Starting phenix.real_space_refine
on Tue Feb 11 06:54:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kwz_23059/02_2025/7kwz_23059.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kwz_23059/02_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_23059/02_2025/7kwz_23059.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kwz_23059/02_2025/7kwz_23059.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kwz_23059/02_2025/7kwz_23059.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kwz_23059/02_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-5592/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: 2.22, per 1000 atoms: 0.47
  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: 1.19
  Conformation dependent library (CDL) restraints added in 642.7 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: 0.91
  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:             0.340
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     12.820
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.420
-------------------------------------------------------------------------------
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  : 0.467 
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: 0.1631
  time to fit residues: 26.3633
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  : 0.516 
-------------------------------------------------------------------------------
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 = 50)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.102712 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: 0.3514 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3514
-------------------------------------------------------------------------------
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  : 0.495 
Fit side-chains
   revert: symmetry clash
REVERT: A  293 ARG cc_start: 0.7891 (mtp180) cc_final: 0.6917 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7418 (mt0) cc_final: 0.6722 (tm-30)
REVERT: A  359 MET cc_start: 0.5671 (tpt) cc_final: 0.5406 (tpt)
REVERT: A  362 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7908 (tm-30)
REVERT: A  365 GLN cc_start: 0.7174 (mp10) cc_final: 0.6858 (mp10)
REVERT: B  293 ARG cc_start: 0.7793 (mtp-110) cc_final: 0.7528 (mtp-110)
REVERT: B  303 GLN cc_start: 0.7341 (mt0) cc_final: 0.6935 (tm-30)
REVERT: B  359 MET cc_start: 0.5423 (tpt) cc_final: 0.5095 (tpt)
REVERT: C  359 MET cc_start: 0.5557 (tpt) cc_final: 0.5166 (tpt)
REVERT: C  360 GLN cc_start: 0.4768 (tt0) cc_final: 0.4472 (tm-30)
REVERT: C  365 GLN cc_start: 0.6300 (mp10) cc_final: 0.5826 (mp10)
REVERT: D  359 MET cc_start: 0.5065 (tpt) cc_final: 0.4805 (tpt)
REVERT: D  405 MET cc_start: 0.7320 (tmm) cc_final: 0.7054 (tmm)
REVERT: E  293 ARG cc_start: 0.8403 (mtp180) cc_final: 0.7151 (pmt-80)
REVERT: E  307 MET cc_start: 0.8408 (ttt) cc_final: 0.8159 (ttm)
REVERT: E  360 GLN cc_start: 0.5367 (tt0) cc_final: 0.5022 (tm-30)
  outliers start: 11
  outliers final: 8
  residues processed: 106
  average time/residue: 0.1694
  time to fit residues: 22.7156
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  : 0.475 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 58 optimal weight:    0.8980
   chunk 22 optimal weight:    9.9990
   chunk 56 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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**
** D 319 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 = 0.4256 r_free = 0.4256 target = 0.140309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.098482 restraints weight = 5873.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 2.80
r_work: 0.3571 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3441 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1921

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= 0.207
  Angle     :  0.681   6.726   6385  Z= 0.351
  Chirality :  0.044   0.119    535
  Planarity :  0.004   0.043    940
  Dihedral  :  5.369  25.795    705
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 12.27 %
    Favored  : 83.86 %
  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: -5.32 (0.15), residues: 685
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.05 (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
  117 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
REVERT: A  293 ARG cc_start: 0.7942 (mtp180) cc_final: 0.6952 (mmp-170)
REVERT: A  336 MET cc_start: 0.8076 (mpp) cc_final: 0.7722 (mtt)
REVERT: A  359 MET cc_start: 0.5986 (tpt) cc_final: 0.5621 (tpt)
REVERT: A  406 ASP cc_start: 0.8001 (m-30) cc_final: 0.7585 (t0)
REVERT: B  303 GLN cc_start: 0.7493 (mt0) cc_final: 0.7141 (tm-30)
REVERT: B  359 MET cc_start: 0.5611 (tpt) cc_final: 0.5281 (tpt)
REVERT: C  359 MET cc_start: 0.5394 (tpt) cc_final: 0.5110 (tpt)
REVERT: C  360 GLN cc_start: 0.5150 (tt0) cc_final: 0.4777 (tm-30)
REVERT: C  365 GLN cc_start: 0.6260 (mp10) cc_final: 0.5647 (mp10)
REVERT: D  303 GLN cc_start: 0.7281 (mt0) cc_final: 0.6849 (tm-30)
REVERT: D  323 MET cc_start: 0.8463 (mtp) cc_final: 0.7926 (mtp)
REVERT: D  359 MET cc_start: 0.5075 (tpt) cc_final: 0.4858 (tpt)
REVERT: D  365 GLN cc_start: 0.6891 (mp10) cc_final: 0.6658 (mp10)
REVERT: E  293 ARG cc_start: 0.8437 (mtp180) cc_final: 0.7162 (pmt-80)
  outliers start: 17
  outliers final: 14
  residues processed: 111
  average time/residue: 0.1695
  time to fit residues: 23.8166
Evaluate side-chains
  101 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
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:    0.2980
   chunk 39 optimal weight:    0.1980
   chunk 17 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 54 optimal weight:   20.0000
   chunk 42 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 57 optimal weight:   10.0000
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 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 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 319 ASN
** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 345 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 = 0.4258 r_free = 0.4258 target = 0.140409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.098954 restraints weight = 5873.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 2.75
r_work: 0.3584 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3459 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4785  Z= 0.179
  Angle     :  0.677   6.615   6385  Z= 0.347
  Chirality :  0.043   0.118    535
  Planarity :  0.004   0.049    940
  Dihedral  :  5.096  24.212    705
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 14.32 %
    Favored  : 81.82 %
  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: -5.25 (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   0.008   0.001   TRP A 412 
 PHE   0.010   0.001   PHE B 283 
 TYR   0.006   0.001   TYR B 374 
 ARG   0.005   0.000   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
  111 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.510 
Fit side-chains
REVERT: A  293 ARG cc_start: 0.7947 (mtp180) cc_final: 0.6922 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7418 (mt0) cc_final: 0.6942 (tm-30)
REVERT: A  319 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.7561 (p0)
REVERT: A  336 MET cc_start: 0.8007 (mpp) cc_final: 0.7659 (mtt)
REVERT: A  359 MET cc_start: 0.5855 (tpt) cc_final: 0.5448 (tpt)
REVERT: A  362 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7674 (tm-30)
REVERT: A  406 ASP cc_start: 0.7998 (m-30) cc_final: 0.7525 (t0)
REVERT: B  293 ARG cc_start: 0.7846 (mtp-110) cc_final: 0.7635 (mtp-110)
REVERT: B  303 GLN cc_start: 0.7442 (mt0) cc_final: 0.7090 (tm-30)
REVERT: B  322 MET cc_start: 0.8069 (ptp) cc_final: 0.7618 (ptt)
REVERT: B  362 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7993 (tm-30)
REVERT: B  406 ASP cc_start: 0.7828 (m-30) cc_final: 0.7332 (t0)
REVERT: C  354 GLN cc_start: 0.7989 (mp10) cc_final: 0.7307 (mp10)
REVERT: C  359 MET cc_start: 0.5309 (tpt) cc_final: 0.5016 (tpt)
REVERT: C  360 GLN cc_start: 0.5396 (tt0) cc_final: 0.5138 (tm-30)
REVERT: C  406 ASP cc_start: 0.7809 (m-30) cc_final: 0.7521 (t0)
REVERT: D  293 ARG cc_start: 0.7702 (mtp-110) cc_final: 0.7440 (mtp-110)
REVERT: D  303 GLN cc_start: 0.7314 (mt0) cc_final: 0.6916 (tm-30)
REVERT: D  323 MET cc_start: 0.8351 (mtp) cc_final: 0.7969 (mtp)
REVERT: E  293 ARG cc_start: 0.8448 (mtp180) cc_final: 0.7079 (pmt-80)
REVERT: E  307 MET cc_start: 0.8435 (ttt) cc_final: 0.8156 (ttm)
REVERT: E  359 MET cc_start: 0.6039 (tpt) cc_final: 0.3934 (tmm)
  outliers start: 17
  outliers final: 14
  residues processed: 106
  average time/residue: 0.1732
  time to fit residues: 23.2638
Evaluate side-chains
  101 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
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  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:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 20 optimal weight:    9.9990
   chunk 61 optimal weight:   10.0000
   chunk 56 optimal weight:    1.9990
   chunk 13 optimal weight:    0.3980
   chunk 8 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 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 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 319 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.141812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.100343 restraints weight = 5818.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 2.75
r_work: 0.3611 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3487 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.2607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   4785  Z= 0.139
  Angle     :  0.638   7.296   6385  Z= 0.326
  Chirality :  0.042   0.115    535
  Planarity :  0.004   0.049    940
  Dihedral  :  4.831  22.436    705
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 15.68 %
    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: -5.18 (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   0.009   0.001   TRP D 385 
 PHE   0.008   0.001   PHE B 283 
 TYR   0.004   0.001   TYR B 374 
 ARG   0.002   0.000   ARG B 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
  111 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.503 
Fit side-chains
REVERT: A  293 ARG cc_start: 0.7940 (mtp180) cc_final: 0.6934 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7375 (mt0) cc_final: 0.6877 (tm-30)
REVERT: A  319 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.7458 (p0)
REVERT: A  336 MET cc_start: 0.7976 (mpp) cc_final: 0.7583 (mtt)
REVERT: A  362 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7973 (tm-30)
REVERT: A  406 ASP cc_start: 0.8043 (m-30) cc_final: 0.7511 (t0)
REVERT: A  414 MET cc_start: 0.5672 (mmm) cc_final: 0.5375 (mmm)
REVERT: B  303 GLN cc_start: 0.7427 (mt0) cc_final: 0.7077 (tm-30)
REVERT: B  354 GLN cc_start: 0.7845 (mp10) cc_final: 0.7448 (mp10)
REVERT: B  359 MET cc_start: 0.5333 (tpt) cc_final: 0.3723 (mmt)
REVERT: B  362 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7965 (tm-30)
REVERT: B  363 PRO cc_start: 0.8623 (Cg_exo) cc_final: 0.8393 (Cg_endo)
REVERT: B  406 ASP cc_start: 0.7769 (m-30) cc_final: 0.7333 (t0)
REVERT: C  359 MET cc_start: 0.4656 (tpt) cc_final: 0.4294 (tpt)
REVERT: C  406 ASP cc_start: 0.7813 (m-30) cc_final: 0.7531 (t0)
REVERT: D  303 GLN cc_start: 0.7295 (mt0) cc_final: 0.6850 (tm-30)
REVERT: D  323 MET cc_start: 0.8302 (mtp) cc_final: 0.7999 (mtp)
REVERT: D  359 MET cc_start: 0.4823 (tpt) cc_final: 0.3166 (mmp)
REVERT: D  362 GLU cc_start: 0.8293 (tm-30) cc_final: 0.8040 (tm-30)
REVERT: D  365 GLN cc_start: 0.6904 (mp10) cc_final: 0.6675 (mp10)
REVERT: E  293 ARG cc_start: 0.8470 (mtp180) cc_final: 0.7072 (pmt-80)
REVERT: E  307 MET cc_start: 0.8384 (ttt) cc_final: 0.8104 (ttm)
REVERT: E  359 MET cc_start: 0.5847 (tpt) cc_final: 0.3608 (tmm)
REVERT: E  406 ASP cc_start: 0.8075 (m-30) cc_final: 0.7851 (t0)
  outliers start: 15
  outliers final: 11
  residues processed: 106
  average time/residue: 0.1687
  time to fit residues: 22.7973
Evaluate side-chains
  101 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
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  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  347 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 47 optimal weight:   20.0000
   chunk 1 optimal weight:    0.0030
   chunk 58 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 44 optimal weight:    0.6980
   chunk 34 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   chunk 24 optimal weight:   10.0000
   chunk 46 optimal weight:    6.9990
   overall best weight:    2.5396

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 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 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.141171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.100004 restraints weight = 5738.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 2.77
r_work: 0.3603 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3464 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   4785  Z= 0.203
  Angle     :  0.682   7.170   6385  Z= 0.350
  Chirality :  0.042   0.119    535
  Planarity :  0.004   0.048    940
  Dihedral  :  5.030  24.119    705
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.88 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 15.45 %
    Favored  : 80.45 %
  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   0.010   0.001   TRP A 412 
 PHE   0.011   0.001   PHE B 283 
 TYR   0.006   0.002   TYR B 374 
 ARG   0.006   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
  112 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.489 
Fit side-chains
REVERT: A  293 ARG cc_start: 0.7946 (mtp180) cc_final: 0.6949 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7370 (mt0) cc_final: 0.6770 (tm-30)
REVERT: A  406 ASP cc_start: 0.8016 (m-30) cc_final: 0.7476 (t0)
REVERT: B  303 GLN cc_start: 0.7380 (mt0) cc_final: 0.6762 (tm-30)
REVERT: B  322 MET cc_start: 0.8121 (ptp) cc_final: 0.7619 (ptt)
REVERT: B  354 GLN cc_start: 0.7720 (mp10) cc_final: 0.7514 (mp10)
REVERT: B  359 MET cc_start: 0.5343 (tpt) cc_final: 0.3669 (mmt)
REVERT: B  406 ASP cc_start: 0.7834 (m-30) cc_final: 0.7426 (t0)
REVERT: C  303 GLN cc_start: 0.7182 (mt0) cc_final: 0.6797 (tm-30)
REVERT: C  354 GLN cc_start: 0.7883 (mp10) cc_final: 0.7412 (mp10)
REVERT: C  359 MET cc_start: 0.4644 (tpt) cc_final: 0.4387 (tpt)
REVERT: C  362 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7329 (tm-30)
REVERT: C  406 ASP cc_start: 0.7842 (m-30) cc_final: 0.7515 (t0)
REVERT: D  303 GLN cc_start: 0.7328 (mt0) cc_final: 0.6794 (tm-30)
REVERT: D  323 MET cc_start: 0.8251 (mtp) cc_final: 0.7952 (mtp)
REVERT: D  405 MET cc_start: 0.7432 (tmm) cc_final: 0.6950 (tpt)
REVERT: E  293 ARG cc_start: 0.8475 (mtp180) cc_final: 0.7109 (pmt-80)
REVERT: E  307 MET cc_start: 0.8466 (ttt) cc_final: 0.8208 (ttm)
REVERT: E  359 MET cc_start: 0.5936 (tpt) cc_final: 0.3738 (tmm)
REVERT: E  406 ASP cc_start: 0.8155 (m-30) cc_final: 0.7850 (t0)
  outliers start: 18
  outliers final: 15
  residues processed: 106
  average time/residue: 0.1668
  time to fit residues: 22.4563
Evaluate side-chains
  104 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
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  337 MET
Chi-restraints excluded: chain B residue  347 SER
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 48 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9980
   chunk 11 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 40 optimal weight:    8.9990
   chunk 12 optimal weight:    7.9990
   chunk 50 optimal weight:    2.9990
   chunk 55 optimal weight:    0.1980
   overall best weight:    2.4386

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 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 358 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 = 0.4243 r_free = 0.4243 target = 0.140954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.099760 restraints weight = 5765.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 2.78
r_work: 0.3603 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3470 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4785  Z= 0.198
  Angle     :  0.699   7.652   6385  Z= 0.359
  Chirality :  0.042   0.118    535
  Planarity :  0.005   0.058    940
  Dihedral  :  5.021  23.454    705
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.32 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 15.68 %
    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: -5.25 (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   0.010   0.001   TRP A 412 
 PHE   0.010   0.001   PHE B 283 
 TYR   0.006   0.001   TYR B 374 
 ARG   0.004   0.001   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
  112 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.465 
Fit side-chains
REVERT: A  293 ARG cc_start: 0.7956 (mtp180) cc_final: 0.6966 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7348 (mt0) cc_final: 0.6742 (tm-30)
REVERT: A  319 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.7558 (p0)
REVERT: A  406 ASP cc_start: 0.7814 (m-30) cc_final: 0.7301 (t0)
REVERT: A  414 MET cc_start: 0.5709 (mmm) cc_final: 0.3776 (mpp)
REVERT: B  303 GLN cc_start: 0.7403 (mt0) cc_final: 0.6784 (tm-30)
REVERT: B  307 MET cc_start: 0.8027 (ttt) cc_final: 0.7627 (ttm)
REVERT: B  322 MET cc_start: 0.8166 (ptp) cc_final: 0.7683 (ptt)
REVERT: B  354 GLN cc_start: 0.7708 (mp10) cc_final: 0.7434 (mp10)
REVERT: B  359 MET cc_start: 0.5225 (tpt) cc_final: 0.3512 (mmt)
REVERT: B  363 PRO cc_start: 0.8674 (Cg_exo) cc_final: 0.8439 (Cg_endo)
REVERT: B  406 ASP cc_start: 0.7801 (m-30) cc_final: 0.7371 (t0)
REVERT: C  303 GLN cc_start: 0.7195 (mt0) cc_final: 0.6835 (tm-30)
REVERT: C  354 GLN cc_start: 0.7841 (mp10) cc_final: 0.7237 (mp10)
REVERT: C  359 MET cc_start: 0.4664 (tpt) cc_final: 0.4397 (tpt)
REVERT: C  406 ASP cc_start: 0.7821 (m-30) cc_final: 0.7498 (t0)
REVERT: D  303 GLN cc_start: 0.7307 (mt0) cc_final: 0.6796 (tm-30)
REVERT: D  323 MET cc_start: 0.8298 (mtp) cc_final: 0.8044 (mtp)
REVERT: D  405 MET cc_start: 0.7489 (tmm) cc_final: 0.7021 (tpt)
REVERT: E  293 ARG cc_start: 0.8427 (mtp180) cc_final: 0.7088 (pmt-80)
REVERT: E  307 MET cc_start: 0.8446 (ttt) cc_final: 0.8192 (ttm)
REVERT: E  322 MET cc_start: 0.8521 (ptp) cc_final: 0.8221 (ptp)
REVERT: E  359 MET cc_start: 0.5900 (tpt) cc_final: 0.3713 (tmm)
REVERT: E  406 ASP cc_start: 0.8156 (m-30) cc_final: 0.7888 (t0)
  outliers start: 18
  outliers final: 14
  residues processed: 107
  average time/residue: 0.1704
  time to fit residues: 23.1063
Evaluate side-chains
  106 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
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  337 MET
Chi-restraints excluded: chain B residue  347 SER
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:    7.9990
   chunk 40 optimal weight:    9.9990
   chunk 28 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 38 optimal weight:   10.0000
   chunk 4 optimal weight:    8.9990
   chunk 39 optimal weight:    1.9990
   chunk 34 optimal weight:    8.9990
   chunk 57 optimal weight:    8.9990
   chunk 32 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 343 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 = 0.4201 r_free = 0.4201 target = 0.134679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.091916 restraints weight = 5937.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 2.80
r_work: 0.3481 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.2796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042   4785  Z= 0.369
  Angle     :  0.828   8.099   6385  Z= 0.430
  Chirality :  0.046   0.124    535
  Planarity :  0.005   0.062    940
  Dihedral  :  5.735  27.517    705
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 14.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.47 %
    Favored  : 84.53 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 15.23 %
    Favored  : 80.45 %
  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: -5.50 (0.15), residues: 685
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.18 (0.11), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 412 
 PHE   0.019   0.002   PHE B 283 
 TYR   0.010   0.002   TYR B 374 
 ARG   0.003   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
  119 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
REVERT: A  293 ARG cc_start: 0.8022 (mtp180) cc_final: 0.7049 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7511 (mt0) cc_final: 0.7091 (tm-30)
REVERT: A  319 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.7844 (p0)
REVERT: A  406 ASP cc_start: 0.7970 (m-30) cc_final: 0.7569 (t0)
REVERT: A  414 MET cc_start: 0.5801 (mmm) cc_final: 0.3822 (mpp)
REVERT: B  303 GLN cc_start: 0.7546 (mt0) cc_final: 0.7116 (tm-30)
REVERT: B  406 ASP cc_start: 0.7933 (m-30) cc_final: 0.7535 (t0)
REVERT: C  303 GLN cc_start: 0.7382 (mt0) cc_final: 0.7040 (tm-30)
REVERT: C  406 ASP cc_start: 0.8023 (m-30) cc_final: 0.7626 (t0)
REVERT: D  303 GLN cc_start: 0.7463 (mt0) cc_final: 0.6947 (tm-30)
REVERT: D  405 MET cc_start: 0.7533 (tmm) cc_final: 0.7192 (tpt)
REVERT: D  406 ASP cc_start: 0.8305 (m-30) cc_final: 0.7832 (t0)
REVERT: E  293 ARG cc_start: 0.8441 (mtp180) cc_final: 0.7085 (pmt-80)
REVERT: E  303 GLN cc_start: 0.7615 (tm-30) cc_final: 0.6931 (tm-30)
REVERT: E  307 MET cc_start: 0.8531 (ttt) cc_final: 0.8235 (ttm)
REVERT: E  359 MET cc_start: 0.6243 (tpt) cc_final: 0.4028 (tmm)
  outliers start: 19
  outliers final: 17
  residues processed: 113
  average time/residue: 0.1855
  time to fit residues: 26.2427
Evaluate side-chains
  112 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
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  337 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 39 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 51 optimal weight:    8.9990
   chunk 50 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 378 ASN
** 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 331 GLN
** 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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.139573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.096547 restraints weight = 5771.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 2.84
r_work: 0.3560 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3432 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4785  Z= 0.182
  Angle     :  0.730   8.209   6385  Z= 0.374
  Chirality :  0.043   0.118    535
  Planarity :  0.005   0.074    940
  Dihedral  :  5.143  23.111    705
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 17.73 %
    Favored  : 78.41 %
  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: -5.42 (0.15), residues: 685
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.12 (0.12), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 385 
 PHE   0.012   0.001   PHE D 283 
 TYR   0.006   0.001   TYR B 374 
 ARG   0.008   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
  112 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.538 
Fit side-chains
REVERT: A  293 ARG cc_start: 0.7893 (mtp180) cc_final: 0.6950 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7440 (mt0) cc_final: 0.6782 (tm-30)
REVERT: A  319 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.7608 (p0)
REVERT: A  406 ASP cc_start: 0.7851 (m-30) cc_final: 0.7464 (t0)
REVERT: A  414 MET cc_start: 0.5821 (mmm) cc_final: 0.3822 (mpp)
REVERT: B  303 GLN cc_start: 0.7428 (mt0) cc_final: 0.6889 (tm-30)
REVERT: B  307 MET cc_start: 0.8092 (ttt) cc_final: 0.7762 (ttm)
REVERT: B  322 MET cc_start: 0.8122 (ptp) cc_final: 0.7784 (ptt)
REVERT: B  359 MET cc_start: 0.5136 (tpt) cc_final: 0.3459 (mmt)
REVERT: B  406 ASP cc_start: 0.7787 (m-30) cc_final: 0.7444 (t0)
REVERT: C  303 GLN cc_start: 0.7213 (mt0) cc_final: 0.6920 (tm-30)
REVERT: C  354 GLN cc_start: 0.7887 (mp10) cc_final: 0.7398 (mp10)
REVERT: C  406 ASP cc_start: 0.7917 (m-30) cc_final: 0.7592 (t0)
REVERT: D  303 GLN cc_start: 0.7379 (mt0) cc_final: 0.6926 (tm-30)
REVERT: D  323 MET cc_start: 0.8350 (mtp) cc_final: 0.7990 (mtp)
REVERT: D  405 MET cc_start: 0.7596 (tmm) cc_final: 0.7104 (tpt)
REVERT: E  289 PHE cc_start: 0.7436 (t80) cc_final: 0.7205 (t80)
REVERT: E  293 ARG cc_start: 0.8474 (mtp180) cc_final: 0.7112 (pmt-80)
REVERT: E  303 GLN cc_start: 0.7588 (tm-30) cc_final: 0.7161 (tm-30)
REVERT: E  307 MET cc_start: 0.8485 (ttt) cc_final: 0.8208 (ttm)
REVERT: E  359 MET cc_start: 0.5873 (tpt) cc_final: 0.3617 (tmm)
  outliers start: 17
  outliers final: 15
  residues processed: 109
  average time/residue: 0.1608
  time to fit residues: 22.3655
Evaluate side-chains
  107 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 50 optimal weight:    9.9990
   chunk 26 optimal weight:    8.9990
   chunk 52 optimal weight:    0.0980
   chunk 29 optimal weight:    8.9990
   chunk 18 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 21 optimal weight:   20.0000
   chunk 60 optimal weight:   10.0000
   chunk 54 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    2.6186

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

Flipped N/Q/H residues before XYZ refinement:
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 312 ASN
** D 327 GLN ** 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 = 0.4261 r_free = 0.4261 target = 0.139013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.096776 restraints weight = 5802.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 2.78
r_work: 0.3550 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3423 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   4785  Z= 0.217
  Angle     :  0.755   8.507   6385  Z= 0.390
  Chirality :  0.043   0.117    535
  Planarity :  0.006   0.075    940
  Dihedral  :  5.161  23.546    705
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.91 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 18.41 %
    Favored  : 77.95 %
  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: -5.42 (0.15), residues: 685
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.12 (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 D 283 
 TYR   0.006   0.001   TYR B 374 
 ARG   0.008   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
  109 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.530 
Fit side-chains
REVERT: A  293 ARG cc_start: 0.7890 (mtp180) cc_final: 0.6927 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7484 (mt0) cc_final: 0.6915 (tm-30)
REVERT: A  319 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.7671 (p0)
REVERT: A  336 MET cc_start: 0.8204 (mpp) cc_final: 0.7881 (mtt)
REVERT: A  406 ASP cc_start: 0.7870 (m-30) cc_final: 0.7518 (t0)
REVERT: A  414 MET cc_start: 0.5818 (mmm) cc_final: 0.3890 (mpp)
REVERT: B  303 GLN cc_start: 0.7468 (mt0) cc_final: 0.6918 (tm-30)
REVERT: B  322 MET cc_start: 0.8081 (ptp) cc_final: 0.7766 (ptt)
REVERT: B  359 MET cc_start: 0.5245 (tpt) cc_final: 0.3530 (mmt)
REVERT: B  406 ASP cc_start: 0.7812 (m-30) cc_final: 0.7462 (t0)
REVERT: C  303 GLN cc_start: 0.7305 (mt0) cc_final: 0.7000 (tm-30)
REVERT: C  354 GLN cc_start: 0.7944 (mp10) cc_final: 0.7488 (mp10)
REVERT: C  406 ASP cc_start: 0.7939 (m-30) cc_final: 0.7594 (t0)
REVERT: D  303 GLN cc_start: 0.7425 (mt0) cc_final: 0.6919 (tm-30)
REVERT: D  323 MET cc_start: 0.8353 (mtp) cc_final: 0.8005 (mtp)
REVERT: D  406 ASP cc_start: 0.8286 (m-30) cc_final: 0.7868 (t0)
REVERT: E  293 ARG cc_start: 0.8439 (mtp180) cc_final: 0.7103 (pmt-80)
REVERT: E  307 MET cc_start: 0.8469 (ttt) cc_final: 0.8200 (ttm)
REVERT: E  359 MET cc_start: 0.6011 (tpt) cc_final: 0.3730 (tmm)
  outliers start: 16
  outliers final: 15
  residues processed: 106
  average time/residue: 0.1747
  time to fit residues: 23.3835
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  : 0.481 
-------------------------------------------------------------------------------
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 41 optimal weight:    8.9990
   chunk 64 optimal weight:    8.9990
   chunk 60 optimal weight:    1.9990
   chunk 3 optimal weight:    7.9990
   chunk 58 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 21 optimal weight:   20.0000
   chunk 9 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 358 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 = 0.4223 r_free = 0.4223 target = 0.136445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.094268 restraints weight = 5924.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 2.75
r_work: 0.3556 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3429 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.3075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   4785  Z= 0.299
  Angle     :  0.827   8.952   6385  Z= 0.428
  Chirality :  0.045   0.120    535
  Planarity :  0.006   0.075    940
  Dihedral  :  5.539  26.050    705
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.78 %
    Favored  : 90.22 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 19.09 %
    Favored  : 77.27 %
  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: -5.53 (0.15), residues: 685
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.21 (0.12), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 412 
 PHE   0.026   0.002   PHE E 289 
 TYR   0.008   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: 2897.58 seconds
wall clock time: 51 minutes 50.60 seconds (3110.60 seconds total)