Starting phenix.real_space_refine
on Thu Mar  6 01:07:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jgg_22326/03_2025/7jgg_22326.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jgg_22326/03_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_22326/03_2025/7jgg_22326.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jgg_22326/03_2025/7jgg_22326.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jgg_22326/03_2025/7jgg_22326.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jgg_22326/03_2025/7jgg_22326.cif"
  }
  resolution = 4.88
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.57, per 1000 atoms: 0.85
  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: 1.15
  Conformation dependent library (CDL) restraints added in 488.3 milliseconds
  

  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: 0.42
  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: 1.09

  Time building geometry restraints manager: 1.37 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:             2.210
  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:             0.110
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.380
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.900
-------------------------------------------------------------------------------
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   4264  Z= 0.143
  Angle     :  0.464  10.363   5710  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 : 54.49
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (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
 TRP   0.027   0.001   TRP A2515 
 HIS   0.000   0.000   HIS A2506 
 PHE   0.017   0.001   PHE A2094 
 TYR   0.007   0.000   TYR A2593 
 ARG   0.001   0.000   ARG A2178 

*********************** 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  : 0.476 
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: 0.1726
  time to fit residues: 8.0062
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  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 37 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 12 optimal weight:    9.9990
   chunk 25 optimal weight:    0.2980
   chunk 20 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 15 optimal weight:    8.9990
   chunk 23 optimal weight:    0.4980
   chunk 29 optimal weight:    0.0970
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3822 r_free = 0.3822 target = 0.068581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.056856 restraints weight = 58915.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.056311 restraints weight = 59028.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.056411 restraints weight = 64990.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3530
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3530 r_free = 0.3530    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3530 r_free = 0.3530    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3530
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6762
moved from start:          0.0816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   4264  Z= 0.112
  Angle     :  0.385   5.166   5710  Z= 0.215
  Chirality :  0.033   0.237    581
  Planarity :  0.003   0.041    728
  Dihedral  :  3.353  29.510    544
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 50.38
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.88 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  3.25 %
    Favored  : 96.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.39), residues: 490
  helix:  2.83 (0.29), residues: 315
  sheet:  None (None), residues: 0
  loop : -0.71 (0.47), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A2511 
 HIS   0.001   0.000   HIS A2506 
 PHE   0.016   0.001   PHE A2072 
 TYR   0.006   0.001   TYR A2095 
 ARG   0.003   0.000   ARG A2463 

*********************** 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: 1
    poor density    : 34
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2060 GLU cc_start: 0.7743 (tp30) cc_final: 0.7270 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1634
  time to fit residues: 7.8438
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  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 37 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 41 optimal weight:    7.9990
   chunk 1 optimal weight:    6.9990
   chunk 29 optimal weight:    0.8980
   chunk 20 optimal weight:    9.9990
   chunk 13 optimal weight:    0.4980
   overall best weight:    2.2786

-------------------------------------------------------------------------------
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
** A2506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.064841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.055625 restraints weight = 61957.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.055548 restraints weight = 64620.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.055777 restraints weight = 64568.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3557
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3557 r_free = 0.3557    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3557 r_free = 0.3557    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3557
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6603
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   4264  Z= 0.181
  Angle     :  0.478   4.996   5710  Z= 0.272
  Chirality :  0.034   0.126    581
  Planarity :  0.003   0.039    728
  Dihedral  :  3.630  30.363    544
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 66.33
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.88 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  3.90 %
    Favored  : 95.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.39), residues: 490
  helix:  2.70 (0.29), residues: 314
  sheet:  None (None), residues: 0
  loop : -0.77 (0.48), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A2511 
 HIS   0.003   0.001   HIS A2506 
 PHE   0.017   0.002   PHE A2176 
 TYR   0.010   0.001   TYR A2580 
 ARG   0.008   0.001   ARG A2038 

*********************** 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: 1
    poor density    : 33
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2249 MET cc_start: 0.4048 (mmt) cc_final: 0.3744 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 34
  average time/residue: 0.1623
  time to fit residues: 7.5159
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  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 27 optimal weight:    9.9990
   chunk 35 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 20 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 40 optimal weight:   30.0000
   chunk 25 optimal weight:    0.0870
   overall best weight:    1.3762

-------------------------------------------------------------------------------
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**
A2557 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.064655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.055473 restraints weight = 61308.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.055394 restraints weight = 63672.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.055581 restraints weight = 64787.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3548
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3548 r_free = 0.3548    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3548 r_free = 0.3548    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3548
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6627
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4264  Z= 0.119
  Angle     :  0.414   8.270   5710  Z= 0.229
  Chirality :  0.033   0.139    581
  Planarity :  0.003   0.031    728
  Dihedral  :  3.644  28.439    544
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 64.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  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 : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.39), residues: 490
  helix:  2.56 (0.28), residues: 322
  sheet:  None (None), residues: 0
  loop : -0.84 (0.50), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A2511 
 HIS   0.002   0.001   HIS A2473 
 PHE   0.016   0.002   PHE A2094 
 TYR   0.020   0.001   TYR A2197 
 ARG   0.005   0.000   ARG A2038 

*********************** 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
  34 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2060 GLU cc_start: 0.7819 (tp30) cc_final: 0.7324 (mm-30)
REVERT: A 2249 MET cc_start: 0.4336 (mmt) cc_final: 0.4120 (mmt)
REVERT: A 2470 ASN cc_start: 0.8467 (m-40) cc_final: 0.8163 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.2107
  time to fit residues: 9.4751
Evaluate side-chains
  31 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0770
   chunk 33 optimal weight:    8.9990
   chunk 1 optimal weight:    9.9990
   chunk 43 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   overall best weight:    2.8146

-------------------------------------------------------------------------------
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 = 0.3645 r_free = 0.3645 target = 0.061132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.051916 restraints weight = 64173.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.052091 restraints weight = 61362.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.052091 restraints weight = 58973.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3435
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3435 r_free = 0.3435    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3435 r_free = 0.3435    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3435
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6926
moved from start:          0.3650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4264  Z= 0.211
  Angle     :  0.507   4.158   5710  Z= 0.288
  Chirality :  0.035   0.126    581
  Planarity :  0.003   0.032    728
  Dihedral  :  3.994  30.079    544
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 83.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.37), residues: 490
  helix:  2.14 (0.28), residues: 318
  sheet:  None (None), residues: 0
  loop : -1.21 (0.45), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A2228 
 HIS   0.002   0.001   HIS A2506 
 PHE   0.020   0.003   PHE A2594 
 TYR   0.014   0.001   TYR A2197 
 ARG   0.006   0.001   ARG A2038 

*********************** 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
  35 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2021 MET cc_start: 0.2055 (mtt) cc_final: 0.1783 (mtt)
REVERT: A 2060 GLU cc_start: 0.8178 (tp30) cc_final: 0.7750 (mm-30)
REVERT: A 2426 TYR cc_start: 0.7603 (t80) cc_final: 0.7113 (t80)
REVERT: A 2430 ASP cc_start: 0.9130 (t0) cc_final: 0.8753 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1760
  time to fit residues: 8.4112
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  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 8 optimal weight:    9.9990
   chunk 24 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0030
   chunk 6 optimal weight:    6.9990
   overall best weight:    1.3996

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.061776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.052649 restraints weight = 63298.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.052407 restraints weight = 63300.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.052568 restraints weight = 65683.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3457
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3457
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6885
moved from start:          0.3746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4264  Z= 0.125
  Angle     :  0.410   4.083   5710  Z= 0.233
  Chirality :  0.033   0.121    581
  Planarity :  0.003   0.032    728
  Dihedral  :  3.848  30.324    544
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 67.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.39), residues: 490
  helix:  2.40 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -1.12 (0.46), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A2475 
 HIS   0.001   0.000   HIS A2506 
 PHE   0.012   0.002   PHE A2176 
 TYR   0.010   0.001   TYR A2580 
 ARG   0.004   0.000   ARG A2038 

*********************** 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
  34 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2021 MET cc_start: 0.1579 (mtt) cc_final: 0.1325 (mtt)
REVERT: A 2060 GLU cc_start: 0.8140 (tp30) cc_final: 0.7773 (mm-30)
REVERT: A 2249 MET cc_start: 0.3801 (mmt) cc_final: 0.3551 (mmt)
REVERT: A 2426 TYR cc_start: 0.7491 (t80) cc_final: 0.7072 (t80)
REVERT: A 2430 ASP cc_start: 0.9157 (t0) cc_final: 0.8800 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.2235
  time to fit residues: 10.2827
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  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0040
   chunk 46 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 26 optimal weight:    8.9990
   chunk 14 optimal weight:    0.0000
   chunk 37 optimal weight:    5.9990
   overall best weight:    2.2002

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

Flipped N/Q/H residues before XYZ refinement:
A2054 ASN
** 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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.059807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.050804 restraints weight = 63976.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.051070 restraints weight = 60889.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 13)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.051266 restraints weight = 57776.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3411
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3411 r_free = 0.3411    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3411 r_free = 0.3411    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3411
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6953
moved from start:          0.4601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4264  Z= 0.161
  Angle     :  0.471   3.839   5710  Z= 0.266
  Chirality :  0.034   0.122    581
  Planarity :  0.003   0.036    728
  Dihedral  :  3.994  30.029    544
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 81.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.38), residues: 490
  helix:  2.14 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -1.29 (0.45), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A2228 
 HIS   0.003   0.001   HIS A2473 
 PHE   0.017   0.003   PHE A2176 
 TYR   0.009   0.001   TYR A2472 
 ARG   0.005   0.001   ARG A2038 

*********************** 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  : 0.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2021 MET cc_start: 0.2368 (mtt) cc_final: 0.2159 (mtt)
REVERT: A 2060 GLU cc_start: 0.8281 (tp30) cc_final: 0.7916 (mm-30)
REVERT: A 2148 MET cc_start: 0.1965 (mmp) cc_final: 0.1665 (mmp)
REVERT: A 2249 MET cc_start: 0.4513 (mmt) cc_final: 0.4083 (mmt)
REVERT: A 2426 TYR cc_start: 0.7886 (t80) cc_final: 0.7290 (t80)
REVERT: A 2430 ASP cc_start: 0.9203 (t0) cc_final: 0.8846 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1845
  time to fit residues: 9.0859
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  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 29 optimal weight:    0.2980
   chunk 28 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 33 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 46 optimal weight:    9.9990
   chunk 21 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0970
   overall best weight:    0.9980

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.061130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.052046 restraints weight = 60955.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.052437 restraints weight = 55723.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.052746 restraints weight = 51752.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3438
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3438 r_free = 0.3438    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3438 r_free = 0.3438    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3438
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6900
moved from start:          0.4607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   4264  Z= 0.113
  Angle     :  0.394   4.644   5710  Z= 0.224
  Chirality :  0.033   0.122    581
  Planarity :  0.003   0.035    728
  Dihedral  :  3.851  29.534    544
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 71.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.39), residues: 490
  helix:  2.37 (0.29), residues: 317
  sheet:  None (None), residues: 0
  loop : -1.10 (0.46), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A2515 
 HIS   0.002   0.001   HIS A2194 
 PHE   0.011   0.002   PHE A2176 
 TYR   0.021   0.001   TYR A2197 
 ARG   0.003   0.000   ARG A2038 

*********************** 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
  37 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2060 GLU cc_start: 0.8244 (tp30) cc_final: 0.7949 (mm-30)
REVERT: A 2249 MET cc_start: 0.4588 (mmt) cc_final: 0.4181 (mmt)
REVERT: A 2426 TYR cc_start: 0.7590 (t80) cc_final: 0.7041 (t80)
REVERT: A 2430 ASP cc_start: 0.9219 (t0) cc_final: 0.8842 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1515
  time to fit residues: 7.6625
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  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 37 optimal weight:    7.9990
   chunk 31 optimal weight:    8.9990
   chunk 36 optimal weight:    8.9990
   chunk 12 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 19 optimal weight:   20.0000
   chunk 47 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    3.3386

-------------------------------------------------------------------------------
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**
** 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 = 0.3580 r_free = 0.3580 target = 0.057442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.048853 restraints weight = 63498.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.049255 restraints weight = 57350.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.049494 restraints weight = 52841.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3362
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3362 r_free = 0.3362    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3362 r_free = 0.3362    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3362
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7026
moved from start:          0.5663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4264  Z= 0.224
  Angle     :  0.578   5.682   5710  Z= 0.326
  Chirality :  0.037   0.129    581
  Planarity :  0.004   0.040    728
  Dihedral  :  4.351  30.571    544
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 97.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.38), residues: 490
  helix:  1.73 (0.29), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.42 (0.45), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A2511 
 HIS   0.003   0.001   HIS A2473 
 PHE   0.019   0.003   PHE A2176 
 TYR   0.016   0.002   TYR A2197 
 ARG   0.006   0.001   ARG A2463 

*********************** 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
  36 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2021 MET cc_start: 0.3227 (mtt) cc_final: 0.2860 (mtt)
REVERT: A 2060 GLU cc_start: 0.8448 (tp30) cc_final: 0.8113 (mm-30)
REVERT: A 2148 MET cc_start: 0.2739 (mmp) cc_final: 0.2402 (mmp)
REVERT: A 2249 MET cc_start: 0.5083 (mmt) cc_final: 0.4574 (mmt)
REVERT: A 2426 TYR cc_start: 0.8059 (t80) cc_final: 0.7454 (t80)
REVERT: A 2430 ASP cc_start: 0.9337 (t0) cc_final: 0.9024 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.1547
  time to fit residues: 7.6138
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  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0980
   chunk 13 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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
** A2211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3631 r_free = 0.3631 target = 0.059070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.050246 restraints weight = 61052.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.050636 restraints weight = 55631.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.050849 restraints weight = 51262.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3410
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3410 r_free = 0.3410    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3410 r_free = 0.3410    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3410
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6960
moved from start:          0.5485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4264  Z= 0.116
  Angle     :  0.420   3.752   5710  Z= 0.236
  Chirality :  0.034   0.124    581
  Planarity :  0.003   0.036    728
  Dihedral  :  4.003  29.825    544
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 74.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.39), residues: 490
  helix:  2.12 (0.29), residues: 322
  sheet:  None (None), residues: 0
  loop : -1.10 (0.48), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A2515 
 HIS   0.002   0.001   HIS A2194 
 PHE   0.013   0.002   PHE A2094 
 TYR   0.007   0.001   TYR A2580 
 ARG   0.002   0.000   ARG A2038 

********************** 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
  38 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2021 MET cc_start: 0.2818 (mtt) cc_final: 0.2529 (mtt)
REVERT: A 2060 GLU cc_start: 0.8403 (tp30) cc_final: 0.8116 (mm-30)
REVERT: A 2148 MET cc_start: 0.2731 (mmp) cc_final: 0.2374 (mmp)
REVERT: A 2249 MET cc_start: 0.4704 (mmt) cc_final: 0.4283 (mmt)
REVERT: A 2426 TYR cc_start: 0.8031 (t80) cc_final: 0.7413 (t80)
REVERT: A 2430 ASP cc_start: 0.9313 (t0) cc_final: 0.8980 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.1450
  time to fit residues: 7.5176
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  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 8 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 26 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0070
   chunk 44 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 37 optimal weight:    8.9990
   chunk 25 optimal weight:    0.0170
   overall best weight:    0.7638

-------------------------------------------------------------------------------
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**
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.059164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.048437 restraints weight = 62849.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.048776 restraints weight = 58634.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.048971 restraints weight = 55364.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3362
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3362 r_free = 0.3362    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3362 r_free = 0.3362    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3362
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.5553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   4264  Z= 0.114
  Angle     :  0.414   4.314   5710  Z= 0.234
  Chirality :  0.033   0.120    581
  Planarity :  0.003   0.037    728
  Dihedral  :  3.843  28.099    544
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 72.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  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 : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.39), residues: 490
  helix:  2.27 (0.29), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.96 (0.48), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A2515 
 HIS   0.003   0.001   HIS A2194 
 PHE   0.012   0.002   PHE A2094 
 TYR   0.013   0.001   TYR A2197 
 ARG   0.002   0.000   ARG A2038 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1771.15 seconds
wall clock time: 32 minutes 52.92 seconds (1972.92 seconds total)