Starting phenix.real_space_refine on Mon Aug 25 04:44:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v3d_42946/08_2025/8v3d_42946_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v3d_42946/08_2025/8v3d_42946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v3d_42946/08_2025/8v3d_42946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v3d_42946/08_2025/8v3d_42946.map" model { file = "/net/cci-nas-00/data/ceres_data/8v3d_42946/08_2025/8v3d_42946_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v3d_42946/08_2025/8v3d_42946_trim.cif" } resolution = 2.95 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= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 100 5.16 5 C 8344 2.51 5 N 2018 2.21 5 O 2174 1.98 5 H 13001 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25637 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 6366 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 383} Chain breaks: 2 Chain: "B" Number of atoms: 6366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 6366 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 383} Chain breaks: 2 Chain: "C" Number of atoms: 6366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 6366 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 383} Chain breaks: 2 Chain: "D" Number of atoms: 6531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 6531 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 9, 'TRANS': 386} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'A1AFC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.00, per 1000 atoms: 0.16 Number of scatterers: 25637 At special positions: 0 Unit cell: (115.649, 122.015, 128.381, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 O 2174 8.00 N 2018 7.00 C 8344 6.00 H 13001 1.00 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: 4.06 Conformation dependent library (CDL) restraints added in 670.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3018 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 63 removed outlier: 3.606A pdb=" N MET A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 93 removed outlier: 3.563A pdb=" N LEU A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Proline residue: A 83 - end of helix Proline residue: A 91 - end of helix Processing helix chain 'A' and resid 93 through 102 Processing helix chain 'A' and resid 103 through 106 removed outlier: 4.538A pdb=" N ASN A 106 " --> pdb=" O ILE A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 113 through 153 removed outlier: 4.165A pdb=" N PHE A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 242 removed outlier: 3.720A pdb=" N VAL A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 4.278A pdb=" N GLU A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 370 removed outlier: 5.312A pdb=" N VAL A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 416 removed outlier: 4.541A pdb=" N MET A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 452 through 474 Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 34 through 63 Processing helix chain 'B' and resid 67 through 93 Proline residue: B 83 - end of helix Proline residue: B 91 - end of helix Processing helix chain 'B' and resid 93 through 102 Processing helix chain 'B' and resid 103 through 106 removed outlier: 4.557A pdb=" N ASN B 106 " --> pdb=" O ILE B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 113 through 153 removed outlier: 3.704A pdb=" N PHE B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 242 removed outlier: 3.749A pdb=" N VAL B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Proline residue: B 236 - end of helix removed outlier: 4.289A pdb=" N GLU B 239 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 370 removed outlier: 5.301A pdb=" N VAL B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ALA B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 416 removed outlier: 4.387A pdb=" N MET B 411 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 422 Processing helix chain 'B' and resid 423 through 438 Processing helix chain 'B' and resid 452 through 474 Processing helix chain 'C' and resid 12 through 22 Processing helix chain 'C' and resid 31 through 63 removed outlier: 3.530A pdb=" N LYS C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) Proline residue: C 37 - end of helix removed outlier: 3.704A pdb=" N ILE C 40 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN C 59 " --> pdb=" O MET C 55 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 93 Proline residue: C 83 - end of helix Proline residue: C 91 - end of helix Processing helix chain 'C' and resid 93 through 102 Processing helix chain 'C' and resid 103 through 106 removed outlier: 4.559A pdb=" N ASN C 106 " --> pdb=" O ILE C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 113 through 153 Processing helix chain 'C' and resid 187 through 242 Proline residue: C 236 - end of helix removed outlier: 4.156A pdb=" N GLU C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 370 removed outlier: 4.004A pdb=" N ILE C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 416 Processing helix chain 'C' and resid 418 through 422 Processing helix chain 'C' and resid 423 through 438 Processing helix chain 'C' and resid 452 through 474 Processing helix chain 'D' and resid 6 through 16 Processing helix chain 'D' and resid 30 through 48 Proline residue: D 44 - end of helix Processing helix chain 'D' and resid 48 through 59 Processing helix chain 'D' and resid 62 through 89 Proline residue: D 72 - end of helix removed outlier: 4.336A pdb=" N GLU D 75 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 109 removed outlier: 3.564A pdb=" N LYS D 109 " --> pdb=" O ASP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 146 Processing helix chain 'D' and resid 146 through 160 Processing helix chain 'D' and resid 181 through 238 Processing helix chain 'D' and resid 240 through 294 removed outlier: 5.580A pdb=" N PHE D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N PHE D 272 " --> pdb=" O GLY D 268 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 338 Proline residue: D 309 - end of helix removed outlier: 3.728A pdb=" N PHE D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL D 332 " --> pdb=" O GLU D 328 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N SER D 333 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP D 334 " --> pdb=" O ARG D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 344 Processing helix chain 'D' and resid 345 through 360 Processing helix chain 'D' and resid 374 through 397 removed outlier: 4.161A pdb=" N PHE D 378 " --> pdb=" O THR D 374 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN D 379 " --> pdb=" O LEU D 375 " (cutoff:3.500A) 1033 hydrogen bonds defined for protein. 3081 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: 4.58 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12971 1.03 - 1.23: 32 1.23 - 1.42: 5391 1.42 - 1.62: 7372 1.62 - 1.81: 169 Bond restraints: 25935 Sorted by residual: bond pdb=" C03 A1AFC D 501 " pdb=" S04 A1AFC D 501 " ideal model delta sigma weight residual 1.730 1.597 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" C05 A1AFC D 501 " pdb=" S04 A1AFC D 501 " ideal model delta sigma weight residual 1.730 1.620 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C05 A1AFC D 501 " pdb=" N06 A1AFC D 501 " ideal model delta sigma weight residual 1.290 1.391 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C02 A1AFC D 501 " pdb=" N06 A1AFC D 501 " ideal model delta sigma weight residual 1.375 1.472 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C02 A1AFC D 501 " pdb=" C03 A1AFC D 501 " ideal model delta sigma weight residual 1.362 1.420 -0.058 2.00e-02 2.50e+03 8.30e+00 ... (remaining 25930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 46591 1.85 - 3.70: 268 3.70 - 5.55: 40 5.55 - 7.41: 5 7.41 - 9.26: 1 Bond angle restraints: 46905 Sorted by residual: angle pdb=" C ALA C 346 " pdb=" N TYR C 347 " pdb=" CA TYR C 347 " ideal model delta sigma weight residual 122.31 115.72 6.59 2.00e+00 2.50e-01 1.09e+01 angle pdb=" C03 A1AFC D 501 " pdb=" S04 A1AFC D 501 " pdb=" C05 A1AFC D 501 " ideal model delta sigma weight residual 90.02 99.28 -9.26 3.00e+00 1.11e-01 9.52e+00 angle pdb=" C GLY B 7 " pdb=" N LEU B 8 " pdb=" CA LEU B 8 " ideal model delta sigma weight residual 121.54 127.43 -5.89 1.91e+00 2.74e-01 9.51e+00 angle pdb=" CA ILE C 40 " pdb=" CB ILE C 40 " pdb=" CG1 ILE C 40 " ideal model delta sigma weight residual 110.40 115.37 -4.97 1.70e+00 3.46e-01 8.56e+00 angle pdb=" C GLY C 348 " pdb=" N VAL C 349 " pdb=" CA VAL C 349 " ideal model delta sigma weight residual 120.46 117.30 3.16 1.37e+00 5.33e-01 5.32e+00 ... (remaining 46900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 10729 17.70 - 35.41: 996 35.41 - 53.11: 352 53.11 - 70.82: 104 70.82 - 88.52: 11 Dihedral angle restraints: 12192 sinusoidal: 6431 harmonic: 5761 Sorted by residual: dihedral pdb=" CA ASP A 421 " pdb=" CB ASP A 421 " pdb=" CG ASP A 421 " pdb=" OD1 ASP A 421 " ideal model delta sinusoidal sigma weight residual -30.00 -88.27 58.27 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CB GLU B 115 " pdb=" CG GLU B 115 " pdb=" CD GLU B 115 " pdb=" OE1 GLU B 115 " ideal model delta sinusoidal sigma weight residual 0.00 -88.52 88.52 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU B 63 " pdb=" CG GLU B 63 " pdb=" CD GLU B 63 " pdb=" OE1 GLU B 63 " ideal model delta sinusoidal sigma weight residual 0.00 88.37 -88.37 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 12189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1524 0.032 - 0.063: 341 0.063 - 0.095: 167 0.095 - 0.127: 38 0.127 - 0.159: 6 Chirality restraints: 2076 Sorted by residual: chirality pdb=" CA TYR C 347 " pdb=" N TYR C 347 " pdb=" C TYR C 347 " pdb=" CB TYR C 347 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ILE A 170 " pdb=" N ILE A 170 " pdb=" C ILE A 170 " pdb=" CB ILE A 170 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CB ILE B 398 " pdb=" CA ILE B 398 " pdb=" CG1 ILE B 398 " pdb=" CG2 ILE B 398 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 2073 not shown) Planarity restraints: 3642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 347 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.94e+00 pdb=" C TYR C 347 " 0.034 2.00e-02 2.50e+03 pdb=" O TYR C 347 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY C 348 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 235 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO A 236 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 170 " 0.031 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO B 171 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 171 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 171 " 0.026 5.00e-02 4.00e+02 ... (remaining 3639 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 230 2.06 - 2.69: 40428 2.69 - 3.33: 77941 3.33 - 3.96: 96598 3.96 - 4.60: 153655 Nonbonded interactions: 368852 Sorted by model distance: nonbonded pdb=" OE1 GLU C 424 " pdb=" H GLU C 424 " model vdw 1.424 2.450 nonbonded pdb=" O ASN B 28 " pdb="HD21 ASN B 28 " model vdw 1.528 2.450 nonbonded pdb="HE21 GLN C 435 " pdb=" OE1 GLN D 360 " model vdw 1.579 2.450 nonbonded pdb=" HZ2 LYS C 86 " pdb=" OD1 ASP C 213 " model vdw 1.599 2.450 nonbonded pdb=" O TYR D 18 " pdb="HH22 ARG D 90 " model vdw 1.606 2.450 ... (remaining 368847 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.850 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: 0.100 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.050 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 0.133 12934 Z= 0.170 Angle : 0.506 9.257 17544 Z= 0.272 Chirality : 0.035 0.159 2076 Planarity : 0.004 0.048 2113 Dihedral : 17.455 88.525 4581 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.59 % Allowed : 26.91 % Favored : 70.50 % 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 aren not related in a simple way. whole: 2.24 (0.21), residues: 1558 helix: 2.19 (0.14), residues: 1259 sheet: -0.27 (1.06), residues: 24 loop : -1.81 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 178 TYR 0.017 0.001 TYR C 347 PHE 0.013 0.001 PHE A 399 TRP 0.007 0.001 TRP B 419 HIS 0.003 0.001 HIS B 24 Details of bonding type rmsd covalent geometry : bond 0.00329 (12934) covalent geometry : angle 0.50599 (17544) hydrogen bonds : bond 0.11703 ( 1033) hydrogen bonds : angle 5.17006 ( 3081) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6974 (m-30) REVERT: A 79 PHE cc_start: 0.7705 (t80) cc_final: 0.7498 (t80) REVERT: B 51 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7904 (tt) REVERT: D 171 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.5622 (p90) outliers start: 36 outliers final: 29 residues processed: 229 average time/residue: 0.9018 time to fit residues: 230.6781 Evaluate side-chains 226 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.151666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.129305 restraints weight = 40225.278| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.29 r_work: 0.3436 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.0489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12934 Z= 0.168 Angle : 0.514 7.196 17544 Z= 0.282 Chirality : 0.036 0.178 2076 Planarity : 0.004 0.049 2113 Dihedral : 6.596 58.926 1750 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.31 % Allowed : 25.18 % Favored : 71.51 % 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 aren not related in a simple way. whole: 2.80 (0.21), residues: 1558 helix: 2.59 (0.14), residues: 1264 sheet: -0.13 (1.10), residues: 24 loop : -1.79 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 129 TYR 0.019 0.001 TYR C 347 PHE 0.016 0.001 PHE A 399 TRP 0.009 0.002 TRP D 104 HIS 0.002 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00356 (12934) covalent geometry : angle 0.51423 (17544) hydrogen bonds : bond 0.06747 ( 1033) hydrogen bonds : angle 3.98482 ( 3081) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: B 36 PHE cc_start: 0.8055 (t80) cc_final: 0.7812 (t80) REVERT: B 51 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7844 (tt) REVERT: B 86 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7811 (mttm) REVERT: D 171 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.5591 (p90) outliers start: 46 outliers final: 20 residues processed: 243 average time/residue: 0.9574 time to fit residues: 259.8448 Evaluate side-chains 216 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 91 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 60 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.150892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.128726 restraints weight = 41228.647| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.22 r_work: 0.3427 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12934 Z= 0.167 Angle : 0.507 7.260 17544 Z= 0.278 Chirality : 0.036 0.181 2076 Planarity : 0.004 0.049 2113 Dihedral : 5.623 59.258 1726 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.60 % Allowed : 24.75 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.85 (0.21), residues: 1558 helix: 2.64 (0.14), residues: 1264 sheet: -0.08 (1.12), residues: 24 loop : -1.83 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 402 TYR 0.021 0.001 TYR C 347 PHE 0.017 0.002 PHE D 185 TRP 0.008 0.002 TRP D 104 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00360 (12934) covalent geometry : angle 0.50747 (17544) hydrogen bonds : bond 0.06702 ( 1033) hydrogen bonds : angle 3.88861 ( 3081) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.6936 (m-30) REVERT: A 438 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.7088 (mp10) REVERT: B 36 PHE cc_start: 0.8059 (t80) cc_final: 0.7772 (t80) REVERT: B 51 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7845 (tt) REVERT: B 86 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7822 (mttm) REVERT: B 178 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7577 (mmt90) REVERT: D 80 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.7998 (m-40) REVERT: D 171 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.5378 (p90) outliers start: 50 outliers final: 30 residues processed: 245 average time/residue: 0.9188 time to fit residues: 251.2416 Evaluate side-chains 232 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 69 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.148797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126420 restraints weight = 41343.907| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.22 r_work: 0.3432 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12934 Z= 0.149 Angle : 0.491 7.016 17544 Z= 0.269 Chirality : 0.035 0.175 2076 Planarity : 0.004 0.049 2113 Dihedral : 5.611 58.739 1726 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.96 % Allowed : 24.68 % Favored : 71.37 % 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 aren not related in a simple way. whole: 2.93 (0.21), residues: 1558 helix: 2.73 (0.14), residues: 1257 sheet: -0.02 (1.12), residues: 24 loop : -1.86 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 178 TYR 0.019 0.001 TYR C 347 PHE 0.015 0.001 PHE A 399 TRP 0.008 0.001 TRP D 104 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00309 (12934) covalent geometry : angle 0.49085 (17544) hydrogen bonds : bond 0.06429 ( 1033) hydrogen bonds : angle 3.82178 ( 3081) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 208 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7333 (m-30) cc_final: 0.6918 (m-30) REVERT: A 438 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.7064 (mp10) REVERT: B 51 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7852 (tt) REVERT: B 178 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7581 (mmt90) REVERT: C 347 TYR cc_start: 0.6637 (OUTLIER) cc_final: 0.6105 (m-80) REVERT: D 80 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.7989 (m-40) REVERT: D 171 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.5214 (p90) outliers start: 55 outliers final: 32 residues processed: 249 average time/residue: 0.9038 time to fit residues: 251.4668 Evaluate side-chains 239 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 55 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 124 optimal weight: 0.2980 chunk 79 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.149191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.126864 restraints weight = 41335.706| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.23 r_work: 0.3445 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12934 Z= 0.140 Angle : 0.484 6.726 17544 Z= 0.264 Chirality : 0.035 0.170 2076 Planarity : 0.004 0.047 2113 Dihedral : 5.550 58.461 1726 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.17 % Allowed : 25.04 % Favored : 71.80 % 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 aren not related in a simple way. whole: 3.02 (0.21), residues: 1558 helix: 2.79 (0.14), residues: 1257 sheet: 0.00 (1.13), residues: 24 loop : -1.85 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 129 TYR 0.018 0.001 TYR C 347 PHE 0.014 0.001 PHE A 36 TRP 0.008 0.001 TRP D 104 HIS 0.004 0.001 HIS C 24 Details of bonding type rmsd covalent geometry : bond 0.00283 (12934) covalent geometry : angle 0.48413 (17544) hydrogen bonds : bond 0.06213 ( 1033) hydrogen bonds : angle 3.76249 ( 3081) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6896 (m-30) REVERT: B 51 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7789 (tt) REVERT: B 178 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7558 (mmt90) REVERT: D 80 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8028 (m-40) REVERT: D 171 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.5227 (p90) outliers start: 44 outliers final: 30 residues processed: 237 average time/residue: 0.9304 time to fit residues: 247.3214 Evaluate side-chains 229 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 136 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.148498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126185 restraints weight = 41619.057| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.22 r_work: 0.3374 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12934 Z= 0.226 Angle : 0.560 7.776 17544 Z= 0.306 Chirality : 0.038 0.198 2076 Planarity : 0.004 0.053 2113 Dihedral : 5.645 59.729 1723 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.24 % Allowed : 24.03 % Favored : 71.73 % 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 aren not related in a simple way. whole: 2.63 (0.21), residues: 1558 helix: 2.46 (0.14), residues: 1269 sheet: 0.02 (1.15), residues: 24 loop : -1.84 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 90 TYR 0.025 0.002 TYR C 347 PHE 0.020 0.002 PHE C 399 TRP 0.012 0.002 TRP D 104 HIS 0.006 0.001 HIS C 229 Details of bonding type rmsd covalent geometry : bond 0.00523 (12934) covalent geometry : angle 0.55962 (17544) hydrogen bonds : bond 0.07267 ( 1033) hydrogen bonds : angle 3.93919 ( 3081) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 198 time to evaluate : 0.693 Fit side-chains REVERT: A 438 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.7018 (mp10) REVERT: A 439 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7827 (mttp) REVERT: B 51 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7894 (tt) REVERT: B 158 ARG cc_start: 0.7875 (mmt90) cc_final: 0.7573 (mmt90) REVERT: B 178 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7588 (mmt90) REVERT: D 80 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8056 (m-40) REVERT: D 171 TYR cc_start: 0.7529 (OUTLIER) cc_final: 0.5064 (p90) outliers start: 59 outliers final: 38 residues processed: 245 average time/residue: 0.9339 time to fit residues: 255.8735 Evaluate side-chains 238 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 52 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 154 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.150838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.128675 restraints weight = 41344.347| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.22 r_work: 0.3421 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12934 Z= 0.150 Angle : 0.498 7.239 17544 Z= 0.273 Chirality : 0.036 0.168 2076 Planarity : 0.004 0.050 2113 Dihedral : 5.581 59.575 1723 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.38 % Allowed : 24.53 % Favored : 72.09 % 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 aren not related in a simple way. whole: 2.84 (0.21), residues: 1558 helix: 2.63 (0.14), residues: 1263 sheet: -0.01 (1.14), residues: 24 loop : -1.82 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 338 TYR 0.019 0.001 TYR C 347 PHE 0.015 0.001 PHE A 399 TRP 0.008 0.001 TRP D 104 HIS 0.003 0.001 HIS B 24 Details of bonding type rmsd covalent geometry : bond 0.00310 (12934) covalent geometry : angle 0.49843 (17544) hydrogen bonds : bond 0.06520 ( 1033) hydrogen bonds : angle 3.82214 ( 3081) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.6971 (mp10) REVERT: A 439 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7825 (mttp) REVERT: B 51 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7860 (tt) REVERT: B 158 ARG cc_start: 0.7910 (mmt90) cc_final: 0.7665 (mmt90) REVERT: B 234 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.6916 (ttt) REVERT: D 80 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8016 (m-40) REVERT: D 171 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.4849 (p90) outliers start: 47 outliers final: 29 residues processed: 238 average time/residue: 0.9763 time to fit residues: 260.3718 Evaluate side-chains 230 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 85 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.148977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126701 restraints weight = 41384.427| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.22 r_work: 0.3398 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12934 Z= 0.204 Angle : 0.546 7.661 17544 Z= 0.297 Chirality : 0.038 0.191 2076 Planarity : 0.004 0.052 2113 Dihedral : 5.679 60.779 1723 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.60 % Allowed : 24.89 % Favored : 71.51 % 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 aren not related in a simple way. whole: 2.65 (0.21), residues: 1558 helix: 2.47 (0.14), residues: 1269 sheet: 0.01 (1.14), residues: 24 loop : -1.82 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 90 TYR 0.023 0.002 TYR C 347 PHE 0.018 0.002 PHE C 399 TRP 0.011 0.002 TRP D 104 HIS 0.005 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00469 (12934) covalent geometry : angle 0.54586 (17544) hydrogen bonds : bond 0.07054 ( 1033) hydrogen bonds : angle 3.90280 ( 3081) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 196 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.6917 (m-30) REVERT: A 438 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.6995 (mp10) REVERT: A 439 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7767 (mttp) REVERT: B 51 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7878 (tt) REVERT: B 158 ARG cc_start: 0.7879 (mmt90) cc_final: 0.7628 (mmt90) REVERT: B 178 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7725 (mmt90) REVERT: B 234 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7294 (ttt) REVERT: D 80 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8083 (m-40) REVERT: D 171 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.4775 (p90) outliers start: 50 outliers final: 34 residues processed: 237 average time/residue: 0.9391 time to fit residues: 249.3813 Evaluate side-chains 235 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 69 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 124 optimal weight: 0.2980 chunk 147 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.150180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.128124 restraints weight = 41320.015| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.21 r_work: 0.3420 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12934 Z= 0.157 Angle : 0.514 7.209 17544 Z= 0.280 Chirality : 0.036 0.175 2076 Planarity : 0.004 0.050 2113 Dihedral : 5.642 60.744 1723 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.45 % Allowed : 25.25 % Favored : 71.29 % 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 aren not related in a simple way. whole: 2.78 (0.21), residues: 1558 helix: 2.58 (0.14), residues: 1263 sheet: 0.06 (1.16), residues: 24 loop : -1.82 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 338 TYR 0.020 0.001 TYR C 347 PHE 0.016 0.001 PHE A 399 TRP 0.008 0.002 TRP D 104 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00332 (12934) covalent geometry : angle 0.51445 (17544) hydrogen bonds : bond 0.06590 ( 1033) hydrogen bonds : angle 3.83559 ( 3081) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6886 (m-30) REVERT: A 402 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7623 (ttp-170) REVERT: A 438 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.6952 (mp10) REVERT: A 439 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7751 (mttp) REVERT: B 51 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7864 (tt) REVERT: B 158 ARG cc_start: 0.7891 (mmt90) cc_final: 0.7639 (mmt90) REVERT: B 178 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7599 (mmt90) REVERT: B 234 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.6935 (ttt) REVERT: D 80 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8053 (m-40) REVERT: D 171 TYR cc_start: 0.7460 (OUTLIER) cc_final: 0.4842 (p90) outliers start: 48 outliers final: 34 residues processed: 234 average time/residue: 0.8988 time to fit residues: 235.0639 Evaluate side-chains 236 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 336 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 109 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 95 optimal weight: 0.0060 chunk 100 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.153009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130937 restraints weight = 41120.548| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.22 r_work: 0.3459 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12934 Z= 0.131 Angle : 0.491 7.238 17544 Z= 0.265 Chirality : 0.035 0.158 2076 Planarity : 0.004 0.049 2113 Dihedral : 5.497 58.890 1723 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.09 % Allowed : 25.47 % Favored : 71.44 % 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 aren not related in a simple way. whole: 3.02 (0.21), residues: 1558 helix: 2.79 (0.14), residues: 1257 sheet: 0.00 (1.15), residues: 24 loop : -1.83 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 174 TYR 0.016 0.001 TYR C 347 PHE 0.017 0.001 PHE B 36 TRP 0.008 0.001 TRP C 146 HIS 0.003 0.001 HIS B 24 Details of bonding type rmsd covalent geometry : bond 0.00256 (12934) covalent geometry : angle 0.49067 (17544) hydrogen bonds : bond 0.06046 ( 1033) hydrogen bonds : angle 3.75049 ( 3081) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 201 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7531 (ttp-170) REVERT: A 438 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.6894 (mp10) REVERT: A 439 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7758 (mttp) REVERT: B 51 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7791 (tt) REVERT: B 158 ARG cc_start: 0.7891 (mmt90) cc_final: 0.7652 (mmt90) REVERT: B 234 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.6789 (ttt) REVERT: C 193 PHE cc_start: 0.7641 (t80) cc_final: 0.7441 (t80) REVERT: D 80 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8041 (m-40) REVERT: D 171 TYR cc_start: 0.7387 (OUTLIER) cc_final: 0.5057 (p90) outliers start: 43 outliers final: 26 residues processed: 236 average time/residue: 0.9093 time to fit residues: 240.2168 Evaluate side-chains 228 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 270 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 288 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 137 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.151822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.129770 restraints weight = 41080.958| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.22 r_work: 0.3422 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12934 Z= 0.153 Angle : 0.510 6.986 17544 Z= 0.275 Chirality : 0.036 0.157 2076 Planarity : 0.004 0.049 2113 Dihedral : 5.430 58.464 1721 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.59 % Allowed : 26.26 % Favored : 71.15 % 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 aren not related in a simple way. whole: 2.97 (0.21), residues: 1558 helix: 2.75 (0.14), residues: 1260 sheet: 0.01 (1.16), residues: 24 loop : -1.87 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 323 TYR 0.021 0.001 TYR C 347 PHE 0.016 0.001 PHE A 399 TRP 0.009 0.002 TRP D 104 HIS 0.005 0.001 HIS C 24 Details of bonding type rmsd covalent geometry : bond 0.00325 (12934) covalent geometry : angle 0.50955 (17544) hydrogen bonds : bond 0.06306 ( 1033) hydrogen bonds : angle 3.77451 ( 3081) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 7084.37 seconds wall clock time: 120 minutes 9.95 seconds (7209.95 seconds total)