Starting phenix.real_space_refine
on Thu Mar  6 02:41:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kwz_23059/03_2025/7kwz_23059.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kwz_23059/03_2025/7kwz_23059.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kwz_23059/03_2025/7kwz_23059.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kwz_23059/03_2025/7kwz_23059.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kwz_23059/03_2025/7kwz_23059.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kwz_23059/03_2025/7kwz_23059.cif"
  }
  resolution = 3.2
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    2770      2.51       5
     N     895      2.21       5
     O     980      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4695
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 939
          Classifications: {'peptide': 139}
          Link IDs: {'PTRANS': 4, 'TRANS': 134}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 2.49, per 1000 atoms: 0.53
  Number of scatterers: 4695
  At special positions: 0
  Unit cell: (94.392, 91.08, 52.992, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O     980      8.00
     N     895      7.00
     C    2770      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.16
  Conformation dependent library (CDL) restraints added in 984.1 milliseconds
  

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1020

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      0 helices and 0 sheets defined
      0.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...

    No hydrogen bonds defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.00

  Time building geometry restraints manager: 1.38 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 865
        1.31 -     1.43: 1405
        1.43 -     1.56: 2415
        1.56 -     1.68: 0
        1.68 -     1.80: 100
  Bond restraints: 4785
  Sorted by residual:
  bond pdb=" CB  ASN D 319 "
       pdb=" CG  ASN D 319 "
    ideal  model  delta    sigma   weight residual
    1.516  1.456  0.060 2.50e-02 1.60e+03 5.82e+00
  bond pdb=" CB  ASN A 319 "
       pdb=" CG  ASN A 319 "
    ideal  model  delta    sigma   weight residual
    1.516  1.456  0.060 2.50e-02 1.60e+03 5.76e+00
  bond pdb=" CB  ASN C 319 "
       pdb=" CG  ASN C 319 "
    ideal  model  delta    sigma   weight residual
    1.516  1.456  0.060 2.50e-02 1.60e+03 5.70e+00
  bond pdb=" CB  ASN E 319 "
       pdb=" CG  ASN E 319 "
    ideal  model  delta    sigma   weight residual
    1.516  1.457  0.059 2.50e-02 1.60e+03 5.65e+00
  bond pdb=" CB  ASN B 319 "
       pdb=" CG  ASN B 319 "
    ideal  model  delta    sigma   weight residual
    1.516  1.457  0.059 2.50e-02 1.60e+03 5.65e+00
  ... (remaining 4780 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 5842
        1.28 -     2.55: 425
        2.55 -     3.83: 78
        3.83 -     5.11: 25
        5.11 -     6.38: 15
  Bond angle restraints: 6385
  Sorted by residual:
  angle pdb=" C   MET D 336 "
        pdb=" N   MET D 337 "
        pdb=" CA  MET D 337 "
      ideal   model   delta    sigma   weight residual
     122.17  117.93    4.24 1.54e+00 4.22e-01 7.57e+00
  angle pdb=" C   MET C 336 "
        pdb=" N   MET C 337 "
        pdb=" CA  MET C 337 "
      ideal   model   delta    sigma   weight residual
     122.17  117.96    4.21 1.54e+00 4.22e-01 7.47e+00
  angle pdb=" C   MET A 336 "
        pdb=" N   MET A 337 "
        pdb=" CA  MET A 337 "
      ideal   model   delta    sigma   weight residual
     122.17  117.99    4.18 1.54e+00 4.22e-01 7.36e+00
  angle pdb=" C   MET B 336 "
        pdb=" N   MET B 337 "
        pdb=" CA  MET B 337 "
      ideal   model   delta    sigma   weight residual
     122.17  117.99    4.18 1.54e+00 4.22e-01 7.36e+00
  angle pdb=" C   MET E 336 "
        pdb=" N   MET E 337 "
        pdb=" CA  MET E 337 "
      ideal   model   delta    sigma   weight residual
     122.17  118.01    4.16 1.54e+00 4.22e-01 7.31e+00
  ... (remaining 6380 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.30: 2119
        9.30 -    18.60: 281
       18.60 -    27.90: 181
       27.90 -    37.20: 59
       37.20 -    46.50: 15
  Dihedral angle restraints: 2655
    sinusoidal: 940
      harmonic: 1715
  Sorted by residual:
  dihedral pdb=" CA  MET C 337 "
           pdb=" C   MET C 337 "
           pdb=" N   GLY C 338 "
           pdb=" CA  GLY C 338 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.03  -24.97     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  MET E 337 "
           pdb=" C   MET E 337 "
           pdb=" N   GLY E 338 "
           pdb=" CA  GLY E 338 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.04  -24.96     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  MET A 337 "
           pdb=" C   MET A 337 "
           pdb=" N   GLY A 338 "
           pdb=" CA  GLY A 338 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.05  -24.95     0      5.00e+00 4.00e-02 2.49e+01
  ... (remaining 2652 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 251
       0.027 -    0.054: 167
       0.054 -    0.081: 57
       0.081 -    0.108: 37
       0.108 -    0.135: 23
  Chirality restraints: 535
  Sorted by residual:
  chirality pdb=" CA  ILE C 318 "
            pdb=" N   ILE C 318 "
            pdb=" C   ILE C 318 "
            pdb=" CB  ILE C 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.52e-01
  chirality pdb=" CA  ILE B 318 "
            pdb=" N   ILE B 318 "
            pdb=" C   ILE B 318 "
            pdb=" CB  ILE B 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.32e-01
  chirality pdb=" CA  ILE A 318 "
            pdb=" N   ILE A 318 "
            pdb=" C   ILE A 318 "
            pdb=" CB  ILE A 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.31e-01
  ... (remaining 532 not shown)

  Planarity restraints: 940
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN D 319 "   -0.006 2.00e-02 2.50e+03   1.17e-02 1.36e+00
        pdb=" C   ASN D 319 "    0.020 2.00e-02 2.50e+03
        pdb=" O   ASN D 319 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   PRO D 320 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN E 319 "   -0.006 2.00e-02 2.50e+03   1.14e-02 1.31e+00
        pdb=" C   ASN E 319 "    0.020 2.00e-02 2.50e+03
        pdb=" O   ASN E 319 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   PRO E 320 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 319 "   -0.006 2.00e-02 2.50e+03   1.14e-02 1.29e+00
        pdb=" C   ASN A 319 "    0.020 2.00e-02 2.50e+03
        pdb=" O   ASN A 319 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   PRO A 320 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 937 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1365
        2.80 -     3.32: 4508
        3.32 -     3.85: 8023
        3.85 -     4.37: 9905
        4.37 -     4.90: 19033
  Nonbonded interactions: 42834
  Sorted by model distance:
  nonbonded pdb=" O   ASN C 279 "
            pdb=" OD1 ASN D 279 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" O   ASN D 279 "
            pdb=" OD1 ASN E 279 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   ASN B 279 "
            pdb=" OD1 ASN C 279 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   ASN A 279 "
            pdb=" OD1 ASN B 279 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OH  TYR B 374 "
            pdb=" O   GLY C 351 "
     model   vdw
     2.310 3.040
  ... (remaining 42829 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.770
  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:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.110
  Find NCS groups from input model:        0.100
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
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      :  0.006   0.060   4785  Z= 0.299
  Angle     :  0.804   6.384   6385  Z= 0.436
  Chirality :  0.048   0.135    535
  Planarity :  0.003   0.027    940
  Dihedral  : 12.477  46.502   1635
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  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: -5.51 (0.15), residues: 685
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.19 (0.11), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 412 
 PHE   0.008   0.002   PHE D 401 
 TYR   0.007   0.002   TYR C 374 
 ARG   0.001   0.000   ARG C 293 

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 ARG cc_start: 0.7950 (mtp180) cc_final: 0.7138 (mmp-170)
REVERT: A  359 MET cc_start: 0.5447 (tpt) cc_final: 0.5232 (tpt)
REVERT: A  360 GLN cc_start: 0.6244 (mt0) cc_final: 0.5871 (tp40)
REVERT: B  359 MET cc_start: 0.5465 (tpt) cc_final: 0.5257 (tpt)
REVERT: B  365 GLN cc_start: 0.6936 (mp10) cc_final: 0.6718 (mp10)
REVERT: C  359 MET cc_start: 0.5600 (tpt) cc_final: 0.5272 (tpt)
REVERT: D  359 MET cc_start: 0.5454 (tpt) cc_final: 0.5232 (tpt)
REVERT: E  293 ARG cc_start: 0.8390 (mtp180) cc_final: 0.7229 (pmt-80)
REVERT: E  307 MET cc_start: 0.8057 (ttt) cc_final: 0.7815 (ttm)
REVERT: E  365 GLN cc_start: 0.7579 (mp10) cc_final: 0.7372 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1812
  time to fit residues: 29.5343
Evaluate side-chains
  78 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 49 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 16 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 26 optimal weight:    0.3980
   chunk 50 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 319 ASN
B 291 ASN
B 319 ASN
B 344 GLN
** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 331 GLN
C 344 GLN
** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 291 ASN
** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 291 ASN
** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.143818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.102715 restraints weight = 5867.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 2.67
r_work: 0.3642 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3515 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.1602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   4785  Z= 0.148
  Angle     :  0.680   7.285   6385  Z= 0.349
  Chirality :  0.044   0.123    535
  Planarity :  0.003   0.050    940
  Dihedral  :  5.370  22.667    705
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 10.68 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -5.39 (0.15), residues: 685
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.10 (0.12), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 385 
 PHE   0.008   0.001   PHE B 283 
 TYR   0.004   0.001   TYR E 374 
 ARG   0.002   0.000   ARG B 293 

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
REVERT: A  293 ARG cc_start: 0.7894 (mtp180) cc_final: 0.6921 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7416 (mt0) cc_final: 0.6727 (tm-30)
REVERT: A  359 MET cc_start: 0.5673 (tpt) cc_final: 0.5408 (tpt)
REVERT: A  362 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7910 (tm-30)
REVERT: A  365 GLN cc_start: 0.7180 (mp10) cc_final: 0.6864 (mp10)
REVERT: B  293 ARG cc_start: 0.7799 (mtp-110) cc_final: 0.7534 (mtp-110)
REVERT: B  303 GLN cc_start: 0.7337 (mt0) cc_final: 0.6939 (tm-30)
REVERT: B  359 MET cc_start: 0.5424 (tpt) cc_final: 0.5096 (tpt)
REVERT: C  359 MET cc_start: 0.5556 (tpt) cc_final: 0.5166 (tpt)
REVERT: C  360 GLN cc_start: 0.4768 (tt0) cc_final: 0.4473 (tm-30)
REVERT: C  365 GLN cc_start: 0.6308 (mp10) cc_final: 0.5831 (mp10)
REVERT: D  359 MET cc_start: 0.5065 (tpt) cc_final: 0.4806 (tpt)
REVERT: D  405 MET cc_start: 0.7320 (tmm) cc_final: 0.7054 (tmm)
REVERT: E  293 ARG cc_start: 0.8407 (mtp180) cc_final: 0.7154 (pmt-80)
REVERT: E  307 MET cc_start: 0.8408 (ttt) cc_final: 0.8160 (ttm)
REVERT: E  360 GLN cc_start: 0.5368 (tt0) cc_final: 0.5023 (tm-30)
  outliers start: 11
  outliers final: 8
  residues processed: 106
  average time/residue: 0.1653
  time to fit residues: 22.2797
Evaluate side-chains
  95 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain C residue  389 SER
Chi-restraints excluded: chain D residue  332 SER
Chi-restraints excluded: chain D residue  389 SER
Chi-restraints excluded: chain D residue  407 SER
Chi-restraints excluded: chain E residue  332 SER
Chi-restraints excluded: chain E residue  405 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 23 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 20 optimal weight:    8.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 319 ASN
** E 319 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 = 0.4263 r_free = 0.4263 target = 0.140987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.099294 restraints weight = 5857.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3724 rms_B_bonded: 2.78
r_work: 0.3584 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3454 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   4785  Z= 0.195
  Angle     :  0.672   6.663   6385  Z= 0.346
  Chirality :  0.044   0.119    535
  Planarity :  0.004   0.044    940
  Dihedral  :  5.315  25.430    705
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 12.05 %
    Favored  : 84.09 %
  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: -5.31 (0.15), residues: 685
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.04 (0.12), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 412 
 PHE   0.012   0.001   PHE B 283 
 TYR   0.007   0.002   TYR B 374 
 ARG   0.002   0.000   ARG D 293 

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
REVERT: A  293 ARG cc_start: 0.7949 (mtp180) cc_final: 0.6965 (mmp-170)
REVERT: A  336 MET cc_start: 0.8053 (mpp) cc_final: 0.7699 (mtt)
REVERT: A  359 MET cc_start: 0.5967 (tpt) cc_final: 0.5568 (tpt)
REVERT: A  406 ASP cc_start: 0.7986 (m-30) cc_final: 0.7576 (t0)
REVERT: B  303 GLN cc_start: 0.7476 (mt0) cc_final: 0.7137 (tm-30)
REVERT: B  359 MET cc_start: 0.5609 (tpt) cc_final: 0.5293 (tpt)
REVERT: C  359 MET cc_start: 0.5503 (tpt) cc_final: 0.5223 (tpt)
REVERT: C  365 GLN cc_start: 0.6282 (mp10) cc_final: 0.5672 (mp10)
REVERT: D  303 GLN cc_start: 0.7238 (mt0) cc_final: 0.6855 (tm-30)
REVERT: D  323 MET cc_start: 0.8466 (mtp) cc_final: 0.7916 (mtp)
REVERT: E  293 ARG cc_start: 0.8440 (mtp180) cc_final: 0.7171 (pmt-80)
  outliers start: 17
  outliers final: 14
  residues processed: 110
  average time/residue: 0.1649
  time to fit residues: 22.9641
Evaluate side-chains
  98 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain C residue  347 SER
Chi-restraints excluded: chain C residue  389 SER
Chi-restraints excluded: chain D residue  332 SER
Chi-restraints excluded: chain D residue  347 SER
Chi-restraints excluded: chain D residue  389 SER
Chi-restraints excluded: chain D residue  407 SER
Chi-restraints excluded: chain E residue  332 SER
Chi-restraints excluded: chain E residue  337 MET
Chi-restraints excluded: chain E residue  347 SER
Chi-restraints excluded: chain E residue  405 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 39 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 18 optimal weight:    9.9990
   chunk 54 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 57 optimal weight:    8.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 319 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 = 0.4223 r_free = 0.4223 target = 0.137082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.094196 restraints weight = 5772.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 2.83
r_work: 0.3509 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3378 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   4785  Z= 0.268
  Angle     :  0.747   6.966   6385  Z= 0.386
  Chirality :  0.045   0.125    535
  Planarity :  0.004   0.047    940
  Dihedral  :  5.539  27.121    705
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.78 %
    Favored  : 90.22 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 15.23 %
    Favored  : 80.91 %
  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: -5.30 (0.16), residues: 685
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.04 (0.12), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 412 
 PHE   0.015   0.002   PHE B 283 
 TYR   0.008   0.002   TYR B 374 
 ARG   0.005   0.001   ARG B 293 

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.505 
Fit side-chains
REVERT: A  293 ARG cc_start: 0.7950 (mtp180) cc_final: 0.6929 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7483 (mt0) cc_final: 0.6838 (tm-30)
REVERT: A  359 MET cc_start: 0.5852 (tpt) cc_final: 0.5422 (tpt)
REVERT: A  362 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7654 (tm-30)
REVERT: A  406 ASP cc_start: 0.8030 (m-30) cc_final: 0.7540 (t0)
REVERT: B  303 GLN cc_start: 0.7495 (mt0) cc_final: 0.6929 (tm-30)
REVERT: B  359 MET cc_start: 0.5616 (tpt) cc_final: 0.5390 (tpt)
REVERT: B  362 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7894 (tm-30)
REVERT: B  406 ASP cc_start: 0.7858 (m-30) cc_final: 0.7439 (t0)
REVERT: C  303 GLN cc_start: 0.7334 (mt0) cc_final: 0.7024 (tm-30)
REVERT: C  354 GLN cc_start: 0.7997 (mp10) cc_final: 0.7286 (mp10)
REVERT: C  406 ASP cc_start: 0.7877 (m-30) cc_final: 0.7541 (t0)
REVERT: D  303 GLN cc_start: 0.7361 (mt0) cc_final: 0.6818 (tm-30)
REVERT: D  323 MET cc_start: 0.8408 (mtp) cc_final: 0.7987 (mtp)
REVERT: E  293 ARG cc_start: 0.8380 (mtp180) cc_final: 0.7052 (pmt-80)
REVERT: E  307 MET cc_start: 0.8436 (ttt) cc_final: 0.8156 (ttm)
REVERT: E  359 MET cc_start: 0.6214 (tpt) cc_final: 0.4011 (tmm)
REVERT: E  406 ASP cc_start: 0.8181 (m-30) cc_final: 0.7902 (t0)
  outliers start: 17
  outliers final: 14
  residues processed: 103
  average time/residue: 0.1644
  time to fit residues: 21.5080
Evaluate side-chains
  102 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain C residue  323 MET
Chi-restraints excluded: chain C residue  347 SER
Chi-restraints excluded: chain C residue  389 SER
Chi-restraints excluded: chain D residue  332 SER
Chi-restraints excluded: chain D residue  347 SER
Chi-restraints excluded: chain D residue  389 SER
Chi-restraints excluded: chain D residue  407 SER
Chi-restraints excluded: chain E residue  332 SER
Chi-restraints excluded: chain E residue  347 SER
Chi-restraints excluded: chain E residue  405 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 26 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 61 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0040
   chunk 52 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0770
   chunk 43 optimal weight:    6.9990
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.5352

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

Flipped N/Q/H residues before XYZ refinement:
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 378 ASN
B 344 GLN
** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 378 ASN
** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 312 ASN
E 319 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.145035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.103440 restraints weight = 5772.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3806 rms_B_bonded: 2.77
r_work: 0.3670 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3548 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4785  Z= 0.107
  Angle     :  0.616   6.162   6385  Z= 0.315
  Chirality :  0.041   0.124    535
  Planarity :  0.004   0.051    940
  Dihedral  :  4.661  20.774    705
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.14 %
    Favored  : 81.36 %
  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: -5.17 (0.16), residues: 685
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.94 (0.12), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 385 
 PHE   0.010   0.001   PHE E 289 
 TYR   0.002   0.001   TYR B 374 
 ARG   0.005   0.001   ARG D 293 

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
REVERT: A  293 ARG cc_start: 0.7855 (mtp180) cc_final: 0.6888 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7406 (mt0) cc_final: 0.6605 (tm-30)
REVERT: A  319 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.7380 (p0)
REVERT: A  336 MET cc_start: 0.7900 (mpp) cc_final: 0.7615 (mtm)
REVERT: A  359 MET cc_start: 0.5791 (tpt) cc_final: 0.5563 (tpt)
REVERT: A  406 ASP cc_start: 0.7994 (m-30) cc_final: 0.7419 (t0)
REVERT: B  303 GLN cc_start: 0.7413 (mt0) cc_final: 0.6978 (tm-30)
REVERT: B  322 MET cc_start: 0.8044 (ptp) cc_final: 0.7661 (ptt)
REVERT: B  354 GLN cc_start: 0.7839 (mp10) cc_final: 0.7430 (mp10)
REVERT: B  359 MET cc_start: 0.5321 (tpt) cc_final: 0.3862 (mmt)
REVERT: B  406 ASP cc_start: 0.7758 (m-30) cc_final: 0.7358 (t0)
REVERT: C  354 GLN cc_start: 0.7776 (mp10) cc_final: 0.7212 (mp10)
REVERT: C  359 MET cc_start: 0.4705 (tpt) cc_final: 0.3098 (mmp)
REVERT: C  406 ASP cc_start: 0.7746 (m-30) cc_final: 0.7470 (t0)
REVERT: D  303 GLN cc_start: 0.7225 (mt0) cc_final: 0.6799 (tm-30)
REVERT: D  323 MET cc_start: 0.8236 (mtp) cc_final: 0.7880 (mtp)
REVERT: D  405 MET cc_start: 0.7512 (tmm) cc_final: 0.6935 (tpt)
REVERT: E  293 ARG cc_start: 0.8478 (mtp180) cc_final: 0.7122 (pmt-80)
REVERT: E  307 MET cc_start: 0.8344 (ttt) cc_final: 0.8061 (ttm)
REVERT: E  359 MET cc_start: 0.5846 (tpt) cc_final: 0.3704 (tmm)
REVERT: E  405 MET cc_start: 0.7823 (ptp) cc_final: 0.7451 (ptp)
  outliers start: 11
  outliers final: 9
  residues processed: 109
  average time/residue: 0.1488
  time to fit residues: 21.0475
Evaluate side-chains
  101 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  319 ASN
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain C residue  347 SER
Chi-restraints excluded: chain C residue  389 SER
Chi-restraints excluded: chain D residue  332 SER
Chi-restraints excluded: chain D residue  347 SER
Chi-restraints excluded: chain D residue  389 SER
Chi-restraints excluded: chain D residue  407 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 57 optimal weight:    0.0870
   chunk 47 optimal weight:   10.0000
   chunk 1 optimal weight:    0.0570
   chunk 58 optimal weight:    0.8980
   chunk 32 optimal weight:    8.9990
   chunk 44 optimal weight:    4.9990
   chunk 34 optimal weight:    6.9990
   chunk 4 optimal weight:    8.9990
   chunk 16 optimal weight:    6.9990
   chunk 24 optimal weight:    9.9990
   chunk 46 optimal weight:   10.0000
   overall best weight:    2.6080

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

Flipped N/Q/H residues before XYZ refinement:
A 378 ASN
** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 378 ASN
** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 358 ASN ** 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 = 0.4254 r_free = 0.4254 target = 0.139724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.097494 restraints weight = 5846.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 2.72
r_work: 0.3583 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3457 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.2755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4785  Z= 0.210
  Angle     :  0.711   7.756   6385  Z= 0.367
  Chirality :  0.043   0.132    535
  Planarity :  0.004   0.058    940
  Dihedral  :  5.039  25.397    705
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.64 %
    Favored  : 90.36 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 15.23 %
    Favored  : 81.14 %
  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: -5.24 (0.16), residues: 685
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.99 (0.12), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 412 
 PHE   0.011   0.001   PHE B 283 
 TYR   0.007   0.002   TYR B 374 
 ARG   0.004   0.001   ARG D 293 

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.490 
Fit side-chains
REVERT: A  293 ARG cc_start: 0.7924 (mtp180) cc_final: 0.6934 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7411 (mt0) cc_final: 0.6903 (tm-30)
REVERT: A  319 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.7513 (p0)
REVERT: A  336 MET cc_start: 0.8007 (mpp) cc_final: 0.7633 (mtt)
REVERT: A  359 MET cc_start: 0.5794 (tpt) cc_final: 0.5538 (tpt)
REVERT: A  406 ASP cc_start: 0.8045 (m-30) cc_final: 0.7542 (t0)
REVERT: A  414 MET cc_start: 0.5686 (mmm) cc_final: 0.3852 (mpp)
REVERT: B  303 GLN cc_start: 0.7461 (mt0) cc_final: 0.6902 (tm-30)
REVERT: B  322 MET cc_start: 0.8128 (ptp) cc_final: 0.7690 (ptt)
REVERT: B  359 MET cc_start: 0.5550 (tpt) cc_final: 0.4240 (mmt)
REVERT: B  406 ASP cc_start: 0.7842 (m-30) cc_final: 0.7423 (t0)
REVERT: C  303 GLN cc_start: 0.7283 (mt0) cc_final: 0.7015 (tm-30)
REVERT: C  362 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7520 (tm-30)
REVERT: C  406 ASP cc_start: 0.7865 (m-30) cc_final: 0.7585 (t0)
REVERT: D  303 GLN cc_start: 0.7320 (mt0) cc_final: 0.6846 (tm-30)
REVERT: D  323 MET cc_start: 0.8287 (mtp) cc_final: 0.7987 (mtp)
REVERT: D  405 MET cc_start: 0.7485 (tmm) cc_final: 0.7041 (tpt)
REVERT: E  293 ARG cc_start: 0.8479 (mtp180) cc_final: 0.7089 (pmt-80)
REVERT: E  307 MET cc_start: 0.8414 (ttt) cc_final: 0.8146 (ttm)
REVERT: E  359 MET cc_start: 0.5959 (tpt) cc_final: 0.3814 (tmm)
  outliers start: 16
  outliers final: 11
  residues processed: 104
  average time/residue: 0.1789
  time to fit residues: 23.7915
Evaluate side-chains
  96 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  319 ASN
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain C residue  330 LEU
Chi-restraints excluded: chain C residue  389 SER
Chi-restraints excluded: chain D residue  332 SER
Chi-restraints excluded: chain D residue  347 SER
Chi-restraints excluded: chain D residue  389 SER
Chi-restraints excluded: chain D residue  407 SER
Chi-restraints excluded: chain E residue  347 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 48 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 40 optimal weight:   10.0000
   chunk 12 optimal weight:    7.9990
   chunk 50 optimal weight:    9.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 327 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 = 0.4211 r_free = 0.4211 target = 0.135374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.092245 restraints weight = 5791.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 2.81
r_work: 0.3492 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3362 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.038   4785  Z= 0.343
  Angle     :  0.816   7.095   6385  Z= 0.425
  Chirality :  0.046   0.123    535
  Planarity :  0.005   0.067    940
  Dihedral  :  5.741  28.769    705
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.97 %
    Favored  : 88.03 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 15.45 %
    Favored  : 80.23 %
  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: -5.46 (0.15), residues: 685
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.16 (0.12), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 412 
 PHE   0.018   0.002   PHE B 283 
 TYR   0.010   0.002   TYR B 374 
 ARG   0.001   0.000   ARG D 293 

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.453 
Fit side-chains
REVERT: A  293 ARG cc_start: 0.7893 (mtp180) cc_final: 0.6895 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7463 (mt0) cc_final: 0.7051 (tm-30)
REVERT: A  319 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.7761 (p0)
REVERT: A  359 MET cc_start: 0.5877 (tpt) cc_final: 0.5514 (tpt)
REVERT: A  406 ASP cc_start: 0.7898 (m-30) cc_final: 0.7462 (t0)
REVERT: A  414 MET cc_start: 0.5782 (mmm) cc_final: 0.3983 (mpp)
REVERT: B  303 GLN cc_start: 0.7499 (mt0) cc_final: 0.7045 (tm-30)
REVERT: B  359 MET cc_start: 0.5615 (tpt) cc_final: 0.4320 (mmt)
REVERT: B  406 ASP cc_start: 0.7906 (m-30) cc_final: 0.7497 (t0)
REVERT: C  303 GLN cc_start: 0.7324 (mt0) cc_final: 0.6981 (tm-30)
REVERT: C  354 GLN cc_start: 0.7988 (mp10) cc_final: 0.7457 (mp10)
REVERT: C  365 GLN cc_start: 0.6503 (mp10) cc_final: 0.5717 (mp10)
REVERT: C  406 ASP cc_start: 0.7998 (m-30) cc_final: 0.7590 (t0)
REVERT: D  303 GLN cc_start: 0.7371 (mt0) cc_final: 0.6875 (tm-30)
REVERT: D  406 ASP cc_start: 0.8400 (m-30) cc_final: 0.7919 (t0)
REVERT: E  293 ARG cc_start: 0.8372 (mtp180) cc_final: 0.7028 (pmt-80)
REVERT: E  303 GLN cc_start: 0.7586 (tm-30) cc_final: 0.6910 (tm-30)
REVERT: E  307 MET cc_start: 0.8473 (ttt) cc_final: 0.8221 (ttm)
REVERT: E  359 MET cc_start: 0.6132 (tpt) cc_final: 0.3830 (tmm)
  outliers start: 19
  outliers final: 16
  residues processed: 110
  average time/residue: 0.1636
  time to fit residues: 22.8938
Evaluate side-chains
  104 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  319 ASN
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain B residue  323 MET
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain B residue  405 MET
Chi-restraints excluded: chain C residue  323 MET
Chi-restraints excluded: chain C residue  330 LEU
Chi-restraints excluded: chain C residue  347 SER
Chi-restraints excluded: chain C residue  389 SER
Chi-restraints excluded: chain D residue  332 SER
Chi-restraints excluded: chain D residue  347 SER
Chi-restraints excluded: chain D residue  389 SER
Chi-restraints excluded: chain D residue  407 SER
Chi-restraints excluded: chain E residue  332 SER
Chi-restraints excluded: chain E residue  347 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 28 optimal weight:   20.0000
   chunk 42 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 4 optimal weight:    0.4980
   chunk 39 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 378 ASN
B 378 ASN
** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 331 GLN
** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 378 ASN
** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 358 ASN ** 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 = 0.4307 r_free = 0.4307 target = 0.142934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.101497 restraints weight = 5813.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3787 rms_B_bonded: 2.74
r_work: 0.3653 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3530 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.3091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4785  Z= 0.128
  Angle     :  0.684   7.241   6385  Z= 0.352
  Chirality :  0.043   0.114    535
  Planarity :  0.005   0.069    940
  Dihedral  :  4.776  21.673    705
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 18.64 %
    Favored  : 78.86 %
  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: -5.28 (0.15), residues: 685
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.02 (0.12), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 385 
 PHE   0.015   0.001   PHE E 289 
 TYR   0.004   0.001   TYR B 374 
 ARG   0.008   0.001   ARG D 293 

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.491 
Fit side-chains
REVERT: A  293 ARG cc_start: 0.7843 (mtp180) cc_final: 0.6916 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7393 (mt0) cc_final: 0.6815 (tm-30)
REVERT: A  319 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.7426 (p0)
REVERT: A  336 MET cc_start: 0.7965 (mpp) cc_final: 0.7579 (mtt)
REVERT: A  359 MET cc_start: 0.5739 (tpt) cc_final: 0.5470 (tpt)
REVERT: A  406 ASP cc_start: 0.7714 (m-30) cc_final: 0.7364 (t0)
REVERT: A  414 MET cc_start: 0.5775 (mmm) cc_final: 0.4001 (mpp)
REVERT: B  303 GLN cc_start: 0.7441 (mt0) cc_final: 0.6886 (tm-30)
REVERT: B  307 MET cc_start: 0.8011 (ttt) cc_final: 0.7683 (ttm)
REVERT: B  322 MET cc_start: 0.8020 (ptp) cc_final: 0.7650 (ptt)
REVERT: B  359 MET cc_start: 0.5389 (tpt) cc_final: 0.4180 (mmt)
REVERT: B  406 ASP cc_start: 0.7717 (m-30) cc_final: 0.7425 (t0)
REVERT: C  303 GLN cc_start: 0.7174 (mt0) cc_final: 0.6949 (tm-30)
REVERT: C  316 PHE cc_start: 0.8733 (m-80) cc_final: 0.8496 (m-80)
REVERT: C  354 GLN cc_start: 0.7877 (mp10) cc_final: 0.7470 (mp10)
REVERT: C  405 MET cc_start: 0.7858 (ptp) cc_final: 0.7391 (ptt)
REVERT: C  406 ASP cc_start: 0.7841 (m-30) cc_final: 0.7569 (t0)
REVERT: C  410 SER cc_start: 0.8622 (m) cc_final: 0.7576 (p)
REVERT: D  303 GLN cc_start: 0.7284 (mt0) cc_final: 0.6877 (tm-30)
REVERT: D  323 MET cc_start: 0.8286 (mtp) cc_final: 0.7932 (mtp)
REVERT: D  405 MET cc_start: 0.7594 (tmm) cc_final: 0.7130 (tpt)
REVERT: E  293 ARG cc_start: 0.8436 (mtp180) cc_final: 0.7117 (pmt-80)
REVERT: E  307 MET cc_start: 0.8434 (ttt) cc_final: 0.8144 (ttm)
REVERT: E  359 MET cc_start: 0.5817 (tpt) cc_final: 0.3605 (tmm)
  outliers start: 11
  outliers final: 10
  residues processed: 100
  average time/residue: 0.1760
  time to fit residues: 22.5306
Evaluate side-chains
  99 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  319 ASN
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain B residue  337 MET
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain C residue  330 LEU
Chi-restraints excluded: chain C residue  389 SER
Chi-restraints excluded: chain D residue  332 SER
Chi-restraints excluded: chain D residue  389 SER
Chi-restraints excluded: chain E residue  332 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 53 optimal weight:    7.9990
   chunk 7 optimal weight:    7.9990
   chunk 48 optimal weight:   10.0000
   chunk 39 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 24 optimal weight:    7.9990
   chunk 51 optimal weight:    8.9990
   chunk 50 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   overall best weight:    7.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 378 ASN
B 378 ASN
** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 378 ASN
** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.131570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.089111 restraints weight = 6030.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.79
r_work: 0.3480 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3347 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.3022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.052   4785  Z= 0.500
  Angle     :  0.944   8.065   6385  Z= 0.499
  Chirality :  0.050   0.135    535
  Planarity :  0.006   0.076    940
  Dihedral  :  6.159  30.096    705
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 16.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.15 %
    Favored  : 79.85 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 18.18 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -5.65 (0.15), residues: 685
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.30 (0.11), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP A 412 
 PHE   0.025   0.003   PHE A 283 
 TYR   0.012   0.003   TYR B 374 
 ARG   0.006   0.001   ARG D 293 

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.499 
Fit side-chains
REVERT: A  293 ARG cc_start: 0.7963 (mtp180) cc_final: 0.6971 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7581 (mt0) cc_final: 0.7036 (tm-30)
REVERT: A  319 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.7869 (p0)
REVERT: A  359 MET cc_start: 0.5821 (tpt) cc_final: 0.5290 (tpt)
REVERT: A  406 ASP cc_start: 0.7981 (m-30) cc_final: 0.7686 (t0)
REVERT: A  414 MET cc_start: 0.5908 (mmm) cc_final: 0.5515 (mmm)
REVERT: B  303 GLN cc_start: 0.7602 (mt0) cc_final: 0.7096 (tm-30)
REVERT: C  303 GLN cc_start: 0.7525 (mt0) cc_final: 0.6984 (tm-30)
REVERT: C  365 GLN cc_start: 0.6476 (mp10) cc_final: 0.5817 (mp10)
REVERT: C  406 ASP cc_start: 0.8047 (m-30) cc_final: 0.7593 (t0)
REVERT: D  303 GLN cc_start: 0.7403 (mt0) cc_final: 0.6722 (tm-30)
REVERT: D  363 PRO cc_start: 0.8883 (Cg_exo) cc_final: 0.8641 (Cg_endo)
REVERT: D  406 ASP cc_start: 0.8407 (m-30) cc_final: 0.7952 (t0)
REVERT: E  293 ARG cc_start: 0.8408 (mtp180) cc_final: 0.7001 (pmt-80)
REVERT: E  303 GLN cc_start: 0.7613 (tm-30) cc_final: 0.7221 (tm-30)
REVERT: E  307 MET cc_start: 0.8527 (ttt) cc_final: 0.8240 (ttm)
  outliers start: 16
  outliers final: 13
  residues processed: 115
  average time/residue: 0.1864
  time to fit residues: 26.6810
Evaluate side-chains
  112 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  319 ASN
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain B residue  337 MET
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain B residue  405 MET
Chi-restraints excluded: chain C residue  389 SER
Chi-restraints excluded: chain D residue  332 SER
Chi-restraints excluded: chain D residue  347 SER
Chi-restraints excluded: chain D residue  389 SER
Chi-restraints excluded: chain D residue  407 SER
Chi-restraints excluded: chain E residue  332 SER
Chi-restraints excluded: chain E residue  347 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 52 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 21 optimal weight:    8.9990
   chunk 60 optimal weight:    7.9990
   chunk 54 optimal weight:    0.0980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 358 ASN
A 378 ASN
** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 358 ASN
D 312 ASN
** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 378 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.142204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.100992 restraints weight = 5833.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3777 rms_B_bonded: 2.75
r_work: 0.3644 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3520 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.3300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4785  Z= 0.144
  Angle     :  0.757   8.914   6385  Z= 0.391
  Chirality :  0.045   0.119    535
  Planarity :  0.006   0.080    940
  Dihedral  :  5.029  22.004    705
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 20.23 %
    Favored  : 77.05 %
  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: -5.43 (0.15), residues: 685
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.13 (0.12), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 385 
 PHE   0.015   0.001   PHE A 289 
 TYR   0.004   0.001   TYR C 374 
 ARG   0.009   0.001   ARG D 293 

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

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

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1370 Ramachandran restraints generated.
    685 Oldfield, 0 Emsley, 685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.503 
Fit side-chains
REVERT: A  293 ARG cc_start: 0.7856 (mtp180) cc_final: 0.6958 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7489 (mt0) cc_final: 0.6869 (tm-30)
REVERT: A  319 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.7495 (p0)
REVERT: A  336 MET cc_start: 0.8139 (mpp) cc_final: 0.7879 (mtm)
REVERT: A  344 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8347 (tp40)
REVERT: A  359 MET cc_start: 0.5784 (tpt) cc_final: 0.5489 (tpt)
REVERT: A  414 MET cc_start: 0.5714 (mmm) cc_final: 0.3948 (mpp)
REVERT: B  303 GLN cc_start: 0.7446 (mt0) cc_final: 0.6996 (tm-30)
REVERT: B  359 MET cc_start: 0.5033 (tpt) cc_final: 0.3507 (mmp)
REVERT: C  303 GLN cc_start: 0.7292 (mt0) cc_final: 0.6999 (tm-30)
REVERT: C  354 GLN cc_start: 0.7942 (mp10) cc_final: 0.7544 (mp10)
REVERT: C  405 MET cc_start: 0.7824 (ptp) cc_final: 0.7375 (ptt)
REVERT: C  406 ASP cc_start: 0.7891 (m-30) cc_final: 0.7602 (t0)
REVERT: D  303 GLN cc_start: 0.7360 (mt0) cc_final: 0.6848 (tm-30)
REVERT: D  323 MET cc_start: 0.8257 (mtp) cc_final: 0.7880 (mtp)
REVERT: E  293 ARG cc_start: 0.8512 (mtp180) cc_final: 0.7166 (pmt-80)
REVERT: E  303 GLN cc_start: 0.7639 (tm-30) cc_final: 0.7232 (tm-30)
REVERT: E  307 MET cc_start: 0.8436 (ttt) cc_final: 0.8173 (ttm)
REVERT: E  359 MET cc_start: 0.6088 (tpt) cc_final: 0.4032 (tmm)
  outliers start: 12
  outliers final: 10
  residues processed: 100
  average time/residue: 0.1764
  time to fit residues: 22.2346
Evaluate side-chains
  100 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  319 ASN
Chi-restraints excluded: chain A residue  332 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain B residue  337 MET
Chi-restraints excluded: chain B residue  347 SER
Chi-restraints excluded: chain C residue  330 LEU
Chi-restraints excluded: chain C residue  389 SER
Chi-restraints excluded: chain D residue  330 LEU
Chi-restraints excluded: chain D residue  332 SER
Chi-restraints excluded: chain D residue  389 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 41 optimal weight:    0.6980
   chunk 64 optimal weight:    8.9990
   chunk 60 optimal weight:    0.0970
   chunk 3 optimal weight:    6.9990
   chunk 58 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 21 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   chunk 44 optimal weight:    9.9990
   overall best weight:    3.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 378 ASN
** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 378 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.137988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.094657 restraints weight = 5850.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3701 rms_B_bonded: 2.82
r_work: 0.3569 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3443 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.3194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   4785  Z= 0.261
  Angle     :  0.809   8.829   6385  Z= 0.421
  Chirality :  0.045   0.120    535
  Planarity :  0.006   0.076    940
  Dihedral  :  5.348  26.496    705
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.14 %
    Favored  : 86.86 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 19.77 %
    Favored  : 77.05 %
  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: -5.48 (0.16), residues: 685
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.17 (0.12), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 412 
 PHE   0.016   0.002   PHE A 289 
 TYR   0.007   0.002   TYR B 374 
 ARG   0.008   0.001   ARG D 293 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3071.25 seconds
wall clock time: 53 minutes 38.05 seconds (3218.05 seconds total)