Starting phenix.real_space_refine on Sat Aug 23 07:49:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9la7_62921/08_2025/9la7_62921.cif Found real_map, /net/cci-nas-00/data/ceres_data/9la7_62921/08_2025/9la7_62921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9la7_62921/08_2025/9la7_62921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9la7_62921/08_2025/9la7_62921.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9la7_62921/08_2025/9la7_62921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9la7_62921/08_2025/9la7_62921.map" } resolution = 2.39 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= 0.029 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 48 5.16 5 C 6856 2.51 5 N 1716 2.21 5 O 1720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 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: 10340 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2585 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 7, 'TRANS': 297} Chain: "D" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2585 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 7, 'TRANS': 297} Chain: "B" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2585 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 7, 'TRANS': 297} Chain: "C" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2585 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 7, 'TRANS': 297} Time building chain proxies: 2.69, per 1000 atoms: 0.26 Number of scatterers: 10340 At special positions: 0 Unit cell: (124.504, 123.716, 88.256, 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 48 16.00 O 1720 8.00 N 1716 7.00 C 6856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 397.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2312 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 5 sheets defined 78.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 65 through 89 Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 97 through 115 Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.730A pdb=" N ARG A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 177 through 191 removed outlier: 4.135A pdb=" N VAL A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 225 removed outlier: 4.270A pdb=" N ILE A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 removed outlier: 4.578A pdb=" N GLY A 232 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 253 through 270 Processing helix chain 'A' and resid 281 through 313 removed outlier: 3.641A pdb=" N GLY A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 333 Processing helix chain 'A' and resid 336 through 349 Processing helix chain 'D' and resid 62 through 90 Proline residue: D 84 - end of helix removed outlier: 3.624A pdb=" N PHE D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 97 through 115 removed outlier: 3.522A pdb=" N GLY D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN D 105 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 131 through 143 Processing helix chain 'D' and resid 143 through 151 Processing helix chain 'D' and resid 153 through 161 Processing helix chain 'D' and resid 164 through 177 Processing helix chain 'D' and resid 178 through 191 Processing helix chain 'D' and resid 195 through 225 Processing helix chain 'D' and resid 227 through 234 removed outlier: 4.534A pdb=" N GLY D 232 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 270 Processing helix chain 'D' and resid 281 through 313 Processing helix chain 'D' and resid 314 through 334 Processing helix chain 'D' and resid 336 through 353 Processing helix chain 'B' and resid 62 through 89 Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 97 through 115 Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 143 through 151 Processing helix chain 'B' and resid 153 through 161 Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 170 through 176 Processing helix chain 'B' and resid 177 through 190 removed outlier: 4.117A pdb=" N VAL B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 226 removed outlier: 3.842A pdb=" N LEU B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 234 removed outlier: 4.747A pdb=" N GLY B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 270 Processing helix chain 'B' and resid 281 through 313 removed outlier: 3.744A pdb=" N GLY B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 334 Processing helix chain 'B' and resid 336 through 351 Processing helix chain 'C' and resid 62 through 90 Proline residue: C 84 - end of helix removed outlier: 3.646A pdb=" N PHE C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 97 through 117 removed outlier: 3.823A pdb=" N PHE C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP C 111 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE C 116 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE C 117 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 153 through 161 Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.541A pdb=" N ARG C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 178 through 191 Processing helix chain 'C' and resid 195 through 226 removed outlier: 3.812A pdb=" N LEU C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 234 removed outlier: 4.370A pdb=" N GLY C 232 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 252 Processing helix chain 'C' and resid 253 through 270 Processing helix chain 'C' and resid 281 through 313 removed outlier: 3.524A pdb=" N VAL C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 334 Processing helix chain 'C' and resid 336 through 353 Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.697A pdb=" N TYR A 120 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.891A pdb=" N TYR B 120 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AA5, first strand: chain 'C' and resid 240 through 241 696 hydrogen bonds defined for protein. 1947 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: 1.75 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3123 1.34 - 1.46: 2812 1.46 - 1.58: 4625 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 10644 Sorted by residual: bond pdb=" N VAL B 267 " pdb=" CA VAL B 267 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 9.92e+00 bond pdb=" N VAL B 272 " pdb=" CA VAL B 272 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 8.97e+00 bond pdb=" N VAL B 311 " pdb=" CA VAL B 311 " ideal model delta sigma weight residual 1.461 1.496 -0.034 1.17e-02 7.31e+03 8.68e+00 bond pdb=" N VAL C 272 " pdb=" CA VAL C 272 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.49e+00 bond pdb=" N VAL C 311 " pdb=" CA VAL C 311 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.34e+00 ... (remaining 10639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 13836 1.97 - 3.94: 530 3.94 - 5.90: 39 5.90 - 7.87: 2 7.87 - 9.84: 1 Bond angle restraints: 14408 Sorted by residual: angle pdb=" CA GLY D 313 " pdb=" C GLY D 313 " pdb=" O GLY D 313 " ideal model delta sigma weight residual 122.29 118.40 3.89 8.10e-01 1.52e+00 2.30e+01 angle pdb=" CA GLY C 313 " pdb=" C GLY C 313 " pdb=" O GLY C 313 " ideal model delta sigma weight residual 122.29 118.48 3.81 8.10e-01 1.52e+00 2.21e+01 angle pdb=" CA ASP A 276 " pdb=" CB ASP A 276 " pdb=" CG ASP A 276 " ideal model delta sigma weight residual 112.60 117.21 -4.61 1.00e+00 1.00e+00 2.12e+01 angle pdb=" N ARG A 91 " pdb=" CA ARG A 91 " pdb=" C ARG A 91 " ideal model delta sigma weight residual 111.71 106.50 5.21 1.15e+00 7.56e-01 2.05e+01 angle pdb=" N ASN A 315 " pdb=" CA ASN A 315 " pdb=" C ASN A 315 " ideal model delta sigma weight residual 111.07 106.48 4.59 1.07e+00 8.73e-01 1.84e+01 ... (remaining 14403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 5120 16.88 - 33.76: 721 33.76 - 50.64: 240 50.64 - 67.52: 49 67.52 - 84.41: 10 Dihedral angle restraints: 6140 sinusoidal: 2520 harmonic: 3620 Sorted by residual: dihedral pdb=" CA LYS D 312 " pdb=" C LYS D 312 " pdb=" N GLY D 313 " pdb=" CA GLY D 313 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASP D 338 " pdb=" CB ASP D 338 " pdb=" CG ASP D 338 " pdb=" OD1 ASP D 338 " ideal model delta sinusoidal sigma weight residual -30.00 -86.97 56.97 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASP D 122 " pdb=" CB ASP D 122 " pdb=" CG ASP D 122 " pdb=" OD1 ASP D 122 " ideal model delta sinusoidal sigma weight residual -30.00 -84.64 54.64 1 2.00e+01 2.50e-03 1.01e+01 ... (remaining 6137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1066 0.045 - 0.090: 363 0.090 - 0.134: 94 0.134 - 0.179: 21 0.179 - 0.224: 4 Chirality restraints: 1548 Sorted by residual: chirality pdb=" CA ILE B 277 " pdb=" N ILE B 277 " pdb=" C ILE B 277 " pdb=" CB ILE B 277 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA VAL C 272 " pdb=" N VAL C 272 " pdb=" C VAL C 272 " pdb=" CB VAL C 272 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA VAL A 167 " pdb=" N VAL A 167 " pdb=" C VAL A 167 " pdb=" CB VAL A 167 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.30e-01 ... (remaining 1545 not shown) Planarity restraints: 1764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 91 " 0.232 9.50e-02 1.11e+02 1.04e-01 6.64e+00 pdb=" NE ARG A 91 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 91 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 91 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 91 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 275 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" C GLY D 275 " 0.044 2.00e-02 2.50e+03 pdb=" O GLY D 275 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP D 276 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 275 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.18e+00 pdb=" C GLY C 275 " -0.043 2.00e-02 2.50e+03 pdb=" O GLY C 275 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP C 276 " 0.015 2.00e-02 2.50e+03 ... (remaining 1761 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1868 2.76 - 3.30: 10552 3.30 - 3.83: 18744 3.83 - 4.37: 21981 4.37 - 4.90: 35998 Nonbonded interactions: 89143 Sorted by model distance: nonbonded pdb=" OD1 ASN B 331 " pdb=" NH2 ARG B 340 " model vdw 2.227 3.120 nonbonded pdb=" OH TYR C 196 " pdb=" NH1 ARG C 200 " model vdw 2.238 3.120 nonbonded pdb=" OH TYR A 126 " pdb=" OD2 ASP D 352 " model vdw 2.243 3.040 nonbonded pdb=" O ASP B 352 " pdb=" NH1 ARG C 332 " model vdw 2.250 3.120 nonbonded pdb=" O SER C 161 " pdb=" OG SER C 161 " model vdw 2.253 3.040 ... (remaining 89138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 4.640 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.400 Find NCS groups from input model: 0.180 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:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 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 : 0.005 0.042 10644 Z= 0.354 Angle : 0.748 9.838 14408 Z= 0.523 Chirality : 0.049 0.224 1548 Planarity : 0.006 0.104 1764 Dihedral : 17.573 84.405 3828 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.74 % Allowed : 22.45 % Favored : 73.81 % 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: 1.11 (0.24), residues: 1212 helix: 0.75 (0.16), residues: 852 sheet: -3.01 (1.13), residues: 20 loop : 1.42 (0.41), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 127 TYR 0.024 0.002 TYR A 263 PHE 0.017 0.002 PHE A 137 TRP 0.014 0.002 TRP A 172 HIS 0.004 0.001 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00528 (10644) covalent geometry : angle 0.74751 (14408) hydrogen bonds : bond 0.14299 ( 696) hydrogen bonds : angle 5.71628 ( 1947) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.6686 (m-10) cc_final: 0.6386 (m100) REVERT: A 96 ARG cc_start: 0.6547 (tpt90) cc_final: 0.6289 (ttp-170) REVERT: A 115 GLN cc_start: 0.7995 (tt0) cc_final: 0.7793 (mm110) REVERT: A 130 TYR cc_start: 0.8724 (m-80) cc_final: 0.8465 (m-80) REVERT: A 141 LYS cc_start: 0.7050 (mtmt) cc_final: 0.6776 (mmtp) REVERT: A 143 HIS cc_start: 0.7908 (OUTLIER) cc_final: 0.6511 (p90) REVERT: A 164 HIS cc_start: 0.7788 (t-170) cc_final: 0.7355 (m90) REVERT: A 165 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8031 (tp30) REVERT: A 168 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.6929 (mtp85) REVERT: A 189 GLU cc_start: 0.6882 (tt0) cc_final: 0.6060 (tp30) REVERT: A 206 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7389 (t80) REVERT: A 210 TYR cc_start: 0.7936 (m-80) cc_final: 0.7716 (m-80) REVERT: A 301 TYR cc_start: 0.7765 (t80) cc_final: 0.7305 (m-80) REVERT: A 320 ARG cc_start: 0.5909 (mmm160) cc_final: 0.5506 (ttt-90) REVERT: A 351 TYR cc_start: 0.4945 (OUTLIER) cc_final: 0.4469 (t80) REVERT: D 61 LYS cc_start: 0.7859 (mttt) cc_final: 0.7610 (tppt) REVERT: D 96 ARG cc_start: 0.6251 (OUTLIER) cc_final: 0.3938 (ptt180) REVERT: D 101 ASP cc_start: 0.6696 (t70) cc_final: 0.6409 (t70) REVERT: D 147 ASP cc_start: 0.7113 (m-30) cc_final: 0.6802 (m-30) REVERT: D 340 ARG cc_start: 0.6054 (ttp-110) cc_final: 0.5598 (ttp-110) REVERT: B 96 ARG cc_start: 0.7660 (tmt90) cc_final: 0.6050 (ttp-170) REVERT: B 115 GLN cc_start: 0.8511 (tp40) cc_final: 0.8011 (mm-40) REVERT: B 168 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8001 (ttp80) REVERT: B 203 LYS cc_start: 0.7742 (mtpp) cc_final: 0.7096 (tmtt) REVERT: B 206 PHE cc_start: 0.7404 (m-80) cc_final: 0.7158 (t80) REVERT: B 301 TYR cc_start: 0.8029 (m-80) cc_final: 0.7786 (m-80) REVERT: B 330 MET cc_start: 0.6396 (mtm) cc_final: 0.6099 (mtt) REVERT: C 61 LYS cc_start: 0.8383 (tppt) cc_final: 0.8147 (ttmm) REVERT: C 96 ARG cc_start: 0.6079 (ttp80) cc_final: 0.4410 (ptt-90) REVERT: C 114 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7362 (tp) REVERT: C 206 PHE cc_start: 0.7902 (t80) cc_final: 0.7461 (t80) outliers start: 41 outliers final: 15 residues processed: 224 average time/residue: 0.6795 time to fit residues: 162.3698 Evaluate side-chains 199 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain C residue 351 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN B 305 ASN C 105 GLN C 278 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.191400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.132078 restraints weight = 11024.627| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.64 r_work: 0.3656 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10644 Z= 0.152 Angle : 0.505 6.261 14408 Z= 0.279 Chirality : 0.041 0.135 1548 Planarity : 0.004 0.053 1764 Dihedral : 6.863 59.558 1450 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.93 % Allowed : 20.53 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.85 (0.24), residues: 1212 helix: 1.32 (0.16), residues: 874 sheet: -3.20 (1.04), residues: 20 loop : 1.67 (0.41), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 332 TYR 0.016 0.002 TYR A 263 PHE 0.033 0.002 PHE B 98 TRP 0.013 0.001 TRP C 255 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00329 (10644) covalent geometry : angle 0.50523 (14408) hydrogen bonds : bond 0.05280 ( 696) hydrogen bonds : angle 4.15206 ( 1947) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.6606 (m-10) cc_final: 0.6296 (m100) REVERT: A 96 ARG cc_start: 0.6372 (tpt90) cc_final: 0.6014 (ttp-170) REVERT: A 115 GLN cc_start: 0.8133 (tt0) cc_final: 0.7820 (mm110) REVERT: A 130 TYR cc_start: 0.8569 (m-80) cc_final: 0.8338 (m-80) REVERT: A 141 LYS cc_start: 0.6832 (mtmt) cc_final: 0.6472 (mmtp) REVERT: A 143 HIS cc_start: 0.7542 (OUTLIER) cc_final: 0.7180 (p90) REVERT: A 168 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7096 (ttp80) REVERT: A 200 ARG cc_start: 0.6462 (OUTLIER) cc_final: 0.4965 (ptm160) REVERT: A 206 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.7185 (t80) REVERT: A 301 TYR cc_start: 0.7479 (t80) cc_final: 0.6892 (m-80) REVERT: A 321 ASP cc_start: 0.6888 (m-30) cc_final: 0.6555 (m-30) REVERT: A 323 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6793 (mmm) REVERT: A 351 TYR cc_start: 0.4797 (OUTLIER) cc_final: 0.4191 (t80) REVERT: D 61 LYS cc_start: 0.7658 (mttt) cc_final: 0.7400 (tppt) REVERT: D 96 ARG cc_start: 0.6087 (tmt170) cc_final: 0.3685 (ptt180) REVERT: D 101 ASP cc_start: 0.6676 (t70) cc_final: 0.6443 (t0) REVERT: D 147 ASP cc_start: 0.6920 (m-30) cc_final: 0.6484 (m-30) REVERT: D 178 VAL cc_start: 0.8430 (p) cc_final: 0.8204 (m) REVERT: D 340 ARG cc_start: 0.5973 (ttp-110) cc_final: 0.5607 (ttp-110) REVERT: B 96 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.5703 (ttp-170) REVERT: B 115 GLN cc_start: 0.8292 (tp40) cc_final: 0.7751 (mm-40) REVERT: B 203 LYS cc_start: 0.7344 (mtpp) cc_final: 0.6554 (tmtt) REVERT: B 206 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.6713 (t80) REVERT: B 301 TYR cc_start: 0.7768 (m-80) cc_final: 0.7465 (m-80) REVERT: B 321 ASP cc_start: 0.7066 (m-30) cc_final: 0.6628 (m-30) REVERT: C 61 LYS cc_start: 0.8201 (tppt) cc_final: 0.7991 (ttmm) REVERT: C 96 ARG cc_start: 0.5925 (ttp80) cc_final: 0.4109 (ptt180) REVERT: C 206 PHE cc_start: 0.7775 (t80) cc_final: 0.7003 (t80) REVERT: C 330 MET cc_start: 0.6863 (mtp) cc_final: 0.6094 (ttp) outliers start: 54 outliers final: 20 residues processed: 228 average time/residue: 0.6918 time to fit residues: 168.0169 Evaluate side-chains 208 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 351 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 12 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.189525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.129969 restraints weight = 11068.003| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.64 r_work: 0.3622 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10644 Z= 0.161 Angle : 0.494 6.950 14408 Z= 0.272 Chirality : 0.040 0.131 1548 Planarity : 0.004 0.050 1764 Dihedral : 5.725 57.785 1423 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.47 % Allowed : 20.44 % Favored : 74.09 % 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: 2.15 (0.24), residues: 1212 helix: 1.44 (0.16), residues: 872 sheet: -3.32 (1.07), residues: 20 loop : 2.11 (0.41), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 250 TYR 0.018 0.002 TYR A 78 PHE 0.017 0.002 PHE A 287 TRP 0.011 0.001 TRP B 255 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00359 (10644) covalent geometry : angle 0.49404 (14408) hydrogen bonds : bond 0.05067 ( 696) hydrogen bonds : angle 3.99529 ( 1947) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 187 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.6658 (m-10) cc_final: 0.6436 (m100) REVERT: A 96 ARG cc_start: 0.6343 (tpt90) cc_final: 0.5822 (ttp80) REVERT: A 115 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7777 (mm110) REVERT: A 130 TYR cc_start: 0.8565 (m-80) cc_final: 0.8288 (m-80) REVERT: A 141 LYS cc_start: 0.6698 (mtmt) cc_final: 0.6323 (mmmm) REVERT: A 143 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.6999 (p90) REVERT: A 168 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7111 (ttp80) REVERT: A 206 PHE cc_start: 0.7361 (OUTLIER) cc_final: 0.7086 (t80) REVERT: A 301 TYR cc_start: 0.7465 (t80) cc_final: 0.6869 (m-80) REVERT: A 321 ASP cc_start: 0.6802 (m-30) cc_final: 0.6493 (m-30) REVERT: A 323 MET cc_start: 0.7074 (OUTLIER) cc_final: 0.6747 (mmt) REVERT: A 335 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5924 (pp) REVERT: A 351 TYR cc_start: 0.4808 (OUTLIER) cc_final: 0.4105 (t80) REVERT: D 61 LYS cc_start: 0.7634 (mttt) cc_final: 0.7356 (tppt) REVERT: D 96 ARG cc_start: 0.5978 (OUTLIER) cc_final: 0.3503 (ptt180) REVERT: D 101 ASP cc_start: 0.6813 (t70) cc_final: 0.6493 (t0) REVERT: D 147 ASP cc_start: 0.6878 (m-30) cc_final: 0.6455 (m-30) REVERT: D 178 VAL cc_start: 0.8377 (p) cc_final: 0.8158 (m) REVERT: D 191 ASP cc_start: 0.6084 (t0) cc_final: 0.5645 (t0) REVERT: D 340 ARG cc_start: 0.5943 (ttp-110) cc_final: 0.5562 (ttp-110) REVERT: B 96 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.5634 (ttp-170) REVERT: B 115 GLN cc_start: 0.8352 (tp40) cc_final: 0.7725 (mm-40) REVERT: B 178 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8600 (m) REVERT: B 203 LYS cc_start: 0.7266 (mtpp) cc_final: 0.6457 (tmtt) REVERT: B 206 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6635 (t80) REVERT: B 301 TYR cc_start: 0.7726 (m-80) cc_final: 0.7449 (m-80) REVERT: B 321 ASP cc_start: 0.6929 (m-30) cc_final: 0.6699 (m-30) REVERT: B 323 MET cc_start: 0.7102 (tpt) cc_final: 0.6765 (mmm) REVERT: C 96 ARG cc_start: 0.5935 (ttp80) cc_final: 0.4026 (ptt-90) REVERT: C 114 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6651 (mp) REVERT: C 168 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8094 (ttp80) REVERT: C 206 PHE cc_start: 0.7699 (t80) cc_final: 0.6868 (t80) REVERT: C 210 TYR cc_start: 0.7371 (OUTLIER) cc_final: 0.7051 (t80) outliers start: 60 outliers final: 26 residues processed: 222 average time/residue: 0.6378 time to fit residues: 151.3765 Evaluate side-chains 218 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 168 ARG Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 TYR Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 351 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.187245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.127180 restraints weight = 11071.001| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.63 r_work: 0.3593 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10644 Z= 0.214 Angle : 0.538 7.640 14408 Z= 0.292 Chirality : 0.042 0.131 1548 Planarity : 0.004 0.050 1764 Dihedral : 5.889 57.281 1423 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.84 % Allowed : 20.53 % Favored : 73.63 % 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: 2.06 (0.24), residues: 1212 helix: 1.34 (0.16), residues: 872 sheet: -3.30 (1.12), residues: 20 loop : 2.21 (0.41), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 340 TYR 0.020 0.002 TYR B 120 PHE 0.025 0.002 PHE B 98 TRP 0.013 0.001 TRP B 255 HIS 0.003 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00500 (10644) covalent geometry : angle 0.53773 (14408) hydrogen bonds : bond 0.05233 ( 696) hydrogen bonds : angle 4.03346 ( 1947) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 182 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7579 (pttp) cc_final: 0.6790 (mmpt) REVERT: A 64 TRP cc_start: 0.6779 (m-10) cc_final: 0.6547 (m100) REVERT: A 96 ARG cc_start: 0.6494 (tpt90) cc_final: 0.5920 (ttp80) REVERT: A 115 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7787 (mm110) REVERT: A 130 TYR cc_start: 0.8550 (m-80) cc_final: 0.8271 (m-80) REVERT: A 168 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7956 (ttp80) REVERT: A 200 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.5029 (ptm160) REVERT: A 206 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.7183 (t80) REVERT: A 282 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8430 (mp) REVERT: A 301 TYR cc_start: 0.7493 (t80) cc_final: 0.6889 (m-80) REVERT: A 323 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6856 (mmt) REVERT: A 335 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5930 (pp) REVERT: A 351 TYR cc_start: 0.4798 (OUTLIER) cc_final: 0.4086 (t80) REVERT: D 61 LYS cc_start: 0.7675 (mttt) cc_final: 0.7394 (tppt) REVERT: D 96 ARG cc_start: 0.5977 (OUTLIER) cc_final: 0.4465 (ttt180) REVERT: D 101 ASP cc_start: 0.6948 (t70) cc_final: 0.6627 (t0) REVERT: D 147 ASP cc_start: 0.7062 (m-30) cc_final: 0.6723 (m-30) REVERT: D 191 ASP cc_start: 0.6245 (t0) cc_final: 0.5903 (t70) REVERT: D 231 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: D 340 ARG cc_start: 0.6033 (ttp-110) cc_final: 0.5674 (ttp-110) REVERT: B 96 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.5797 (ttp-170) REVERT: B 115 GLN cc_start: 0.8440 (tp40) cc_final: 0.7780 (mm-40) REVERT: B 203 LYS cc_start: 0.7377 (mtpp) cc_final: 0.6518 (tmtt) REVERT: B 206 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.6698 (t80) REVERT: B 251 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7941 (mm-30) REVERT: B 301 TYR cc_start: 0.7811 (m-80) cc_final: 0.7561 (m-80) REVERT: B 323 MET cc_start: 0.7217 (tpt) cc_final: 0.6838 (mmm) REVERT: C 96 ARG cc_start: 0.5941 (ttp80) cc_final: 0.3945 (ptt180) REVERT: C 115 GLN cc_start: 0.7651 (mt0) cc_final: 0.7372 (mt0) REVERT: C 206 PHE cc_start: 0.7741 (t80) cc_final: 0.6888 (t80) REVERT: C 210 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.7054 (t80) REVERT: C 240 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.7549 (tmtm) REVERT: C 340 ARG cc_start: 0.6170 (ttm-80) cc_final: 0.5495 (tpp80) outliers start: 64 outliers final: 29 residues processed: 219 average time/residue: 0.6786 time to fit residues: 158.3565 Evaluate side-chains 224 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 TYR Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 311 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 18 optimal weight: 0.9980 chunk 107 optimal weight: 0.0770 chunk 97 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 68 optimal weight: 0.0980 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 HIS C 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.190109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.130922 restraints weight = 11086.664| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.65 r_work: 0.3642 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10644 Z= 0.131 Angle : 0.469 7.974 14408 Z= 0.256 Chirality : 0.039 0.132 1548 Planarity : 0.004 0.052 1764 Dihedral : 5.527 54.869 1419 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.29 % Allowed : 21.72 % Favored : 72.99 % 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: 2.33 (0.24), residues: 1212 helix: 1.59 (0.16), residues: 870 sheet: -3.18 (1.16), residues: 20 loop : 2.15 (0.41), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 250 TYR 0.018 0.002 TYR B 120 PHE 0.019 0.002 PHE C 98 TRP 0.011 0.001 TRP A 255 HIS 0.002 0.001 HIS C 213 Details of bonding type rmsd covalent geometry : bond 0.00282 (10644) covalent geometry : angle 0.46865 (14408) hydrogen bonds : bond 0.04651 ( 696) hydrogen bonds : angle 3.83818 ( 1947) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 183 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.6722 (m-10) cc_final: 0.6484 (m100) REVERT: A 96 ARG cc_start: 0.6413 (tpt90) cc_final: 0.5828 (ttp80) REVERT: A 115 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7843 (mm110) REVERT: A 130 TYR cc_start: 0.8503 (m-80) cc_final: 0.8257 (m-80) REVERT: A 143 HIS cc_start: 0.7351 (OUTLIER) cc_final: 0.6976 (p90) REVERT: A 168 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7898 (ttp80) REVERT: A 200 ARG cc_start: 0.6502 (OUTLIER) cc_final: 0.5012 (ptm160) REVERT: A 206 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.7159 (t80) REVERT: A 282 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8336 (mp) REVERT: A 301 TYR cc_start: 0.7492 (t80) cc_final: 0.6879 (m-80) REVERT: A 323 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6894 (mmt) REVERT: A 335 LEU cc_start: 0.6084 (OUTLIER) cc_final: 0.5801 (pp) REVERT: A 351 TYR cc_start: 0.4801 (OUTLIER) cc_final: 0.4135 (t80) REVERT: D 61 LYS cc_start: 0.7595 (mttt) cc_final: 0.7344 (tppt) REVERT: D 101 ASP cc_start: 0.6881 (t70) cc_final: 0.6547 (t0) REVERT: D 114 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7072 (mp) REVERT: D 147 ASP cc_start: 0.6966 (m-30) cc_final: 0.6550 (m-30) REVERT: D 175 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7793 (tp) REVERT: D 178 VAL cc_start: 0.8369 (OUTLIER) cc_final: 0.8166 (m) REVERT: D 340 ARG cc_start: 0.6022 (ttp-110) cc_final: 0.5717 (ttp-110) REVERT: B 96 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.5574 (ttp-170) REVERT: B 115 GLN cc_start: 0.8396 (tp40) cc_final: 0.7731 (mm110) REVERT: B 203 LYS cc_start: 0.7228 (mtpp) cc_final: 0.6455 (tmtt) REVERT: B 206 PHE cc_start: 0.7009 (OUTLIER) cc_final: 0.6665 (t80) REVERT: B 251 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7904 (mm-30) REVERT: B 301 TYR cc_start: 0.7696 (m-80) cc_final: 0.7439 (m-80) REVERT: B 321 ASP cc_start: 0.7035 (m-30) cc_final: 0.6830 (m-30) REVERT: B 323 MET cc_start: 0.7169 (tpt) cc_final: 0.6826 (mmm) REVERT: B 346 HIS cc_start: 0.6825 (OUTLIER) cc_final: 0.6579 (t-90) REVERT: C 96 ARG cc_start: 0.5875 (ttp80) cc_final: 0.3868 (ptt180) REVERT: C 115 GLN cc_start: 0.7632 (mt0) cc_final: 0.7363 (mt0) REVERT: C 168 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7411 (mtp85) REVERT: C 200 ARG cc_start: 0.7703 (mmm-85) cc_final: 0.6464 (mmt180) REVERT: C 206 PHE cc_start: 0.7674 (t80) cc_final: 0.6849 (t80) REVERT: C 210 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.7119 (t80) REVERT: C 240 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.7411 (tmtm) outliers start: 58 outliers final: 21 residues processed: 219 average time/residue: 0.6111 time to fit residues: 143.3425 Evaluate side-chains 210 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 168 ARG Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 TYR Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain C residue 295 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 62 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4281 r_free = 0.4281 target = 0.188703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.129983 restraints weight = 11159.131| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.63 r_work: 0.3614 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10644 Z= 0.164 Angle : 0.496 8.031 14408 Z= 0.270 Chirality : 0.040 0.125 1548 Planarity : 0.004 0.051 1764 Dihedral : 5.598 55.716 1419 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 6.02 % Allowed : 21.44 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.34 (0.24), residues: 1212 helix: 1.58 (0.16), residues: 872 sheet: -3.03 (1.16), residues: 20 loop : 2.21 (0.41), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 318 TYR 0.019 0.002 TYR A 120 PHE 0.028 0.002 PHE B 98 TRP 0.011 0.001 TRP A 255 HIS 0.004 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00372 (10644) covalent geometry : angle 0.49551 (14408) hydrogen bonds : bond 0.04812 ( 696) hydrogen bonds : angle 3.85869 ( 1947) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 172 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7499 (pttp) cc_final: 0.6884 (mmtp) REVERT: A 64 TRP cc_start: 0.6790 (m-10) cc_final: 0.6556 (m100) REVERT: A 96 ARG cc_start: 0.6470 (tpt90) cc_final: 0.5848 (ttp80) REVERT: A 115 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7812 (mm110) REVERT: A 130 TYR cc_start: 0.8465 (m-80) cc_final: 0.8189 (m-80) REVERT: A 143 HIS cc_start: 0.7387 (OUTLIER) cc_final: 0.7039 (p90) REVERT: A 168 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7969 (ttp80) REVERT: A 200 ARG cc_start: 0.6546 (OUTLIER) cc_final: 0.5042 (ptm160) REVERT: A 206 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.7133 (t80) REVERT: A 282 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8385 (mp) REVERT: A 301 TYR cc_start: 0.7520 (t80) cc_final: 0.6899 (m-80) REVERT: A 321 ASP cc_start: 0.6905 (m-30) cc_final: 0.6686 (m-30) REVERT: A 323 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6850 (mmt) REVERT: A 335 LEU cc_start: 0.6102 (OUTLIER) cc_final: 0.5804 (pp) REVERT: A 351 TYR cc_start: 0.4772 (OUTLIER) cc_final: 0.4064 (t80) REVERT: D 61 LYS cc_start: 0.7537 (mttt) cc_final: 0.7227 (mptp) REVERT: D 96 ARG cc_start: 0.5992 (OUTLIER) cc_final: 0.4604 (ttt180) REVERT: D 101 ASP cc_start: 0.6869 (t70) cc_final: 0.6513 (t0) REVERT: D 114 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7024 (mp) REVERT: D 147 ASP cc_start: 0.6965 (m-30) cc_final: 0.6590 (m-30) REVERT: D 175 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7941 (tp) REVERT: D 340 ARG cc_start: 0.6016 (ttp-110) cc_final: 0.5677 (ttp-110) REVERT: B 96 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.5664 (ttp-170) REVERT: B 115 GLN cc_start: 0.8409 (tp40) cc_final: 0.7782 (mm110) REVERT: B 203 LYS cc_start: 0.7308 (mtpp) cc_final: 0.6510 (tmtt) REVERT: B 206 PHE cc_start: 0.7036 (OUTLIER) cc_final: 0.6695 (t80) REVERT: B 231 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: B 251 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7888 (mm-30) REVERT: B 254 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8417 (tp) REVERT: B 301 TYR cc_start: 0.7747 (m-80) cc_final: 0.7502 (m-80) REVERT: B 321 ASP cc_start: 0.6975 (m-30) cc_final: 0.6737 (m-30) REVERT: B 323 MET cc_start: 0.7125 (tpt) cc_final: 0.6821 (mmm) REVERT: B 346 HIS cc_start: 0.6846 (OUTLIER) cc_final: 0.6593 (t-90) REVERT: C 96 ARG cc_start: 0.5897 (ttp80) cc_final: 0.3875 (ptt180) REVERT: C 115 GLN cc_start: 0.7586 (mt0) cc_final: 0.7320 (mt0) REVERT: C 168 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7431 (mtp85) REVERT: C 206 PHE cc_start: 0.7700 (t80) cc_final: 0.6875 (t80) REVERT: C 210 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.7115 (t80) REVERT: C 240 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.7486 (tmtm) outliers start: 66 outliers final: 28 residues processed: 215 average time/residue: 0.6286 time to fit residues: 144.7990 Evaluate side-chains 218 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 168 ARG Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 TYR Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 311 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 69 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4270 r_free = 0.4270 target = 0.188319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.128625 restraints weight = 11040.548| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.63 r_work: 0.3610 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10644 Z= 0.168 Angle : 0.507 8.495 14408 Z= 0.274 Chirality : 0.041 0.129 1548 Planarity : 0.004 0.050 1764 Dihedral : 5.661 56.816 1419 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 5.20 % Allowed : 21.90 % Favored : 72.90 % 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: 2.30 (0.24), residues: 1212 helix: 1.56 (0.16), residues: 872 sheet: -3.01 (1.12), residues: 20 loop : 2.17 (0.41), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 134 TYR 0.022 0.002 TYR B 120 PHE 0.019 0.002 PHE C 98 TRP 0.011 0.001 TRP A 255 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00383 (10644) covalent geometry : angle 0.50666 (14408) hydrogen bonds : bond 0.04800 ( 696) hydrogen bonds : angle 3.86781 ( 1947) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 173 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7539 (pttp) cc_final: 0.6788 (mmpt) REVERT: A 64 TRP cc_start: 0.6809 (m-10) cc_final: 0.6594 (m100) REVERT: A 96 ARG cc_start: 0.6596 (tpt90) cc_final: 0.5894 (ttp80) REVERT: A 115 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7889 (mm110) REVERT: A 130 TYR cc_start: 0.8481 (m-80) cc_final: 0.8214 (m-80) REVERT: A 143 HIS cc_start: 0.7430 (OUTLIER) cc_final: 0.7053 (p90) REVERT: A 146 MET cc_start: 0.7850 (mmp) cc_final: 0.7523 (mmt) REVERT: A 168 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8021 (ttp80) REVERT: A 200 ARG cc_start: 0.6566 (OUTLIER) cc_final: 0.5064 (ptm160) REVERT: A 206 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.7205 (t80) REVERT: A 254 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8440 (tp) REVERT: A 282 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8452 (mp) REVERT: A 301 TYR cc_start: 0.7529 (t80) cc_final: 0.6915 (m-80) REVERT: A 317 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.5430 (mt-10) REVERT: A 323 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6950 (mmt) REVERT: A 335 LEU cc_start: 0.6091 (OUTLIER) cc_final: 0.5800 (pp) REVERT: A 351 TYR cc_start: 0.4701 (OUTLIER) cc_final: 0.4023 (t80) REVERT: D 61 LYS cc_start: 0.7538 (mttt) cc_final: 0.7185 (mptp) REVERT: D 96 ARG cc_start: 0.6000 (OUTLIER) cc_final: 0.4697 (ttt180) REVERT: D 101 ASP cc_start: 0.6931 (t70) cc_final: 0.6554 (t0) REVERT: D 114 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.6863 (mp) REVERT: D 147 ASP cc_start: 0.7011 (m-30) cc_final: 0.6632 (m-30) REVERT: D 340 ARG cc_start: 0.6065 (ttp-110) cc_final: 0.5746 (ttp-110) REVERT: B 96 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.5670 (ttp-170) REVERT: B 115 GLN cc_start: 0.8476 (tp40) cc_final: 0.8181 (mm110) REVERT: B 203 LYS cc_start: 0.7293 (mtpp) cc_final: 0.6522 (tmtt) REVERT: B 206 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.6772 (t80) REVERT: B 231 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: B 301 TYR cc_start: 0.7766 (m-80) cc_final: 0.7526 (m-80) REVERT: B 321 ASP cc_start: 0.6973 (m-30) cc_final: 0.6697 (m-30) REVERT: B 323 MET cc_start: 0.7123 (tpt) cc_final: 0.6857 (mmt) REVERT: C 96 ARG cc_start: 0.5891 (ttp80) cc_final: 0.5463 (ttp80) REVERT: C 115 GLN cc_start: 0.7585 (mt0) cc_final: 0.7327 (mt0) REVERT: C 168 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7451 (mtp85) REVERT: C 196 TYR cc_start: 0.7341 (t80) cc_final: 0.7017 (t80) REVERT: C 200 ARG cc_start: 0.7736 (mmm-85) cc_final: 0.6580 (mmt180) REVERT: C 206 PHE cc_start: 0.7677 (t80) cc_final: 0.6905 (t80) REVERT: C 210 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.7108 (t80) REVERT: C 240 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.7527 (tmtm) outliers start: 57 outliers final: 24 residues processed: 207 average time/residue: 0.6382 time to fit residues: 141.2029 Evaluate side-chains 205 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 168 ARG Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 TYR Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain C residue 295 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 47 optimal weight: 0.0970 chunk 114 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.4276 r_free = 0.4276 target = 0.188962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.129572 restraints weight = 11036.032| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.63 r_work: 0.3621 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10644 Z= 0.149 Angle : 0.489 7.720 14408 Z= 0.265 Chirality : 0.040 0.129 1548 Planarity : 0.004 0.051 1764 Dihedral : 5.339 56.034 1417 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.02 % Allowed : 22.26 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.36 (0.24), residues: 1212 helix: 1.61 (0.16), residues: 872 sheet: -2.93 (1.11), residues: 20 loop : 2.15 (0.41), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 318 TYR 0.021 0.002 TYR B 120 PHE 0.029 0.002 PHE B 98 TRP 0.011 0.001 TRP A 255 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00334 (10644) covalent geometry : angle 0.48914 (14408) hydrogen bonds : bond 0.04651 ( 696) hydrogen bonds : angle 3.82401 ( 1947) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 171 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7462 (pttp) cc_final: 0.6712 (mmpt) REVERT: A 96 ARG cc_start: 0.6602 (tpt90) cc_final: 0.5876 (ttp80) REVERT: A 115 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7866 (mm110) REVERT: A 130 TYR cc_start: 0.8434 (m-80) cc_final: 0.8135 (m-80) REVERT: A 168 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7987 (ttp80) REVERT: A 200 ARG cc_start: 0.6548 (OUTLIER) cc_final: 0.5072 (ptm160) REVERT: A 201 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6778 (pp) REVERT: A 206 PHE cc_start: 0.7421 (OUTLIER) cc_final: 0.7189 (t80) REVERT: A 282 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8445 (mp) REVERT: A 301 TYR cc_start: 0.7515 (t80) cc_final: 0.6903 (m-80) REVERT: A 317 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6368 (tt0) REVERT: A 323 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.7015 (mmt) REVERT: A 335 LEU cc_start: 0.6029 (OUTLIER) cc_final: 0.5742 (pp) REVERT: A 351 TYR cc_start: 0.4668 (OUTLIER) cc_final: 0.3989 (t80) REVERT: D 61 LYS cc_start: 0.7561 (mttt) cc_final: 0.7197 (mptp) REVERT: D 101 ASP cc_start: 0.6864 (t70) cc_final: 0.6509 (t0) REVERT: D 114 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6785 (mp) REVERT: D 147 ASP cc_start: 0.6982 (m-30) cc_final: 0.6588 (m-30) REVERT: D 178 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8208 (m) REVERT: D 340 ARG cc_start: 0.6055 (ttp-110) cc_final: 0.5735 (ttp-110) REVERT: B 96 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.5874 (ttp80) REVERT: B 115 GLN cc_start: 0.8453 (tp40) cc_final: 0.8144 (mm110) REVERT: B 203 LYS cc_start: 0.7321 (mtpp) cc_final: 0.6543 (tmtt) REVERT: B 206 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.6782 (t80) REVERT: B 231 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: B 251 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7903 (mm-30) REVERT: B 254 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8414 (tp) REVERT: B 301 TYR cc_start: 0.7746 (m-80) cc_final: 0.7501 (m-80) REVERT: B 323 MET cc_start: 0.7095 (tpt) cc_final: 0.6824 (mmt) REVERT: C 96 ARG cc_start: 0.5912 (ttp80) cc_final: 0.5520 (ttp80) REVERT: C 114 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6751 (mp) REVERT: C 115 GLN cc_start: 0.7610 (mt0) cc_final: 0.7378 (mt0) REVERT: C 168 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7426 (mtp85) REVERT: C 196 TYR cc_start: 0.7361 (t80) cc_final: 0.7157 (t80) REVERT: C 200 ARG cc_start: 0.7735 (mmm-85) cc_final: 0.6498 (mmt180) REVERT: C 206 PHE cc_start: 0.7637 (t80) cc_final: 0.6875 (t80) REVERT: C 208 GLU cc_start: 0.8059 (tt0) cc_final: 0.7818 (mt-10) REVERT: C 210 TYR cc_start: 0.7474 (OUTLIER) cc_final: 0.7102 (t80) REVERT: C 240 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.7493 (tmtm) outliers start: 55 outliers final: 23 residues processed: 202 average time/residue: 0.6567 time to fit residues: 141.5858 Evaluate side-chains 211 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 168 ARG Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 TYR Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain C residue 295 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 114 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 113 optimal weight: 0.0980 chunk 84 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4294 r_free = 0.4294 target = 0.189987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.131861 restraints weight = 11107.895| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.85 r_work: 0.3623 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10644 Z= 0.133 Angle : 0.483 9.081 14408 Z= 0.260 Chirality : 0.039 0.131 1548 Planarity : 0.003 0.051 1764 Dihedral : 5.249 56.569 1417 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.84 % Allowed : 22.54 % Favored : 72.63 % 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: 2.48 (0.24), residues: 1212 helix: 1.72 (0.16), residues: 872 sheet: -2.87 (1.10), residues: 20 loop : 2.09 (0.41), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 134 TYR 0.021 0.002 TYR B 120 PHE 0.021 0.002 PHE C 98 TRP 0.010 0.001 TRP D 68 HIS 0.002 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00293 (10644) covalent geometry : angle 0.48305 (14408) hydrogen bonds : bond 0.04500 ( 696) hydrogen bonds : angle 3.76945 ( 1947) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 170 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.6636 (tpt90) cc_final: 0.5840 (ttp80) REVERT: A 115 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7883 (mp10) REVERT: A 143 HIS cc_start: 0.7270 (OUTLIER) cc_final: 0.6901 (p90) REVERT: A 146 MET cc_start: 0.7815 (mmp) cc_final: 0.7571 (mmt) REVERT: A 168 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7961 (ttp80) REVERT: A 200 ARG cc_start: 0.6496 (OUTLIER) cc_final: 0.4990 (ptm160) REVERT: A 201 ILE cc_start: 0.7018 (OUTLIER) cc_final: 0.6759 (pp) REVERT: A 206 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7240 (t80) REVERT: A 301 TYR cc_start: 0.7576 (t80) cc_final: 0.6954 (m-80) REVERT: A 317 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6041 (tm-30) REVERT: A 321 ASP cc_start: 0.6894 (m-30) cc_final: 0.6659 (m-30) REVERT: A 323 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6973 (mmt) REVERT: A 351 TYR cc_start: 0.4683 (OUTLIER) cc_final: 0.3996 (t80) REVERT: D 61 LYS cc_start: 0.7533 (mttt) cc_final: 0.7177 (mptp) REVERT: D 101 ASP cc_start: 0.6881 (t70) cc_final: 0.6511 (t0) REVERT: D 147 ASP cc_start: 0.6957 (m-30) cc_final: 0.6543 (m-30) REVERT: D 178 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8205 (m) REVERT: D 340 ARG cc_start: 0.6034 (ttp-110) cc_final: 0.5716 (ttp-110) REVERT: B 96 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.5841 (ttp80) REVERT: B 115 GLN cc_start: 0.8397 (tp40) cc_final: 0.8088 (mm110) REVERT: B 203 LYS cc_start: 0.7335 (mtpp) cc_final: 0.6570 (tmtt) REVERT: B 206 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6828 (t80) REVERT: B 301 TYR cc_start: 0.7791 (m-80) cc_final: 0.7545 (m-80) REVERT: B 323 MET cc_start: 0.7079 (tpt) cc_final: 0.6834 (mmt) REVERT: C 115 GLN cc_start: 0.7619 (mt0) cc_final: 0.7410 (mt0) REVERT: C 168 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7396 (mtp85) REVERT: C 196 TYR cc_start: 0.7343 (t80) cc_final: 0.7131 (t80) REVERT: C 200 ARG cc_start: 0.7741 (mmm-85) cc_final: 0.6480 (mmt180) REVERT: C 206 PHE cc_start: 0.7616 (t80) cc_final: 0.6866 (t80) REVERT: C 208 GLU cc_start: 0.8091 (tt0) cc_final: 0.7848 (mt-10) REVERT: C 210 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.7150 (t80) REVERT: C 240 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.7478 (tmtm) REVERT: C 322 LYS cc_start: 0.6729 (tttt) cc_final: 0.6246 (ttpt) outliers start: 53 outliers final: 23 residues processed: 198 average time/residue: 0.6262 time to fit residues: 132.4214 Evaluate side-chains 199 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 168 ARG Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 TYR Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain C residue 295 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 24 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 55 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 27 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.188768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.128770 restraints weight = 10868.073| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.69 r_work: 0.3628 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10644 Z= 0.148 Angle : 0.516 10.673 14408 Z= 0.273 Chirality : 0.040 0.145 1548 Planarity : 0.004 0.050 1764 Dihedral : 5.277 56.821 1417 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.01 % Allowed : 23.45 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.46 (0.24), residues: 1212 helix: 1.69 (0.16), residues: 872 sheet: -2.80 (1.10), residues: 20 loop : 2.15 (0.41), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 318 TYR 0.022 0.002 TYR B 120 PHE 0.028 0.002 PHE B 98 TRP 0.011 0.001 TRP A 255 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00333 (10644) covalent geometry : angle 0.51560 (14408) hydrogen bonds : bond 0.04583 ( 696) hydrogen bonds : angle 3.79447 ( 1947) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.6657 (tpt90) cc_final: 0.5896 (ttp80) REVERT: A 115 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7803 (mp10) REVERT: A 168 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7977 (ttp80) REVERT: A 200 ARG cc_start: 0.6529 (OUTLIER) cc_final: 0.5015 (ptm160) REVERT: A 201 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6767 (pp) REVERT: A 206 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.7235 (t80) REVERT: A 301 TYR cc_start: 0.7481 (t80) cc_final: 0.6835 (m-80) REVERT: A 317 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.6081 (tm-30) REVERT: A 321 ASP cc_start: 0.6865 (m-30) cc_final: 0.6627 (m-30) REVERT: A 323 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6984 (mmt) REVERT: A 351 TYR cc_start: 0.4675 (OUTLIER) cc_final: 0.4005 (t80) REVERT: D 61 LYS cc_start: 0.7560 (mttt) cc_final: 0.7175 (mptp) REVERT: D 101 ASP cc_start: 0.6827 (t70) cc_final: 0.6454 (t0) REVERT: D 147 ASP cc_start: 0.6926 (m-30) cc_final: 0.6509 (m-30) REVERT: D 178 VAL cc_start: 0.8369 (OUTLIER) cc_final: 0.8162 (m) REVERT: D 200 ARG cc_start: 0.7743 (mmm-85) cc_final: 0.7525 (mmm-85) REVERT: D 340 ARG cc_start: 0.6045 (ttp-110) cc_final: 0.5721 (ttp-110) REVERT: B 96 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.5895 (ttp80) REVERT: B 115 GLN cc_start: 0.8421 (tp40) cc_final: 0.8110 (mm110) REVERT: B 203 LYS cc_start: 0.7264 (mtpp) cc_final: 0.6505 (tmtt) REVERT: B 206 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.6731 (t80) REVERT: B 301 TYR cc_start: 0.7709 (m-80) cc_final: 0.7452 (m-80) REVERT: B 323 MET cc_start: 0.7031 (tpt) cc_final: 0.6795 (mmt) REVERT: C 114 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6726 (mp) REVERT: C 115 GLN cc_start: 0.7632 (mt0) cc_final: 0.7425 (mt0) REVERT: C 168 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7392 (mtp85) REVERT: C 206 PHE cc_start: 0.7527 (t80) cc_final: 0.6780 (t80) REVERT: C 208 GLU cc_start: 0.8027 (tt0) cc_final: 0.7805 (mt-10) REVERT: C 210 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.7126 (t80) REVERT: C 240 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.7446 (tmtm) REVERT: C 322 LYS cc_start: 0.6625 (tttt) cc_final: 0.6186 (ttpt) outliers start: 44 outliers final: 26 residues processed: 187 average time/residue: 0.6547 time to fit residues: 130.4582 Evaluate side-chains 205 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 168 ARG Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 210 TYR Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain C residue 295 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 20 optimal weight: 0.2980 chunk 72 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.188956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.128744 restraints weight = 11009.703| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.71 r_work: 0.3630 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10644 Z= 0.146 Angle : 0.516 9.345 14408 Z= 0.275 Chirality : 0.040 0.129 1548 Planarity : 0.004 0.050 1764 Dihedral : 5.281 57.090 1417 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.11 % Allowed : 23.81 % Favored : 72.08 % 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: 2.46 (0.24), residues: 1212 helix: 1.70 (0.16), residues: 872 sheet: -2.73 (1.10), residues: 20 loop : 2.12 (0.41), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 318 TYR 0.022 0.002 TYR B 120 PHE 0.021 0.002 PHE C 98 TRP 0.011 0.001 TRP A 255 HIS 0.002 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00328 (10644) covalent geometry : angle 0.51632 (14408) hydrogen bonds : bond 0.04547 ( 696) hydrogen bonds : angle 3.79333 ( 1947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5672.68 seconds wall clock time: 97 minutes 6.88 seconds (5826.88 seconds total)