TRP A2228 
 HIS   0.004   0.001   HIS A2473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 4264)
  covalent geometry    : angle       0.56297 ( 5710)
  SS BOND              : bond        0.00545 (    5)
  SS BOND              : angle       2.42007 (   10)
  hydrogen bonds       : bond        0.04411 (  243)
  hydrogen bonds       : angle       4.17596 (  717)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2021 MET cc_start: 0.3539 (mtt) cc_final: 0.2695 (mtt)
REVERT: A 2060 GLU cc_start: 0.8296 (tp30) cc_final: 0.7886 (mm-30)
REVERT: A 2249 MET cc_start: 0.4370 (mmt) cc_final: 0.3881 (mmt)
REVERT: A 2426 TYR cc_start: 0.7828 (t80) cc_final: 0.7226 (t80)
REVERT: A 2430 ASP cc_start: 0.9230 (t0) cc_final: 0.8867 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0627
  time to fit residues: 3.0912
Evaluate side-chains
  26 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 10 optimal weight:    8.9990
   chunk 28 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 33 optimal weight:    7.9990
   chunk 44 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A2140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2470 ASN
** A2506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.059244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.049225 restraints weight = 64656.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.049126 restraints weight = 62000.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.049261 restraints weight = 63401.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.049431 restraints weight = 58543.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.049596 restraints weight = 56427.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3364
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3365 r_free = 0.3365    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3365
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7002
moved from start:          0.5037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4269  Z= 0.150
  Angle     :  0.485   3.948   5720  Z= 0.278
  Chirality :  0.035   0.136    581
  Planarity :  0.004   0.037    728
  Dihedral  :  4.287  32.426    544
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 83.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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:  1.16 (0.38), residues: 490
  helix:  1.84 (0.29), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.41 (0.46), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A2038 
 TYR   0.014   0.001   TYR A2197 
 PHE   0.016   0.003   PHE A2176 
 TRP   0.010   0.001   TRP A2511 
 HIS   0.002   0.001   HIS A2506 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 4264)
  covalent geometry    : angle       0.48271 ( 5710)
  SS BOND              : bond        0.00415 (    5)
  SS BOND              : angle       1.17543 (   10)
  hydrogen bonds       : bond        0.04183 (  243)
  hydrogen bonds       : angle       4.21151 (  717)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2021 MET cc_start: 0.3680 (mtt) cc_final: 0.3389 (mtt)
REVERT: A 2060 GLU cc_start: 0.8171 (tp30) cc_final: 0.7847 (mm-30)
REVERT: A 2106 MET cc_start: 0.8152 (mmp) cc_final: 0.7681 (mmp)
REVERT: A 2249 MET cc_start: 0.4611 (mmt) cc_final: 0.4119 (mmt)
REVERT: A 2426 TYR cc_start: 0.8012 (t80) cc_final: 0.7414 (t80)
REVERT: A 2430 ASP cc_start: 0.9284 (t0) cc_final: 0.8990 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0610
  time to fit residues: 2.9929
Evaluate side-chains
  24 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 43 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9980
   chunk 15 optimal weight:    9.9990
   chunk 32 optimal weight:   10.0000
   chunk 34 optimal weight:    1.9990
   chunk 8 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A2140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2529 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 = 0.3567 r_free = 0.3567 target = 0.057379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.047902 restraints weight = 65294.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.047962 restraints weight = 60322.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.048201 restraints weight = 57926.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.048295 restraints weight = 53686.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.048345 restraints weight = 52701.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3327
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3327 r_free = 0.3327    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3327 r_free = 0.3327    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3327
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7048
moved from start:          0.5767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   4269  Z= 0.183
  Angle     :  0.547   5.484   5720  Z= 0.320
  Chirality :  0.038   0.294    581
  Planarity :  0.004   0.039    728
  Dihedral  :  4.461  32.511    544
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 95.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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:  0.85 (0.38), residues: 490
  helix:  1.60 (0.29), residues: 322
  sheet:  None (None), residues: 0
  loop : -1.55 (0.47), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A2038 
 TYR   0.021   0.001   TYR A2197 
 PHE   0.016   0.003   PHE A2176 
 TRP   0.063   0.003   TRP A2136 
 HIS   0.003   0.001   HIS A2473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 4264)
  covalent geometry    : angle       0.54535 ( 5710)
  SS BOND              : bond        0.00305 (    5)
  SS BOND              : angle       1.22212 (   10)
  hydrogen bonds       : bond        0.04597 (  243)
  hydrogen bonds       : angle       4.43764 (  717)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
REVERT: A 2021 MET cc_start: 0.4126 (mtt) cc_final: 0.3840 (mtt)
REVERT: A 2060 GLU cc_start: 0.8333 (tp30) cc_final: 0.8025 (mm-30)
REVERT: A 2426 TYR cc_start: 0.7975 (t80) cc_final: 0.7378 (t80)
REVERT: A 2430 ASP cc_start: 0.9407 (t0) cc_final: 0.9103 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0645
  time to fit residues: 3.0317
Evaluate side-chains
  22 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 20 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A2175 GLN
** A2374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.057209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.047258 restraints weight = 65409.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.047072 restraints weight = 63841.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.047289 restraints weight = 64382.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.047454 restraints weight = 60054.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.047578 restraints weight = 57560.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3330
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3330 r_free = 0.3330    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3330 r_free = 0.3330    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3330
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
moved from start:          0.5903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4269  Z= 0.130
  Angle     :  0.490   5.351   5720  Z= 0.276
  Chirality :  0.035   0.147    581
  Planarity :  0.003   0.038    728
  Dihedral  :  4.350  32.492    544
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 84.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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:  1.04 (0.38), residues: 490
  helix:  1.71 (0.29), residues: 323
  sheet:  None (None), residues: 0
  loop : -1.40 (0.48), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A2038 
 TYR   0.017   0.001   TYR A2387 
 PHE   0.016   0.003   PHE A2512 
 TRP   0.041   0.002   TRP A2136 
 HIS   0.003   0.001   HIS A2506 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 4264)
  covalent geometry    : angle       0.48787 ( 5710)
  SS BOND              : bond        0.00267 (    5)
  SS BOND              : angle       1.13780 (   10)
  hydrogen bonds       : bond        0.04205 (  243)
  hydrogen bonds       : angle       4.20798 (  717)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2021 MET cc_start: 0.4007 (mtt) cc_final: 0.3798 (mtt)
REVERT: A 2060 GLU cc_start: 0.8379 (tp30) cc_final: 0.8028 (mm-30)
REVERT: A 2426 TYR cc_start: 0.8020 (t80) cc_final: 0.7434 (t80)
REVERT: A 2430 ASP cc_start: 0.9423 (t0) cc_final: 0.9121 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0625
  time to fit residues: 2.7625
Evaluate side-chains
  25 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 24 optimal weight:    7.9990
   chunk 46 optimal weight:    7.9990
   chunk 47 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 30 optimal weight:    0.4980
   chunk 15 optimal weight:    0.5980
   chunk 35 optimal weight:    7.9990
   chunk 34 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A2175 GLN
** A2330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.057770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.047329 restraints weight = 63833.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.047506 restraints weight = 59647.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.047795 restraints weight = 57331.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.047978 restraints weight = 54859.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.048151 restraints weight = 52858.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3347
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3347
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7079
moved from start:          0.5949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4269  Z= 0.104
  Angle     :  0.444   4.036   5720  Z= 0.253
  Chirality :  0.035   0.119    581
  Planarity :  0.003   0.038    728
  Dihedral  :  4.152  30.973    544
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 78.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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:  1.22 (0.39), residues: 490
  helix:  1.85 (0.29), residues: 323
  sheet:  None (None), residues: 0
  loop : -1.33 (0.49), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2038 
 TYR   0.023   0.001   TYR A2197 
 PHE   0.013   0.002   PHE A2394 
 TRP   0.021   0.001   TRP A2515 
 HIS   0.003   0.001   HIS A2194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 4264)
  covalent geometry    : angle       0.44222 ( 5710)
  SS BOND              : bond        0.00280 (    5)
  SS BOND              : angle       1.15293 (   10)
  hydrogen bonds       : bond        0.04009 (  243)
  hydrogen bonds       : angle       4.08264 (  717)

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

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

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  980 Ramachandran restraints generated.
    490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2021 MET cc_start: 0.3663 (mtt) cc_final: 0.3433 (mtt)
REVERT: A 2060 GLU cc_start: 0.8445 (tp30) cc_final: 0.8098 (mm-30)
REVERT: A 2249 MET cc_start: 0.5019 (mmt) cc_final: 0.4679 (mmt)
REVERT: A 2426 TYR cc_start: 0.8095 (t80) cc_final: 0.7495 (t80)
REVERT: A 2430 ASP cc_start: 0.9385 (t0) cc_final: 0.9063 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0634
  time to fit residues: 3.0751
Evaluate side-chains
  24 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0040
   chunk 42 optimal weight:    9.9990
   chunk 46 optimal weight:    1.9990
   chunk 36 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 5 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9990
   chunk 30 optimal weight:    0.4980
   overall best weight:    0.6394

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

Flipped N/Q/H residues before XYZ refinement:
A2175 GLN
** A2330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.058699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.047959 restraints weight = 64533.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.048232 restraints weight = 60257.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.048571 restraints weight = 57011.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.048714 restraints weight = 54260.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.048899 restraints weight = 52593.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3364
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3364 r_free = 0.3364    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3364
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.5863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   4269  Z= 0.090
  Angle     :  0.429   3.847   5720  Z= 0.241
  Chirality :  0.034   0.119    581
  Planarity :  0.003   0.038    728
  Dihedral  :  3.940  28.956    544
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 71.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.51 (0.39), residues: 490
  helix:  2.08 (0.29), residues: 322
  sheet:  None (None), residues: 0
  loop : -1.21 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2038 
 TYR   0.018   0.001   TYR A2197 
 PHE   0.011   0.001   PHE A2072 
 TRP   0.020   0.001   TRP A2136 
 HIS   0.001   0.000   HIS A2506 

Details of bonding type rmsd
  covalent geometry    : bond        0.00172 ( 4264)
  covalent geometry    : angle       0.42684 ( 5710)
  SS BOND              : bond        0.00208 (    5)
  SS BOND              : angle       1.07066 (   10)
  hydrogen bonds       : bond        0.03861 (  243)
  hydrogen bonds       : angle       4.00149 (  717)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 947.82 seconds
wall clock time: 17 minutes 13.70 seconds (1033.70 seconds total)