Starting phenix.real_space_refine
on Tue Mar  3 12:47:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kwz_23059/03_2026/7kwz_23059.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kwz_23059/03_2026/7kwz_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kwz_23059/03_2026/7kwz_23059.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kwz_23059/03_2026/7kwz_23059.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kwz_23059/03_2026/7kwz_23059.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kwz_23059/03_2026/7kwz_23059.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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:
    B, C, D, E
  Time building chain proxies: 0.60, per 1000 atoms: 0.13
  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: 0.49
  Conformation dependent library (CDL) restraints added in 231.2 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: 0.35
  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: 0.65 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             0.650
  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:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.620
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.740
-------------------------------------------------------------------------------
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 : 13.83
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.001   0.000   ARG C 293 
 TYR   0.007   0.002   TYR C 374 
 PHE   0.008   0.002   PHE D 401 
 TRP   0.010   0.002   TRP A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00608 ( 4785)
  covalent geometry    : angle       0.80401 ( 6385)

*********************** 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  : 0.122 
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: 0.6719 (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: 0.0656
  time to fit residues: 10.7312
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  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 319 ASN
B 344 GLN
** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 331 GLN
C 344 GLN
** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 319 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 = 0.4248 r_free = 0.4248 target = 0.140498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.098602 restraints weight = 6045.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 2.74
r_work: 0.3587 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3462 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.1621

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= 0.245
  Angle     :  0.740   7.059   6385  Z= 0.382
  Chirality :  0.046   0.127    535
  Planarity :  0.003   0.048    940
  Dihedral  :  5.735  25.303    705
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.64 %
    Favored  : 90.36 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 11.59 %
    Favored  : 85.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.47 (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
 ARG   0.002   0.000   ARG B 293 
 TYR   0.007   0.002   TYR B 374 
 PHE   0.014   0.001   PHE B 283 
 TRP   0.011   0.002   TRP A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 4785)
  covalent geometry    : angle       0.74023 ( 6385)

*********************** 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
  109 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 ARG cc_start: 0.7927 (mtp180) cc_final: 0.6929 (mmp-170)
REVERT: A  359 MET cc_start: 0.5857 (tpt) cc_final: 0.5510 (tpt)
REVERT: A  362 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7960 (tm-30)
REVERT: A  406 ASP cc_start: 0.7924 (m-30) cc_final: 0.7559 (t0)
REVERT: B  293 ARG cc_start: 0.7857 (mtp-110) cc_final: 0.7605 (mtp-110)
REVERT: B  303 GLN cc_start: 0.7467 (mt0) cc_final: 0.7088 (tm-30)
REVERT: B  356 GLN cc_start: 0.8434 (mp10) cc_final: 0.8151 (mp10)
REVERT: B  359 MET cc_start: 0.5534 (tpt) cc_final: 0.5212 (tpt)
REVERT: C  356 GLN cc_start: 0.8469 (mp10) cc_final: 0.8228 (mp10)
REVERT: C  359 MET cc_start: 0.5603 (tpt) cc_final: 0.5229 (tpt)
REVERT: C  360 GLN cc_start: 0.4915 (tt0) cc_final: 0.4565 (tm-30)
REVERT: D  359 MET cc_start: 0.5025 (tpt) cc_final: 0.4793 (tpt)
REVERT: E  293 ARG cc_start: 0.8378 (mtp180) cc_final: 0.7131 (pmt-80)
REVERT: E  360 GLN cc_start: 0.5257 (tt0) cc_final: 0.5036 (tm-30)
  outliers start: 11
  outliers final: 8
  residues processed: 105
  average time/residue: 0.0719
  time to fit residues: 9.6676
Evaluate side-chains
  93 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
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 7 optimal weight:    0.0970
   chunk 17 optimal weight:    0.7980
   chunk 44 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 63 optimal weight:    3.9990
   chunk 28 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 56 optimal weight:    8.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    1.5182

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

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

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.144469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.102554 restraints weight = 6013.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 2.84
r_work: 0.3628 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3501 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4785  Z= 0.146
  Angle     :  0.648   6.731   6385  Z= 0.333
  Chirality :  0.043   0.118    535
  Planarity :  0.004   0.044    940
  Dihedral  :  5.133  22.104    705
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 12.73 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.30 (0.15), residues: 685
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.03 (0.12), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 293 
 TYR   0.004   0.001   TYR B 374 
 PHE   0.008   0.001   PHE B 283 
 TRP   0.009   0.001   TRP B 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4785)
  covalent geometry    : angle       0.64799 ( 6385)

*********************** 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
  109 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
REVERT: A  293 ARG cc_start: 0.7885 (mtp180) cc_final: 0.6907 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7438 (mt0) cc_final: 0.6602 (tm-30)
REVERT: A  336 MET cc_start: 0.8026 (mpp) cc_final: 0.7675 (mtt)
REVERT: A  359 MET cc_start: 0.5906 (tpt) cc_final: 0.5557 (tpt)
REVERT: A  365 GLN cc_start: 0.7357 (mp10) cc_final: 0.7058 (mp10)
REVERT: A  406 ASP cc_start: 0.7938 (m-30) cc_final: 0.7513 (t0)
REVERT: B  303 GLN cc_start: 0.7473 (mt0) cc_final: 0.6980 (tm-30)
REVERT: B  356 GLN cc_start: 0.8358 (mp10) cc_final: 0.8107 (mp10)
REVERT: B  359 MET cc_start: 0.5504 (tpt) cc_final: 0.5137 (tpt)
REVERT: B  365 GLN cc_start: 0.6839 (mp10) cc_final: 0.6551 (mp10)
REVERT: C  359 MET cc_start: 0.5283 (tpt) cc_final: 0.5023 (tpt)
REVERT: E  293 ARG cc_start: 0.8484 (mtp180) cc_final: 0.7157 (pmt-80)
REVERT: E  337 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8061 (ttm)
REVERT: E  359 MET cc_start: 0.6044 (tpt) cc_final: 0.3855 (tmm)
  outliers start: 12
  outliers final: 10
  residues processed: 106
  average time/residue: 0.0723
  time to fit residues: 9.8059
Evaluate side-chains
  94 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  405 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 48 optimal weight:   10.0000
   chunk 27 optimal weight:    6.9990
   chunk 61 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 51 optimal weight:   10.0000
   chunk 15 optimal weight:   20.0000
   chunk 33 optimal weight:   10.0000
   chunk 59 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9980
   chunk 62 optimal weight:    9.9990
   overall best weight:    5.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 344 GLN
** 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 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 = 0.4182 r_free = 0.4182 target = 0.134306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.091083 restraints weight = 5869.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 2.84
r_work: 0.3449 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3319 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.042   4785  Z= 0.391
  Angle     :  0.836   7.764   6385  Z= 0.436
  Chirality :  0.047   0.132    535
  Planarity :  0.005   0.046    940
  Dihedral  :  5.956  28.704    705
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.47 %
    Favored  : 84.53 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 17.73 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.49 (0.15), 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
 ARG   0.004   0.000   ARG B 293 
 TYR   0.010   0.003   TYR B 374 
 PHE   0.020   0.002   PHE B 283 
 TRP   0.013   0.002   TRP A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00781 ( 4785)
  covalent geometry    : angle       0.83608 ( 6385)

*********************** 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
  112 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: A  293 ARG cc_start: 0.8023 (mtp180) cc_final: 0.6999 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7543 (mt0) cc_final: 0.7084 (tm-30)
REVERT: A  359 MET cc_start: 0.6071 (tpt) cc_final: 0.5567 (tpt)
REVERT: A  365 GLN cc_start: 0.7480 (mp10) cc_final: 0.7141 (mp10)
REVERT: A  406 ASP cc_start: 0.8101 (m-30) cc_final: 0.7671 (t0)
REVERT: A  414 MET cc_start: 0.5814 (mmm) cc_final: 0.5598 (mmm)
REVERT: B  303 GLN cc_start: 0.7613 (mt0) cc_final: 0.7164 (tm-30)
REVERT: B  359 MET cc_start: 0.5602 (tpt) cc_final: 0.5331 (tpt)
REVERT: B  365 GLN cc_start: 0.6838 (mp10) cc_final: 0.6476 (mp10)
REVERT: C  303 GLN cc_start: 0.7429 (mt0) cc_final: 0.6964 (tm-30)
REVERT: C  362 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7703 (tm-30)
REVERT: C  406 ASP cc_start: 0.8048 (m-30) cc_final: 0.7582 (t0)
REVERT: D  303 GLN cc_start: 0.7501 (mt0) cc_final: 0.6832 (tm-30)
REVERT: D  406 ASP cc_start: 0.8241 (m-30) cc_final: 0.7863 (t0)
REVERT: E  293 ARG cc_start: 0.8426 (mtp180) cc_final: 0.7109 (pmt-80)
REVERT: E  307 MET cc_start: 0.8500 (ttt) cc_final: 0.8243 (ttm)
  outliers start: 16
  outliers final: 14
  residues processed: 106
  average time/residue: 0.0710
  time to fit residues: 9.6428
Evaluate side-chains
  103 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  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 3 optimal weight:    5.9990
   chunk 9 optimal weight:    0.4980
   chunk 34 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    1.4584

-------------------------------------------------------------------------------
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**
B 358 ASN
** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 331 GLN
** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 358 ASN
C 378 ASN
D 358 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.144351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.102176 restraints weight = 5928.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3721 rms_B_bonded: 2.82
r_work: 0.3605 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3479 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4785  Z= 0.147
  Angle     :  0.668   7.080   6385  Z= 0.342
  Chirality :  0.042   0.116    535
  Planarity :  0.004   0.046    940
  Dihedral  :  5.121  22.625    705
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.95 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.27 (0.16), residues: 685
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.01 (0.12), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 293 
 TYR   0.005   0.001   TYR B 374 
 PHE   0.009   0.001   PHE E 289 
 TRP   0.010   0.001   TRP B 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 4785)
  covalent geometry    : angle       0.66808 ( 6385)

*********************** 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
  106 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A  293 ARG cc_start: 0.7893 (mtp180) cc_final: 0.6943 (mmp-170)
REVERT: A  319 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.7567 (p0)
REVERT: A  336 MET cc_start: 0.8022 (mpp) cc_final: 0.7626 (mtt)
REVERT: A  359 MET cc_start: 0.6023 (tpt) cc_final: 0.5556 (tpt)
REVERT: A  362 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7651 (tm-30)
REVERT: A  365 GLN cc_start: 0.7348 (mp10) cc_final: 0.7092 (mp10)
REVERT: A  406 ASP cc_start: 0.8070 (m-30) cc_final: 0.7651 (t0)
REVERT: A  414 MET cc_start: 0.5814 (mmm) cc_final: 0.5544 (mmm)
REVERT: B  303 GLN cc_start: 0.7463 (mt0) cc_final: 0.6915 (tm-30)
REVERT: B  322 MET cc_start: 0.8063 (ptp) cc_final: 0.7569 (ptt)
REVERT: B  359 MET cc_start: 0.5356 (tpt) cc_final: 0.5040 (tpt)
REVERT: C  303 GLN cc_start: 0.7239 (mt0) cc_final: 0.6873 (tm-30)
REVERT: C  322 MET cc_start: 0.8185 (ptp) cc_final: 0.7762 (ptt)
REVERT: C  354 GLN cc_start: 0.7874 (mp10) cc_final: 0.7356 (mp10)
REVERT: C  359 MET cc_start: 0.4769 (tpt) cc_final: 0.3083 (mmp)
REVERT: C  362 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7631 (tm-30)
REVERT: C  406 ASP cc_start: 0.7894 (m-30) cc_final: 0.7496 (t0)
REVERT: D  303 GLN cc_start: 0.7384 (mt0) cc_final: 0.6890 (tm-30)
REVERT: D  405 MET cc_start: 0.7594 (tmm) cc_final: 0.7129 (tpt)
REVERT: D  410 SER cc_start: 0.8668 (m) cc_final: 0.7667 (p)
REVERT: E  293 ARG cc_start: 0.8459 (mtp180) cc_final: 0.7110 (pmt-80)
REVERT: E  303 GLN cc_start: 0.7705 (tm-30) cc_final: 0.7290 (tm-30)
REVERT: E  307 MET cc_start: 0.8423 (ttt) cc_final: 0.8173 (ttm)
REVERT: E  322 MET cc_start: 0.8526 (ptp) cc_final: 0.8287 (ptt)
REVERT: E  323 MET cc_start: 0.8580 (mtp) cc_final: 0.8322 (mtp)
REVERT: E  337 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.8003 (ttm)
REVERT: E  359 MET cc_start: 0.6079 (tpt) cc_final: 0.3881 (tmm)
REVERT: E  406 ASP cc_start: 0.8182 (m-30) cc_final: 0.7846 (t0)
  outliers start: 13
  outliers final: 9
  residues processed: 102
  average time/residue: 0.0612
  time to fit residues: 8.1521
Evaluate side-chains
  98 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  337 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 23 optimal weight:    9.9990
   chunk 56 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 4 optimal weight:    7.9990
   chunk 40 optimal weight:    9.9990
   chunk 1 optimal weight:    0.8980
   chunk 59 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 44 optimal weight:    0.7980
   overall best weight:    4.7386

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.134834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.091634 restraints weight = 6001.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 2.85
r_work: 0.3513 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3383 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.041   4785  Z= 0.338
  Angle     :  0.799   7.331   6385  Z= 0.417
  Chirality :  0.046   0.133    535
  Planarity :  0.005   0.051    940
  Dihedral  :  5.720  27.800    705
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.06 %
    Favored  : 83.94 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 19.32 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.47 (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
 ARG   0.005   0.001   ARG D 293 
 TYR   0.010   0.002   TYR B 374 
 PHE   0.017   0.002   PHE B 283 
 TRP   0.011   0.002   TRP A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00679 ( 4785)
  covalent geometry    : angle       0.79947 ( 6385)

*********************** 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
  110 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: A  293 ARG cc_start: 0.7978 (mtp180) cc_final: 0.6985 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7490 (mt0) cc_final: 0.6997 (tm-30)
REVERT: A  359 MET cc_start: 0.6005 (tpt) cc_final: 0.5504 (tpt)
REVERT: A  406 ASP cc_start: 0.8160 (m-30) cc_final: 0.7668 (t0)
REVERT: B  303 GLN cc_start: 0.7532 (mt0) cc_final: 0.6985 (tm-30)
REVERT: B  359 MET cc_start: 0.5315 (tpt) cc_final: 0.5064 (tpt)
REVERT: C  303 GLN cc_start: 0.7353 (mt0) cc_final: 0.6843 (tm-30)
REVERT: C  362 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7569 (tm-30)
REVERT: C  406 ASP cc_start: 0.7977 (m-30) cc_final: 0.7474 (t0)
REVERT: D  303 GLN cc_start: 0.7455 (mt0) cc_final: 0.6853 (tm-30)
REVERT: D  405 MET cc_start: 0.7390 (tmm) cc_final: 0.7093 (tpt)
REVERT: D  406 ASP cc_start: 0.8307 (m-30) cc_final: 0.7749 (t0)
REVERT: E  293 ARG cc_start: 0.8428 (mtp180) cc_final: 0.7065 (pmt-80)
REVERT: E  303 GLN cc_start: 0.7635 (tm-30) cc_final: 0.7174 (tm-30)
REVERT: E  307 MET cc_start: 0.8455 (ttt) cc_final: 0.8163 (ttm)
  outliers start: 15
  outliers final: 11
  residues processed: 104
  average time/residue: 0.0720
  time to fit residues: 9.4767
Evaluate side-chains
  101 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  347 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   chunk 29 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 18 optimal weight:    8.9990
   chunk 4 optimal weight:    0.0870
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.7760

-------------------------------------------------------------------------------
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 344 GLN
** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 378 ASN
** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 319 ASN
C 344 GLN
** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 378 ASN
E 312 ASN
E 345 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.142524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.101542 restraints weight = 5877.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3770 rms_B_bonded: 2.74
r_work: 0.3631 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3506 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4785  Z= 0.124
  Angle     :  0.667   7.279   6385  Z= 0.343
  Chirality :  0.042   0.115    535
  Planarity :  0.005   0.055    940
  Dihedral  :  4.893  21.027    705
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 18.86 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.29 (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
 ARG   0.008   0.001   ARG D 293 
 TYR   0.003   0.001   TYR B 374 
 PHE   0.011   0.001   PHE E 289 
 TRP   0.017   0.002   TRP D 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 4785)
  covalent geometry    : angle       0.66745 ( 6385)

*********************** 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
  110 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A  293 ARG cc_start: 0.7840 (mtp180) cc_final: 0.6897 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7411 (mt0) cc_final: 0.6764 (tm-30)
REVERT: A  319 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.7450 (p0)
REVERT: A  336 MET cc_start: 0.8012 (mpp) cc_final: 0.7803 (mtm)
REVERT: A  359 MET cc_start: 0.6051 (tpt) cc_final: 0.5633 (tpt)
REVERT: A  362 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7904 (tm-30)
REVERT: A  406 ASP cc_start: 0.8033 (m-30) cc_final: 0.7634 (t0)
REVERT: B  303 GLN cc_start: 0.7450 (mt0) cc_final: 0.6865 (tm-30)
REVERT: B  307 MET cc_start: 0.7983 (ttt) cc_final: 0.7662 (ttm)
REVERT: B  322 MET cc_start: 0.7987 (ptp) cc_final: 0.7661 (ptt)
REVERT: B  359 MET cc_start: 0.5357 (tpt) cc_final: 0.5106 (tpt)
REVERT: B  408 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8197 (mtpp)
REVERT: C  303 GLN cc_start: 0.7239 (mt0) cc_final: 0.6866 (tm-30)
REVERT: C  322 MET cc_start: 0.8018 (ptp) cc_final: 0.7716 (ptt)
REVERT: C  354 GLN cc_start: 0.7856 (mp10) cc_final: 0.7452 (mp10)
REVERT: C  362 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7538 (tm-30)
REVERT: C  406 ASP cc_start: 0.7925 (m-30) cc_final: 0.7565 (t0)
REVERT: D  303 GLN cc_start: 0.7357 (mt0) cc_final: 0.6857 (tm-30)
REVERT: D  405 MET cc_start: 0.7629 (tmm) cc_final: 0.7155 (tpt)
REVERT: D  410 SER cc_start: 0.8710 (m) cc_final: 0.7859 (p)
REVERT: E  293 ARG cc_start: 0.8458 (mtp180) cc_final: 0.7122 (pmt-80)
REVERT: E  303 GLN cc_start: 0.7642 (tm-30) cc_final: 0.6698 (tm-30)
REVERT: E  307 MET cc_start: 0.8434 (ttt) cc_final: 0.8135 (ttm)
REVERT: E  322 MET cc_start: 0.8393 (ptp) cc_final: 0.8161 (ptt)
REVERT: E  359 MET cc_start: 0.5924 (tpt) cc_final: 0.3748 (tmm)
REVERT: E  405 MET cc_start: 0.7968 (ptp) cc_final: 0.7602 (ptp)
REVERT: E  406 ASP cc_start: 0.8230 (m-30) cc_final: 0.7855 (t0)
  outliers start: 15
  outliers final: 11
  residues processed: 108
  average time/residue: 0.0677
  time to fit residues: 9.4529
Evaluate side-chains
  103 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  340 LEU
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 28 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 49 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   overall best weight:    4.7990

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.135002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.091935 restraints weight = 5945.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 2.81
r_work: 0.3473 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3345 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.2893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.041   4785  Z= 0.341
  Angle     :  0.820   7.923   6385  Z= 0.426
  Chirality :  0.046   0.122    535
  Planarity :  0.005   0.056    940
  Dihedral  :  5.727  28.902    705
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.08 %
    Favored  : 82.92 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 18.86 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.48 (0.15), 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
 ARG   0.006   0.001   ARG D 293 
 TYR   0.009   0.002   TYR B 374 
 PHE   0.018   0.002   PHE A 283 
 TRP   0.011   0.002   TRP A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00689 ( 4785)
  covalent geometry    : angle       0.81964 ( 6385)

*********************** 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
  106 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
REVERT: A  293 ARG cc_start: 0.7961 (mtp180) cc_final: 0.7010 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7520 (mt0) cc_final: 0.7037 (tm-30)
REVERT: A  319 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.7864 (p0)
REVERT: A  359 MET cc_start: 0.6032 (tpt) cc_final: 0.5567 (tpt)
REVERT: A  362 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7944 (tm-30)
REVERT: A  406 ASP cc_start: 0.8037 (m-30) cc_final: 0.7669 (t0)
REVERT: B  303 GLN cc_start: 0.7552 (mt0) cc_final: 0.7082 (tm-30)
REVERT: B  322 MET cc_start: 0.8190 (ptp) cc_final: 0.7716 (ptt)
REVERT: B  359 MET cc_start: 0.5395 (tpt) cc_final: 0.5085 (tpt)
REVERT: B  365 GLN cc_start: 0.6904 (mp10) cc_final: 0.6639 (mp10)
REVERT: C  303 GLN cc_start: 0.7417 (mt0) cc_final: 0.6942 (tm-30)
REVERT: C  362 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7656 (tm-30)
REVERT: C  406 ASP cc_start: 0.8036 (m-30) cc_final: 0.7560 (t0)
REVERT: D  303 GLN cc_start: 0.7502 (mt0) cc_final: 0.6853 (tm-30)
REVERT: D  362 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7923 (tm-30)
REVERT: D  405 MET cc_start: 0.7578 (tmm) cc_final: 0.7274 (tpt)
REVERT: D  406 ASP cc_start: 0.8368 (m-30) cc_final: 0.7849 (t0)
REVERT: E  293 ARG cc_start: 0.8416 (mtp180) cc_final: 0.7086 (pmt-80)
REVERT: E  307 MET cc_start: 0.8544 (ttt) cc_final: 0.8264 (ttm)
REVERT: E  322 MET cc_start: 0.8597 (ptp) cc_final: 0.8312 (ptt)
  outliers start: 16
  outliers final: 11
  residues processed: 103
  average time/residue: 0.0615
  time to fit residues: 8.1609
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  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  340 LEU
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 7 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 56 optimal weight:    6.9990
   chunk 35 optimal weight:   10.0000
   chunk 4 optimal weight:    0.0040
   chunk 61 optimal weight:    0.0970
   chunk 28 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9990
   overall best weight:    1.0196

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

Flipped N/Q/H residues before XYZ refinement:
** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 378 ASN
** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 358 ASN
C 378 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.142399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.100706 restraints weight = 5796.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3762 rms_B_bonded: 2.75
r_work: 0.3629 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3501 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.3099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4785  Z= 0.134
  Angle     :  0.712   8.239   6385  Z= 0.361
  Chirality :  0.043   0.117    535
  Planarity :  0.004   0.056    940
  Dihedral  :  4.934  22.332    705
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 20.91 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.34 (0.15), residues: 685
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.06 (0.12), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 293 
 TYR   0.004   0.001   TYR B 374 
 PHE   0.019   0.001   PHE E 289 
 TRP   0.016   0.002   TRP B 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 4785)
  covalent geometry    : angle       0.71192 ( 6385)

*********************** 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
  101 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A  293 ARG cc_start: 0.7868 (mtp180) cc_final: 0.6932 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7399 (mt0) cc_final: 0.6754 (tm-30)
REVERT: A  319 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.7613 (p0)
REVERT: A  336 MET cc_start: 0.8088 (mpp) cc_final: 0.7863 (mtm)
REVERT: A  359 MET cc_start: 0.6037 (tpt) cc_final: 0.5610 (tpt)
REVERT: A  362 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8031 (tm-30)
REVERT: A  406 ASP cc_start: 0.7968 (m-30) cc_final: 0.7651 (t0)
REVERT: B  303 GLN cc_start: 0.7453 (mt0) cc_final: 0.6873 (tm-30)
REVERT: B  307 MET cc_start: 0.8007 (ttt) cc_final: 0.7686 (ttm)
REVERT: B  322 MET cc_start: 0.7921 (ptp) cc_final: 0.7503 (ptt)
REVERT: B  365 GLN cc_start: 0.6752 (mp10) cc_final: 0.6459 (mp10)
REVERT: C  303 GLN cc_start: 0.7246 (mt0) cc_final: 0.6921 (tm-30)
REVERT: C  322 MET cc_start: 0.7969 (ptp) cc_final: 0.7661 (ptt)
REVERT: C  354 GLN cc_start: 0.7906 (mp10) cc_final: 0.7493 (mp10)
REVERT: C  406 ASP cc_start: 0.7901 (m-30) cc_final: 0.7545 (t0)
REVERT: D  303 GLN cc_start: 0.7386 (mt0) cc_final: 0.6860 (tm-30)
REVERT: D  405 MET cc_start: 0.7632 (tmm) cc_final: 0.7202 (tpt)
REVERT: D  410 SER cc_start: 0.8671 (m) cc_final: 0.7872 (p)
REVERT: E  293 ARG cc_start: 0.8460 (mtp180) cc_final: 0.7099 (pmt-80)
REVERT: E  307 MET cc_start: 0.8408 (ttt) cc_final: 0.7829 (mtp)
REVERT: E  322 MET cc_start: 0.8483 (ptp) cc_final: 0.8232 (ptt)
REVERT: E  359 MET cc_start: 0.6033 (tpt) cc_final: 0.3934 (tmm)
  outliers start: 11
  outliers final: 9
  residues processed: 99
  average time/residue: 0.0608
  time to fit residues: 7.7729
Evaluate side-chains
  99 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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  347 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 37 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 7 optimal weight:    7.9990
   chunk 49 optimal weight:    8.9990
   chunk 24 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 378 ASN
** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 378 ASN
D 312 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.138348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.095014 restraints weight = 5816.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 2.82
r_work: 0.3543 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3407 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.3016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   4785  Z= 0.231
  Angle     :  0.759   8.195   6385  Z= 0.389
  Chirality :  0.043   0.117    535
  Planarity :  0.005   0.058    940
  Dihedral  :  5.229  25.587    705
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.36 %
    Favored  : 89.64 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 20.68 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.41 (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
 ARG   0.005   0.001   ARG D 293 
 TYR   0.007   0.002   TYR B 374 
 PHE   0.018   0.002   PHE E 289 
 TRP   0.008   0.001   TRP A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 ( 4785)
  covalent geometry    : angle       0.75937 ( 6385)

********************** 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
  100 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A  293 ARG cc_start: 0.7945 (mtp180) cc_final: 0.7024 (mmp-170)
REVERT: A  303 GLN cc_start: 0.7529 (mt0) cc_final: 0.6878 (tm-30)
REVERT: A  319 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.7776 (p0)
REVERT: A  336 MET cc_start: 0.8296 (mpp) cc_final: 0.8071 (mtm)
REVERT: A  359 MET cc_start: 0.5931 (tpt) cc_final: 0.5592 (tpt)
REVERT: A  362 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8044 (tm-30)
REVERT: A  406 ASP cc_start: 0.7958 (m-30) cc_final: 0.7643 (t0)
REVERT: B  303 GLN cc_start: 0.7498 (mt0) cc_final: 0.7014 (tm-30)
REVERT: B  322 MET cc_start: 0.8094 (ptp) cc_final: 0.7610 (ptt)
REVERT: C  303 GLN cc_start: 0.7362 (mt0) cc_final: 0.6972 (tm-30)
REVERT: C  354 GLN cc_start: 0.8003 (mp10) cc_final: 0.7522 (mp10)
REVERT: C  359 MET cc_start: 0.4634 (tpt) cc_final: 0.3137 (mmp)
REVERT: C  362 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7401 (tm-30)
REVERT: C  406 ASP cc_start: 0.7981 (m-30) cc_final: 0.7546 (t0)
REVERT: D  303 GLN cc_start: 0.7414 (mt0) cc_final: 0.6893 (tm-30)
REVERT: D  406 ASP cc_start: 0.8292 (m-30) cc_final: 0.7894 (t0)
REVERT: E  293 ARG cc_start: 0.8463 (mtp180) cc_final: 0.7117 (pmt-80)
REVERT: E  307 MET cc_start: 0.8517 (ttt) cc_final: 0.8246 (ttm)
REVERT: E  322 MET cc_start: 0.8560 (ptp) cc_final: 0.8291 (ptt)
REVERT: E  359 MET cc_start: 0.6242 (tpt) cc_final: 0.4089 (tmm)
  outliers start: 12
  outliers final: 10
  residues processed: 99
  average time/residue: 0.0655
  time to fit residues: 8.3732
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  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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 30 optimal weight:    0.8980
   chunk 39 optimal weight:    6.9990
   chunk 55 optimal weight:    3.9990
   chunk 40 optimal weight:    9.9990
   chunk 47 optimal weight:   30.0000
   chunk 12 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 35 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 345 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 = 0.4275 r_free = 0.4275 target = 0.140219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.097334 restraints weight = 5714.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 2.78
r_work: 0.3576 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3447 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.3102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4785  Z= 0.179
  Angle     :  0.738   8.641   6385  Z= 0.378
  Chirality :  0.043   0.144    535
  Planarity :  0.004   0.052    940
  Dihedral  :  5.104  24.137    705
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 21.14 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.38 (0.16), 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
 ARG   0.005   0.001   ARG D 293 
 TYR   0.006   0.001   TYR B 374 
 PHE   0.017   0.001   PHE E 289 
 TRP   0.010   0.001   TRP B 385 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 4785)
  covalent geometry    : angle       0.73840 ( 6385)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1414.13 seconds
wall clock time: 24 minutes 49.38 seconds (1489.38 seconds total)