Starting phenix.real_space_refine
on Wed Jun  4 12:00:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tz0_26201/06_2025/7tz0_26201.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tz0_26201/06_2025/7tz0_26201.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tz0_26201/06_2025/7tz0_26201.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tz0_26201/06_2025/7tz0_26201.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tz0_26201/06_2025/7tz0_26201.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tz0_26201/06_2025/7tz0_26201.cif"
  }
  resolution = 4.17
  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=   0.100
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      12      5.16       5
     C    1699      2.51       5
     N     453      2.21       5
     O     510      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-5710/modules/chem_data/mon_lib"
  Total number of atoms: 2674
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1521
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1521
          Classifications: {'peptide': 192}
          Link IDs: {'PTRANS': 10, 'TRANS': 181}
    Chain: "B"
      Number of atoms: 1153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 1153
          Classifications: {'peptide': 155}
          Link IDs: {'PTRANS': 4, 'TRANS': 150}
  Time building chain proxies: 2.14, per 1000 atoms: 0.80
  Number of scatterers: 2674
  At special positions: 0
  Unit cell: (58.491, 66.348, 96.903, 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      12     16.00
     O     510      8.00
     N     453      7.00
     C    1699      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.62
  Conformation dependent library (CDL) restraints added in 331.1 milliseconds
  

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  632

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 2 sheets defined
      36.9% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 365 through 370
      removed outlier: 4.304A  pdb=" N   TYR A 369 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ASN A 370 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 365 through 370'
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'B' and resid 16 through 25
      removed outlier: 3.542A  pdb=" N   GLU B  20 " --> pdb=" O   LYS B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 35
    Processing helix  chain 'B' and resid 49 through 58
      removed outlier: 3.522A  pdb=" N   LEU B  53 " --> pdb=" O   THR B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 69
      removed outlier: 4.064A  pdb=" N   TYR B  69 " --> pdb=" O   VAL B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 91
    Processing helix  chain 'B' and resid 93 through 103
      removed outlier: 4.008A  pdb=" N   GLU B  97 " --> pdb=" O   LEU B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 124
      removed outlier: 3.528A  pdb=" N   ARG B 123 " --> pdb=" O   LEU B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 135
      removed outlier: 3.617A  pdb=" N   VAL B 129 " --> pdb=" O   HIS B 125 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   GLU B 130 " --> pdb=" O   LEU B 126 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ASN B 135 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 157
      removed outlier: 3.599A  pdb=" N   ASP B 155 " --> pdb=" O   ASP B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 168
      removed outlier: 3.839A  pdb=" N   ALA B 162 " --> pdb=" O   ASN B 158 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   GLU B 163 " --> pdb=" O   GLU B 159 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ILE B 164 " --> pdb=" O   ASP B 160 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LEU B 165 " --> pdb=" O   LEU B 161 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 397 through 402
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454

    72 hydrogen bonds defined for protein.
    207 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.56

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 889
        1.35 -     1.46: 646
        1.46 -     1.58: 1184
        1.58 -     1.70: 1
        1.70 -     1.81: 14
  Bond restraints: 2734
  Sorted by residual:
  bond pdb=" CB  PRO A 384 "
       pdb=" CG  PRO A 384 "
    ideal  model  delta    sigma   weight residual
    1.492  1.605 -0.113 5.00e-02 4.00e+02 5.13e+00
  bond pdb=" CB  PRO B  50 "
       pdb=" CG  PRO B  50 "
    ideal  model  delta    sigma   weight residual
    1.492  1.553 -0.061 5.00e-02 4.00e+02 1.47e+00
  bond pdb=" CB  LYS A 458 "
       pdb=" CG  LYS A 458 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.11e-01
  bond pdb=" CG  PRO A 384 "
       pdb=" CD  PRO A 384 "
    ideal  model  delta    sigma   weight residual
    1.503  1.533 -0.030 3.40e-02 8.65e+02 8.03e-01
  bond pdb=" CB  ARG B  31 "
       pdb=" CG  ARG B  31 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 6.69e-01
  ... (remaining 2729 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.87: 3639
        1.87 -     3.75: 64
        3.75 -     5.62: 9
        5.62 -     7.50: 2
        7.50 -     9.37: 1
  Bond angle restraints: 3715
  Sorted by residual:
  angle pdb=" CA  PRO A 384 "
        pdb=" N   PRO A 384 "
        pdb=" CD  PRO A 384 "
      ideal   model   delta    sigma   weight residual
     112.00  104.86    7.14 1.40e+00 5.10e-01 2.60e+01
  angle pdb=" N   VAL A 341 "
        pdb=" CA  VAL A 341 "
        pdb=" C   VAL A 341 "
      ideal   model   delta    sigma   weight residual
     113.42  108.54    4.88 1.17e+00 7.31e-01 1.74e+01
  angle pdb=" CA  PRO B  50 "
        pdb=" N   PRO B  50 "
        pdb=" CD  PRO B  50 "
      ideal   model   delta    sigma   weight residual
     112.00  107.42    4.58 1.40e+00 5.10e-01 1.07e+01
  angle pdb=" CA  LEU A 518 "
        pdb=" CB  LEU A 518 "
        pdb=" CG  LEU A 518 "
      ideal   model   delta    sigma   weight residual
     116.30  125.67   -9.37 3.50e+00 8.16e-02 7.17e+00
  angle pdb=" CA  LYS A 458 "
        pdb=" CB  LYS A 458 "
        pdb=" CG  LYS A 458 "
      ideal   model   delta    sigma   weight residual
     114.10  119.44   -5.34 2.00e+00 2.50e-01 7.14e+00
  ... (remaining 3710 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.80: 1429
       14.80 -    29.59: 143
       29.59 -    44.39: 32
       44.39 -    59.18: 8
       59.18 -    73.98: 2
  Dihedral angle restraints: 1614
    sinusoidal: 619
      harmonic: 995
  Sorted by residual:
  dihedral pdb=" CB  CYS A 480 "
           pdb=" SG  CYS A 480 "
           pdb=" SG  CYS A 488 "
           pdb=" CB  CYS A 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   19.02   73.98     1      1.00e+01 1.00e-02 6.95e+01
  dihedral pdb=" CB  CYS A 379 "
           pdb=" SG  CYS A 379 "
           pdb=" SG  CYS A 432 "
           pdb=" CB  CYS A 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -144.38   58.38     1      1.00e+01 1.00e-02 4.57e+01
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   46.65   46.35     1      1.00e+01 1.00e-02 2.97e+01
  ... (remaining 1611 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 223
       0.028 -    0.056: 115
       0.056 -    0.084: 45
       0.084 -    0.112: 19
       0.112 -    0.140: 6
  Chirality restraints: 408
  Sorted by residual:
  chirality pdb=" CA  PRO B  50 "
            pdb=" N   PRO B  50 "
            pdb=" C   PRO B  50 "
            pdb=" CB  PRO B  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.92e-01
  chirality pdb=" CA  PRO A 491 "
            pdb=" N   PRO A 491 "
            pdb=" C   PRO A 491 "
            pdb=" CB  PRO A 491 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.13 2.00e-01 2.50e+01 4.52e-01
  chirality pdb=" CA  VAL A 382 "
            pdb=" N   VAL A 382 "
            pdb=" C   VAL A 382 "
            pdb=" CB  VAL A 382 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.82e-01
  ... (remaining 405 not shown)

  Planarity restraints: 489
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 383 "   -0.075 5.00e-02 4.00e+02   1.10e-01 1.94e+01
        pdb=" N   PRO A 384 "    0.190 5.00e-02 4.00e+02
        pdb=" CA  PRO A 384 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO A 384 "   -0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  49 "   -0.056 5.00e-02 4.00e+02   8.32e-02 1.11e+01
        pdb=" N   PRO B  50 "    0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO B  50 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B  50 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 360 "   -0.010 2.00e-02 2.50e+03   2.09e-02 4.37e+00
        pdb=" C   ASN A 360 "    0.036 2.00e-02 2.50e+03
        pdb=" O   ASN A 360 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   CYS A 361 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 486 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 715
        2.79 -     3.32: 2669
        3.32 -     3.85: 4201
        3.85 -     4.37: 4974
        4.37 -     4.90: 7820
  Nonbonded interactions: 20379
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 415 "
            pdb=" OD2 ASP A 420 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   ASN A 439 "
            pdb=" OG  SER A 443 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" NH1 ARG A 346 "
            pdb=" O   PHE A 347 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" NH1 ARG A 357 "
            pdb=" O   ILE A 358 "
     model   vdw
     2.281 3.120
  nonbonded pdb=" OG1 THR B  82 "
            pdb=" ND1 HIS B  85 "
     model   vdw
     2.306 3.120
  ... (remaining 20374 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.090
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.340
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6217
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      :  0.003   0.113   2738  Z= 0.114
  Angle     :  0.626   9.374   3723  Z= 0.331
  Chirality :  0.041   0.140    408
  Planarity :  0.007   0.110    489
  Dihedral  : 12.380  69.766    970
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.42), residues: 343
  helix: -0.69 (0.47), residues: 106
  sheet: -1.48 (1.07), residues: 24
  loop : -1.37 (0.40), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  79 
 HIS   0.004   0.001   HIS B  52 
 PHE   0.032   0.001   PHE A 429 
 TYR   0.012   0.001   TYR A 495 
 ARG   0.004   0.000   ARG B  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.26316 (   72)
  hydrogen bonds       : angle       7.56412 (  207)
  SS BOND              : bond        0.00223 (    4)
  SS BOND              : angle       1.28132 (    8)
  covalent geometry    : bond        0.00333 ( 2734)
  covalent geometry    : angle       0.62432 ( 3715)

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

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

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
REVERT: A  418 ILE cc_start: 0.8385 (mp) cc_final: 0.7934 (mp)
REVERT: A  498 GLN cc_start: 0.8587 (mp10) cc_final: 0.8268 (mp10)
REVERT: B   66 LEU cc_start: 0.8491 (mt) cc_final: 0.8260 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1253
  time to fit residues: 12.2911
Evaluate side-chains
  72 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 28 optimal weight:   20.0000
   chunk 25 optimal weight:    2.9990
   chunk 14 optimal weight:   30.0000
   chunk 8 optimal weight:    0.1980
   chunk 17 optimal weight:   30.0000
   chunk 13 optimal weight:    8.9990
   chunk 26 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   overall best weight:    3.0388

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

Flipped N/Q/H residues before XYZ refinement:
** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.189757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.160942 restraints weight = 6867.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.164829 restraints weight = 5011.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.168052 restraints weight = 3865.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.4216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6398
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   2738  Z= 0.112
  Angle     :  0.577   6.468   3723  Z= 0.292
  Chirality :  0.043   0.137    408
  Planarity :  0.005   0.060    489
  Dihedral  :  4.598  18.322    376
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.42), residues: 343
  helix: -0.60 (0.45), residues: 113
  sheet: -1.17 (0.90), residues: 30
  loop : -1.38 (0.42), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 353 
 HIS   0.006   0.002   HIS B  85 
 PHE   0.009   0.001   PHE A 490 
 TYR   0.011   0.001   TYR A 495 
 ARG   0.003   0.001   ARG A 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03022 (   72)
  hydrogen bonds       : angle       5.47454 (  207)
  SS BOND              : bond        0.00266 (    4)
  SS BOND              : angle       1.44452 (    8)
  covalent geometry    : bond        0.00262 ( 2734)
  covalent geometry    : angle       0.57339 ( 3715)

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

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

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: A  409 GLN cc_start: 0.7827 (mt0) cc_final: 0.7258 (mt0)
REVERT: A  418 ILE cc_start: 0.8076 (mp) cc_final: 0.7534 (mp)
REVERT: A  429 PHE cc_start: 0.7569 (t80) cc_final: 0.7208 (t80)
REVERT: A  498 GLN cc_start: 0.8552 (mp10) cc_final: 0.8235 (mp10)
REVERT: B   76 MET cc_start: 0.8354 (pmm) cc_final: 0.7965 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1159
  time to fit residues: 11.9930
Evaluate side-chains
  72 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 32 optimal weight:   20.0000
   chunk 14 optimal weight:    0.0010
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 24 optimal weight:   30.0000
   chunk 23 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    3.9994

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.186657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.157805 restraints weight = 6832.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.161899 restraints weight = 4918.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.165015 restraints weight = 3741.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.4187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6459
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   2738  Z= 0.129
  Angle     :  0.618   8.163   3723  Z= 0.308
  Chirality :  0.044   0.135    408
  Planarity :  0.005   0.050    489
  Dihedral  :  4.901  20.312    376
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.42), residues: 343
  helix: -0.48 (0.45), residues: 115
  sheet: -1.58 (0.86), residues: 30
  loop : -1.52 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 353 
 HIS   0.003   0.001   HIS B  52 
 PHE   0.012   0.002   PHE B 150 
 TYR   0.012   0.001   TYR A 380 
 ARG   0.004   0.001   ARG A 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02910 (   72)
  hydrogen bonds       : angle       5.21170 (  207)
  SS BOND              : bond        0.00515 (    4)
  SS BOND              : angle       1.87117 (    8)
  covalent geometry    : bond        0.00292 ( 2734)
  covalent geometry    : angle       0.61240 ( 3715)

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

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

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A  374 PHE cc_start: 0.7493 (m-10) cc_final: 0.7224 (m-10)
REVERT: A  418 ILE cc_start: 0.8174 (mp) cc_final: 0.7560 (mp)
REVERT: A  429 PHE cc_start: 0.7621 (t80) cc_final: 0.7237 (t80)
REVERT: A  498 GLN cc_start: 0.8439 (mp10) cc_final: 0.8056 (mp10)
REVERT: B   76 MET cc_start: 0.8381 (pmm) cc_final: 0.7992 (pmm)
REVERT: B  112 ASN cc_start: 0.7478 (t0) cc_final: 0.7153 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1194
  time to fit residues: 12.0344
Evaluate side-chains
  69 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0980
   chunk 20 optimal weight:    5.9990
   chunk 27 optimal weight:   20.0000
   chunk 10 optimal weight:    5.9990
   chunk 13 optimal weight:   20.0000
   chunk 23 optimal weight:    0.5980
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    0.0980
   chunk 9 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B 135 ASN
B 142 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.192323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.163430 restraints weight = 6808.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.167672 restraints weight = 4874.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.170924 restraints weight = 3684.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.4242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6352
moved from start:          0.2484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   2738  Z= 0.091
  Angle     :  0.575   8.214   3723  Z= 0.282
  Chirality :  0.042   0.136    408
  Planarity :  0.005   0.052    489
  Dihedral  :  4.435  19.197    376
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  3.17 %
    Favored  : 96.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.43), residues: 343
  helix:  0.02 (0.49), residues: 114
  sheet: -1.49 (0.82), residues: 31
  loop : -1.31 (0.41), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  79 
 HIS   0.003   0.001   HIS B  52 
 PHE   0.007   0.001   PHE A 464 
 TYR   0.012   0.001   TYR A 380 
 ARG   0.002   0.000   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02373 (   72)
  hydrogen bonds       : angle       4.99009 (  207)
  SS BOND              : bond        0.00261 (    4)
  SS BOND              : angle       1.51169 (    8)
  covalent geometry    : bond        0.00200 ( 2734)
  covalent geometry    : angle       0.57135 ( 3715)

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

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

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  409 GLN cc_start: 0.7909 (mt0) cc_final: 0.7345 (mt0)
REVERT: A  418 ILE cc_start: 0.8205 (mp) cc_final: 0.7630 (mp)
REVERT: A  429 PHE cc_start: 0.7648 (t80) cc_final: 0.7248 (t80)
REVERT: A  498 GLN cc_start: 0.8484 (mp10) cc_final: 0.8113 (mp10)
REVERT: B   76 MET cc_start: 0.8413 (pmm) cc_final: 0.8026 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1524
  time to fit residues: 14.4869
Evaluate side-chains
  67 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 6 optimal weight:    6.9990
   chunk 24 optimal weight:   40.0000
   chunk 14 optimal weight:   20.0000
   chunk 21 optimal weight:    0.6980
   chunk 23 optimal weight:    7.9990
   chunk 11 optimal weight:    0.5980
   chunk 32 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 12 optimal weight:    8.9990
   overall best weight:    4.4586

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
B  36 ASN
B 135 ASN
B 142 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.189519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.161808 restraints weight = 7150.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.166053 restraints weight = 5088.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.169182 restraints weight = 3837.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.4199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6460
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   2738  Z= 0.138
  Angle     :  0.629   8.757   3723  Z= 0.313
  Chirality :  0.043   0.134    408
  Planarity :  0.005   0.049    489
  Dihedral  :  4.894  20.327    376
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  3.17 %
    Favored  : 96.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.43), residues: 343
  helix: -0.06 (0.47), residues: 115
  sheet: -1.54 (0.83), residues: 31
  loop : -1.53 (0.42), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 353 
 HIS   0.005   0.001   HIS B  85 
 PHE   0.014   0.002   PHE A 490 
 TYR   0.012   0.001   TYR A 380 
 ARG   0.005   0.001   ARG A 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02825 (   72)
  hydrogen bonds       : angle       5.01076 (  207)
  SS BOND              : bond        0.00331 (    4)
  SS BOND              : angle       2.28442 (    8)
  covalent geometry    : bond        0.00317 ( 2734)
  covalent geometry    : angle       0.62019 ( 3715)

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

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

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A  374 PHE cc_start: 0.7660 (m-10) cc_final: 0.7308 (m-10)
REVERT: A  418 ILE cc_start: 0.8253 (mp) cc_final: 0.7559 (mp)
REVERT: A  429 PHE cc_start: 0.7623 (t80) cc_final: 0.7239 (t80)
REVERT: A  498 GLN cc_start: 0.8430 (mp10) cc_final: 0.8029 (mp10)
REVERT: B   76 MET cc_start: 0.8343 (pmm) cc_final: 0.7867 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1277
  time to fit residues: 12.0941
Evaluate side-chains
  69 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 12 optimal weight:    0.0020
   chunk 20 optimal weight:    6.9990
   chunk 19 optimal weight:    8.9990
   chunk 17 optimal weight:   20.0000
   chunk 21 optimal weight:    0.5980
   chunk 3 optimal weight:   20.0000
   chunk 28 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 16 optimal weight:    4.9990
   chunk 14 optimal weight:   10.0000
   chunk 6 optimal weight:    6.9990
   overall best weight:    3.9194

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

Flipped N/Q/H residues before XYZ refinement:
** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.188380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.160966 restraints weight = 7072.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.165451 restraints weight = 4895.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.168718 restraints weight = 3596.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.4196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6453
moved from start:          0.3246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   2738  Z= 0.124
  Angle     :  0.631   9.948   3723  Z= 0.309
  Chirality :  0.043   0.137    408
  Planarity :  0.005   0.048    489
  Dihedral  :  4.877  19.176    376
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.43), residues: 343
  helix: -0.08 (0.46), residues: 115
  sheet: -1.86 (0.82), residues: 30
  loop : -1.56 (0.42), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 353 
 HIS   0.004   0.001   HIS B  85 
 PHE   0.012   0.002   PHE B 150 
 TYR   0.009   0.001   TYR A 380 
 ARG   0.004   0.001   ARG A 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02624 (   72)
  hydrogen bonds       : angle       5.01133 (  207)
  SS BOND              : bond        0.00268 (    4)
  SS BOND              : angle       1.85240 (    8)
  covalent geometry    : bond        0.00286 ( 2734)
  covalent geometry    : angle       0.62559 ( 3715)

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

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

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
REVERT: A  418 ILE cc_start: 0.8272 (mp) cc_final: 0.7542 (mp)
REVERT: A  429 PHE cc_start: 0.7703 (t80) cc_final: 0.7320 (t80)
REVERT: A  498 GLN cc_start: 0.8260 (mp10) cc_final: 0.7854 (mp10)
REVERT: B   76 MET cc_start: 0.8386 (pmm) cc_final: 0.7939 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.1276
  time to fit residues: 12.4997
Evaluate side-chains
  68 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 2 optimal weight:   20.0000
   chunk 18 optimal weight:    0.7980
   chunk 27 optimal weight:    6.9990
   chunk 7 optimal weight:    8.9990
   chunk 20 optimal weight:    8.9990
   chunk 3 optimal weight:   10.0000
   chunk 14 optimal weight:    0.4980
   chunk 11 optimal weight:    5.9990
   chunk 22 optimal weight:   20.0000
   chunk 33 optimal weight:   20.0000
   chunk 23 optimal weight:    9.9990
   overall best weight:    4.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 422 ASN
B 112 ASN
** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.187193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.160084 restraints weight = 7274.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.164549 restraints weight = 4918.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.167872 restraints weight = 3582.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.4183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6490
moved from start:          0.3767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   2738  Z= 0.141
  Angle     :  0.672  12.146   3723  Z= 0.329
  Chirality :  0.044   0.138    408
  Planarity :  0.005   0.048    489
  Dihedral  :  5.162  19.610    376
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 14.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.04 %
    Favored  : 90.96 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  1.06 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.43), residues: 343
  helix: -0.12 (0.47), residues: 113
  sheet: -2.18 (0.76), residues: 33
  loop : -1.63 (0.43), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 353 
 HIS   0.004   0.001   HIS B  85 
 PHE   0.015   0.002   PHE A 490 
 TYR   0.012   0.002   TYR A 396 
 ARG   0.005   0.001   ARG A 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02725 (   72)
  hydrogen bonds       : angle       5.08269 (  207)
  SS BOND              : bond        0.00431 (    4)
  SS BOND              : angle       2.21399 (    8)
  covalent geometry    : bond        0.00325 ( 2734)
  covalent geometry    : angle       0.66452 ( 3715)

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

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

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A  418 ILE cc_start: 0.8313 (mp) cc_final: 0.7610 (mp)
REVERT: A  429 PHE cc_start: 0.7720 (t80) cc_final: 0.7310 (t80)
REVERT: A  498 GLN cc_start: 0.8116 (mp10) cc_final: 0.7721 (mp10)
REVERT: B   76 MET cc_start: 0.8326 (pmm) cc_final: 0.7881 (pmm)
  outliers start: 2
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1229
  time to fit residues: 12.2476
Evaluate side-chains
  67 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 14 optimal weight:    8.9990
   chunk 8 optimal weight:   10.0000
   chunk 1 optimal weight:    0.7980
   chunk 23 optimal weight:    7.9990
   chunk 33 optimal weight:   20.0000
   chunk 26 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 29 optimal weight:   30.0000
   chunk 17 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    5.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
** B  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 112 ASN
** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.184453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.157572 restraints weight = 6865.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.161946 restraints weight = 4618.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.165009 restraints weight = 3345.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.4153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6532
moved from start:          0.4316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   2738  Z= 0.168
  Angle     :  0.726  14.196   3723  Z= 0.358
  Chirality :  0.045   0.141    408
  Planarity :  0.005   0.047    489
  Dihedral  :  5.615  19.419    376
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 16.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.20 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  1.76 %
    Favored  : 97.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.06 (0.43), residues: 343
  helix: -0.40 (0.46), residues: 113
  sheet: -2.35 (0.75), residues: 33
  loop : -1.81 (0.43), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 353 
 HIS   0.004   0.001   HIS B  52 
 PHE   0.018   0.002   PHE A 490 
 TYR   0.015   0.002   TYR A 495 
 ARG   0.006   0.001   ARG A 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03103 (   72)
  hydrogen bonds       : angle       5.33650 (  207)
  SS BOND              : bond        0.00397 (    4)
  SS BOND              : angle       1.95107 (    8)
  covalent geometry    : bond        0.00382 ( 2734)
  covalent geometry    : angle       0.72122 ( 3715)

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

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

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 78
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A  392 PHE cc_start: 0.8065 (m-80) cc_final: 0.7853 (m-80)
REVERT: A  418 ILE cc_start: 0.8335 (mp) cc_final: 0.7636 (mp)
REVERT: A  429 PHE cc_start: 0.7674 (t80) cc_final: 0.7295 (t80)
REVERT: A  498 GLN cc_start: 0.7957 (mp10) cc_final: 0.7614 (mp10)
REVERT: B   76 MET cc_start: 0.8175 (pmm) cc_final: 0.7766 (pmm)
  outliers start: 2
  outliers final: 1
  residues processed: 78
  average time/residue: 0.1179
  time to fit residues: 11.2292
Evaluate side-chains
  69 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 17 optimal weight:   20.0000
   chunk 23 optimal weight:   20.0000
   chunk 30 optimal weight:   30.0000
   chunk 28 optimal weight:    3.9990
   chunk 11 optimal weight:    6.9990
   chunk 29 optimal weight:    7.9990
   chunk 3 optimal weight:    0.0470
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 21 optimal weight:    0.0980
   chunk 25 optimal weight:    2.9990
   overall best weight:    2.8284

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

Flipped N/Q/H residues before XYZ refinement:
** B 135 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 = 0.4394 r_free = 0.4394 target = 0.188757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.161504 restraints weight = 6658.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.165931 restraints weight = 4513.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.169249 restraints weight = 3268.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6453
moved from start:          0.4424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2738  Z= 0.113
  Angle     :  0.648  11.484   3723  Z= 0.319
  Chirality :  0.043   0.135    408
  Planarity :  0.005   0.047    489
  Dihedral  :  5.037  19.507    376
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.16 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.43), residues: 343
  helix: -0.09 (0.47), residues: 111
  sheet: -2.87 (0.79), residues: 27
  loop : -1.59 (0.43), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 353 
 HIS   0.004   0.001   HIS B  85 
 PHE   0.009   0.001   PHE B 150 
 TYR   0.017   0.001   TYR A 396 
 ARG   0.003   0.000   ARG A 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02529 (   72)
  hydrogen bonds       : angle       5.02287 (  207)
  SS BOND              : bond        0.00301 (    4)
  SS BOND              : angle       1.87450 (    8)
  covalent geometry    : bond        0.00260 ( 2734)
  covalent geometry    : angle       0.64256 ( 3715)

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

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

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A  418 ILE cc_start: 0.8334 (mp) cc_final: 0.7594 (mp)
REVERT: A  429 PHE cc_start: 0.7623 (t80) cc_final: 0.7240 (t80)
REVERT: A  498 GLN cc_start: 0.8133 (mp10) cc_final: 0.7844 (mp10)
REVERT: B   76 MET cc_start: 0.8202 (pmm) cc_final: 0.7804 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1194
  time to fit residues: 10.9657
Evaluate side-chains
  67 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 3 optimal weight:    0.3980
   chunk 7 optimal weight:   10.0000
   chunk 10 optimal weight:    5.9990
   chunk 30 optimal weight:   30.0000
   chunk 20 optimal weight:    8.9990
   chunk 11 optimal weight:   20.0000
   chunk 29 optimal weight:    4.9990
   chunk 23 optimal weight:   20.0000
   chunk 28 optimal weight:    7.9990
   chunk 22 optimal weight:    9.9990
   chunk 13 optimal weight:    8.9990
   overall best weight:    5.6788

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

Flipped N/Q/H residues before XYZ refinement:
** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.185067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.157712 restraints weight = 6802.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.161960 restraints weight = 4571.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.165268 restraints weight = 3322.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.4152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6533
moved from start:          0.4810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   2738  Z= 0.165
  Angle     :  0.715  13.523   3723  Z= 0.357
  Chirality :  0.044   0.168    408
  Planarity :  0.005   0.047    489
  Dihedral  :  5.451  19.796    376
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 17.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.79 %
    Favored  : 89.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.43), residues: 343
  helix: -0.41 (0.45), residues: 112
  sheet: -2.36 (0.74), residues: 32
  loop : -1.89 (0.43), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP A 353 
 HIS   0.004   0.001   HIS B  85 
 PHE   0.015   0.002   PHE A 490 
 TYR   0.013   0.002   TYR A 495 
 ARG   0.006   0.001   ARG A 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03028 (   72)
  hydrogen bonds       : angle       5.32852 (  207)
  SS BOND              : bond        0.00267 (    4)
  SS BOND              : angle       2.26430 (    8)
  covalent geometry    : bond        0.00377 ( 2734)
  covalent geometry    : angle       0.70852 ( 3715)

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

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

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  686 Ramachandran restraints generated.
    343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A  418 ILE cc_start: 0.8368 (mp) cc_final: 0.7692 (mp)
REVERT: A  429 PHE cc_start: 0.7743 (t80) cc_final: 0.7394 (t80)
REVERT: A  498 GLN cc_start: 0.8015 (mp10) cc_final: 0.7686 (mp10)
REVERT: B   76 MET cc_start: 0.8151 (pmm) cc_final: 0.7739 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.1315
  time to fit residues: 11.8228
Evaluate side-chains
  67 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 19 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0370
   chunk 13 optimal weight:    0.9980
   chunk 11 optimal weight:    5.9990
   chunk 7 optimal weight:   20.0000
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 29 optimal weight:   20.0000
   chunk 4 optimal weight:    6.9990
   chunk 32 optimal weight:   10.0000
   overall best weight:    1.8062

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

Flipped N/Q/H residues before XYZ refinement:
B 112 ASN
** B 135 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 = 0.4400 r_free = 0.4400 target = 0.189458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.163998 restraints weight = 6934.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.168175 restraints weight = 4761.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.171411 restraints weight = 3496.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.4220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6407
moved from start:          0.4812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   2738  Z= 0.103
  Angle     :  0.644  10.407   3723  Z= 0.316
  Chirality :  0.043   0.131    408
  Planarity :  0.005   0.048    489
  Dihedral  :  4.754  18.916    376
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  0.35 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.44), residues: 343
  helix: -0.22 (0.46), residues: 118
  sheet: -2.90 (0.79), residues: 27
  loop : -1.57 (0.44), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B  79 
 HIS   0.003   0.001   HIS B  85 
 PHE   0.008   0.001   PHE B 150 
 TYR   0.014   0.001   TYR A 495 
 ARG   0.004   0.000   ARG A 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02497 (   72)
  hydrogen bonds       : angle       4.88316 (  207)
  SS BOND              : bond        0.00140 (    4)
  SS BOND              : angle       1.62338 (    8)
  covalent geometry    : bond        0.00238 ( 2734)
  covalent geometry    : angle       0.64011 ( 3715)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1289.72 seconds
wall clock time: 23 minutes 16.85 seconds (1396.85 seconds total)