Starting phenix.real_space_refine
on Tue Feb 11 05:44:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jgg_22326/02_2025/7jgg_22326.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jgg_22326/02_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_22326/02_2025/7jgg_22326.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jgg_22326/02_2025/7jgg_22326.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jgg_22326/02_2025/7jgg_22326.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jgg_22326/02_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-5592/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: 3.27, per 1000 atoms: 0.78
  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: 1.07
  Conformation dependent library (CDL) restraints added in 467.5 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: 0.38
  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: 1.05

  Time building geometry restraints manager: 1.25 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:             1.370
  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:             0.130
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.340
  Find NCS groups from input model:        0.040
  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:             0.010
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.130
-------------------------------------------------------------------------------
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  : 0.507 
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: 0.1792
  time to fit residues: 8.2320
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  : 0.500 
-------------------------------------------------------------------------------
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 = 0.068579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.056857 restraints weight = 58908.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.056295 restraints weight = 59024.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.056394 restraints weight = 65089.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3529
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3529 r_free = 0.3529    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: 0.6763
moved from start:          0.0818

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   5.162   5710  Z= 0.215
  Chirality :  0.033   0.235    581
  Planarity :  0.003   0.041    728
  Dihedral  :  3.352  29.474    544
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 50.14
  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 (0.40), 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  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2060 GLU cc_start: 0.7742 (tp30) cc_final: 0.7268 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1620
  time to fit residues: 7.7204
Evaluate side-chains
  29 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 33 optimal weight:    8.9990
   chunk 31 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 41 optimal weight:   10.0000
   chunk 1 optimal weight:    8.9990
   chunk 29 optimal weight:    9.9990
   chunk 20 optimal weight:   10.0000
   chunk 13 optimal weight:    0.3980
   overall best weight:    3.2386

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

Flipped N/Q/H residues before XYZ refinement:
A2109 ASN
** 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
A2473 HIS
** A2506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.062200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.053238 restraints weight = 63542.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.053185 restraints weight = 65027.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.053391 restraints weight = 65119.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3488
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3488 r_free = 0.3488    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3488 r_free = 0.3488    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3488
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6696
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4264  Z= 0.247
  Angle     :  0.605   6.591   5710  Z= 0.342
  Chirality :  0.037   0.150    581
  Planarity :  0.004   0.032    728
  Dihedral  :  4.108  32.322    544
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 81.31
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.69 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  6.72 %
    Favored  : 93.06 %
  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:  1.55 (0.37), residues: 490
  helix:  2.05 (0.28), residues: 315
  sheet:  None (None), residues: 0
  loop : -0.90 (0.47), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A2511 
 HIS   0.004   0.001   HIS A2506 
 PHE   0.023   0.003   PHE A2512 
 TYR   0.015   0.002   TYR A2472 
 ARG   0.010   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
  33 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 32
  time to evaluate  : 0.595 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2249 MET cc_start: 0.4368 (mmt) cc_final: 0.4128 (mmt)
REVERT: A 2558 TYR cc_start: 0.8577 (t80) cc_final: 0.8109 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 33
  average time/residue: 0.1551
  time to fit residues: 7.0992
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  : 0.491 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 27 optimal weight:   10.0000
   chunk 35 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 20 optimal weight:    8.9990
   chunk 12 optimal weight:    8.9990
   chunk 46 optimal weight:    0.9990
   chunk 40 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A2109 ASN
** 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 = 0.3666 r_free = 0.3666 target = 0.062047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.053141 restraints weight = 62917.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.053105 restraints weight = 62828.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.053256 restraints weight = 63901.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3465
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3465 r_free = 0.3465    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3465 r_free = 0.3465    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3465
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6832
moved from start:          0.3398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4264  Z= 0.160
  Angle     :  0.452   4.867   5710  Z= 0.258
  Chirality :  0.034   0.142    581
  Planarity :  0.003   0.030    728
  Dihedral  :  3.984  30.045    544
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 71.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  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:  1.49 (0.38), residues: 490
  helix:  2.10 (0.28), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.24 (0.46), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A2183 
 HIS   0.002   0.001   HIS A2194 
 PHE   0.014   0.002   PHE A2176 
 TYR   0.021   0.001   TYR A2197 
 ARG   0.007   0.001   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
  35 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2021 MET cc_start: 0.1833 (mtt) cc_final: 0.1556 (mtt)
REVERT: A 2060 GLU cc_start: 0.8208 (tp30) cc_final: 0.7790 (mm-30)
REVERT: A 2426 TYR cc_start: 0.7408 (t80) cc_final: 0.7016 (t80)
REVERT: A 2430 ASP cc_start: 0.9156 (t0) cc_final: 0.8795 (m-30)
REVERT: A 2441 MET cc_start: 0.9089 (ptt) cc_final: 0.8220 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1480
  time to fit residues: 7.1404
Evaluate side-chains
  29 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 35 optimal weight:   20.0000
   chunk 15 optimal weight:    7.9990
   chunk 46 optimal weight:    6.9990
   chunk 4 optimal weight:    9.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3653 r_free = 0.3653 target = 0.061329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.051646 restraints weight = 63478.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.051835 restraints weight = 60128.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.052074 restraints weight = 57729.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3437
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3437 r_free = 0.3437    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3437 r_free = 0.3437    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3437
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6922
moved from start:          0.3837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4264  Z= 0.159
  Angle     :  0.443   4.322   5710  Z= 0.254
  Chirality :  0.033   0.130    581
  Planarity :  0.003   0.031    728
  Dihedral  :  3.927  30.725    544
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 72.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  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:  1.58 (0.38), residues: 490
  helix:  2.18 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.24 (0.45), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A2183 
 HIS   0.002   0.001   HIS A2506 
 PHE   0.014   0.002   PHE A2176 
 TYR   0.018   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
  36 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  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: 0.1719 (mtt) cc_final: 0.1410 (mtt)
REVERT: A 2060 GLU cc_start: 0.8212 (tp30) cc_final: 0.7780 (mm-30)
REVERT: A 2249 MET cc_start: 0.4059 (mmt) cc_final: 0.3718 (mmt)
REVERT: A 2426 TYR cc_start: 0.7624 (t80) cc_final: 0.7152 (t80)
REVERT: A 2430 ASP cc_start: 0.9155 (t0) cc_final: 0.8793 (m-30)
REVERT: A 2441 MET cc_start: 0.9054 (ptt) cc_final: 0.8236 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.1600
  time to fit residues: 7.8693
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  : 0.615 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   chunk 14 optimal weight:    8.9990
   chunk 33 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    1.5586

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.061090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.051502 restraints weight = 63142.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.051742 restraints weight = 60253.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.051856 restraints weight = 57896.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3430
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3430 r_free = 0.3430    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3430 r_free = 0.3430    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3430
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6938
moved from start:          0.4134

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= 0.126
  Angle     :  0.402   4.047   5710  Z= 0.228
  Chirality :  0.033   0.115    581
  Planarity :  0.003   0.031    728
  Dihedral  :  3.842  30.168    544
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 71.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  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 : 0.21 %

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:  1.84 (0.39), residues: 490
  helix:  2.36 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -1.08 (0.48), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A2183 
 HIS   0.001   0.000   HIS A2506 
 PHE   0.013   0.002   PHE A2176 
 TYR   0.009   0.001   TYR A2580 
 ARG   0.005   0.001   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
  39 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2021 MET cc_start: 0.2063 (mtt) cc_final: 0.1791 (mtt)
REVERT: A 2060 GLU cc_start: 0.8223 (tp30) cc_final: 0.7785 (mm-30)
REVERT: A 2249 MET cc_start: 0.4307 (mmt) cc_final: 0.3905 (mmt)
REVERT: A 2426 TYR cc_start: 0.7718 (t80) cc_final: 0.7184 (t80)
REVERT: A 2430 ASP cc_start: 0.9161 (t0) cc_final: 0.8814 (m-30)
REVERT: A 2441 MET cc_start: 0.9062 (ptt) cc_final: 0.8271 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.1534
  time to fit residues: 8.2206
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  : 0.570 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 7 optimal weight:    0.2980
   chunk 38 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 35 optimal weight:   20.0000
   chunk 32 optimal weight:    8.9990
   chunk 26 optimal weight:    8.9990
   chunk 14 optimal weight:    0.0970
   chunk 37 optimal weight:    5.9990
   overall best weight:    2.6784

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

Flipped N/Q/H residues before XYZ refinement:
A2054 ASN
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.059803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.049290 restraints weight = 62509.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.048992 restraints weight = 63487.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.049188 restraints weight = 65447.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3352
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3352
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.4857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4264  Z= 0.184
  Angle     :  0.510  10.177   5710  Z= 0.291
  Chirality :  0.035   0.232    581
  Planarity :  0.004   0.033    728
  Dihedral  :  4.051  30.164    544
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 84.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  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 (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 (0.39), residues: 490
  helix:  2.13 (0.29), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.26 (0.46), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.066   0.002   TRP A2136 
 HIS   0.002   0.001   HIS A2473 
 PHE   0.017   0.003   PHE A2594 
 TYR   0.025   0.001   TYR A2197 
 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  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2021 MET cc_start: 0.2717 (mtt) cc_final: 0.2411 (mtt)
REVERT: A 2060 GLU cc_start: 0.8425 (tp30) cc_final: 0.8002 (mm-30)
REVERT: A 2106 MET cc_start: 0.8125 (mmp) cc_final: 0.7798 (mmp)
REVERT: A 2136 TRP cc_start: 0.9421 (m-90) cc_final: 0.9173 (t-100)
REVERT: A 2140 ASN cc_start: 0.9471 (m110) cc_final: 0.8994 (m-40)
REVERT: A 2148 MET cc_start: 0.1388 (mmp) cc_final: 0.1085 (mmp)
REVERT: A 2426 TYR cc_start: 0.7946 (t80) cc_final: 0.7413 (t80)
REVERT: A 2430 ASP cc_start: 0.9339 (t0) cc_final: 0.9046 (m-30)
REVERT: A 2441 MET cc_start: 0.9095 (ptt) cc_final: 0.8298 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1599
  time to fit residues: 7.8625
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  : 0.583 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 28 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 4 optimal weight:    0.7980
   chunk 46 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    1.2784

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.060503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.051021 restraints weight = 57656.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 18)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.051410 restraints weight = 52179.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.051664 restraints weight = 48276.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3421
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3421 r_free = 0.3421    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 = 0.3421 r_free = 0.3421    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3421
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6938
moved from start:          0.4890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4264  Z= 0.137
  Angle     :  0.435   7.774   5710  Z= 0.247
  Chirality :  0.034   0.132    581
  Planarity :  0.003   0.035    728
  Dihedral  :  3.949  30.058    544
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 73.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  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 : 0.21 %

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:  2.21 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.12 (0.47), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP A2136 
 HIS   0.001   0.000   HIS A2194 
 PHE   0.021   0.002   PHE A2512 
 TYR   0.019   0.001   TYR A2197 
 ARG   0.004   0.001   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  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2021 MET cc_start: 0.2485 (mtt) cc_final: 0.2147 (mtt)
REVERT: A 2060 GLU cc_start: 0.8334 (tp30) cc_final: 0.7949 (mm-30)
REVERT: A 2148 MET cc_start: 0.1350 (mmp) cc_final: 0.1090 (mmp)
REVERT: A 2426 TYR cc_start: 0.7667 (t80) cc_final: 0.7128 (t80)
REVERT: A 2430 ASP cc_start: 0.9288 (t0) cc_final: 0.8964 (m-30)
REVERT: A 2441 MET cc_start: 0.9103 (ptt) cc_final: 0.8297 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1482
  time to fit residues: 7.6027
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  : 0.540 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 37 optimal weight:    8.9990
   chunk 31 optimal weight:    7.9990
   chunk 36 optimal weight:    9.9990
   chunk 12 optimal weight:    0.8980
   chunk 49 optimal weight:    0.3980
   chunk 35 optimal weight:    9.9990
   chunk 19 optimal weight:   20.0000
   chunk 47 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 42 optimal weight:   10.0000
   overall best weight:    2.8384

-------------------------------------------------------------------------------
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**
** 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 = 0.3575 r_free = 0.3575 target = 0.056707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.046324 restraints weight = 65086.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.046635 restraints weight = 60839.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.046776 restraints weight = 57457.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3296
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3296 r_free = 0.3296    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3296 r_free = 0.3296    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3296
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7139
moved from start:          0.6029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4264  Z= 0.221
  Angle     :  0.595   7.768   5710  Z= 0.339
  Chirality :  0.037   0.129    581
  Planarity :  0.004   0.041    728
  Dihedral  :  4.426  30.124    544
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 97.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  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 (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:  1.02 (0.38), residues: 490
  helix:  1.72 (0.29), residues: 322
  sheet:  None (None), residues: 0
  loop : -1.45 (0.47), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.080   0.004   TRP A2136 
 HIS   0.004   0.002   HIS A2194 
 PHE   0.025   0.003   PHE A2512 
 TYR   0.017   0.002   TYR A2243 
 ARG   0.005   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  : 0.526 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2021 MET cc_start: 0.3755 (mtt) cc_final: 0.3266 (mtt)
REVERT: A 2060 GLU cc_start: 0.8461 (tp30) cc_final: 0.8055 (mm-30)
REVERT: A 2148 MET cc_start: 0.2080 (mmp) cc_final: 0.1697 (mmp)
REVERT: A 2249 MET cc_start: 0.5241 (mmt) cc_final: 0.4835 (mmt)
REVERT: A 2426 TYR cc_start: 0.8318 (t80) cc_final: 0.7792 (t80)
REVERT: A 2430 ASP cc_start: 0.9451 (t0) cc_final: 0.9174 (m-30)
REVERT: A 2441 MET cc_start: 0.9184 (ptt) cc_final: 0.8482 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.1651
  time to fit residues: 8.0661
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  : 0.475 
-------------------------------------------------------------------------------
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:    0.0770
   chunk 40 optimal weight:   20.0000
   chunk 13 optimal weight:    5.9990
   chunk 48 optimal weight:    0.0470
   chunk 18 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0970
   chunk 22 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   chunk 34 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.4034

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3631 r_free = 0.3631 target = 0.058869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.048640 restraints weight = 62279.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.048187 restraints weight = 61100.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.048420 restraints weight = 63549.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3351
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3351 r_free = 0.3351    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3351 r_free = 0.3351    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3351
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.5751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   4264  Z= 0.112
  Angle     :  0.433   5.311   5710  Z= 0.248
  Chirality :  0.034   0.125    581
  Planarity :  0.003   0.036    728
  Dihedral  :  4.047  29.260    544
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 70.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  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:  1.60 (0.39), residues: 490
  helix:  2.11 (0.29), residues: 322
  sheet:  None (None), residues: 0
  loop : -1.07 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.074   0.003   TRP A2136 
 HIS   0.002   0.000   HIS A2473 
 PHE   0.011   0.001   PHE A2072 
 TYR   0.027   0.001   TYR A2197 
 ARG   0.002   0.000   ARG A2037 

********************** 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
  39 residues out of total 463 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2021 MET cc_start: 0.3050 (mtt) cc_final: 0.2634 (mtt)
REVERT: A 2060 GLU cc_start: 0.8461 (tp30) cc_final: 0.8074 (mm-30)
REVERT: A 2148 MET cc_start: 0.2014 (mmp) cc_final: 0.1694 (mmp)
REVERT: A 2249 MET cc_start: 0.4893 (mmt) cc_final: 0.4580 (mmt)
REVERT: A 2426 TYR cc_start: 0.7995 (t80) cc_final: 0.7415 (t80)
REVERT: A 2430 ASP cc_start: 0.9438 (t0) cc_final: 0.9135 (m-30)
REVERT: A 2441 MET cc_start: 0.9075 (ptt) cc_final: 0.8307 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.1780
  time to fit residues: 8.9652
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 26 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 44 optimal weight:   20.0000
   chunk 18 optimal weight:    0.4980
   chunk 37 optimal weight:    0.9990
   chunk 25 optimal weight:    9.9990
   overall best weight:    1.0988

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3620 r_free = 0.3620 target = 0.058368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.047674 restraints weight = 63336.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.047992 restraints weight = 59212.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.048182 restraints weight = 56038.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3341
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3341
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7076
moved from start:          0.5882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4264  Z= 0.116
  Angle     :  0.433   5.391   5710  Z= 0.250
  Chirality :  0.034   0.121    581
  Planarity :  0.003   0.038    728
  Dihedral  :  3.899  30.073    544
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 73.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  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 : 0.21 %

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:  1.76 (0.39), residues: 490
  helix:  2.26 (0.29), residues: 321
  sheet:  None (None), residues: 0
  loop : -1.04 (0.49), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.081   0.003   TRP A2136 
 HIS   0.001   0.001   HIS A2473 
 PHE   0.011   0.002   PHE A2072 
 TYR   0.016   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: 1623.50 seconds
wall clock time: 30 minutes 8.69 seconds (1808.69 seconds total)