Starting phenix.real_space_refine on Thu Jun 5 09:39:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ur7_42486/06_2025/8ur7_42486.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ur7_42486/06_2025/8ur7_42486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ur7_42486/06_2025/8ur7_42486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ur7_42486/06_2025/8ur7_42486.map" model { file = "/net/cci-nas-00/data/ceres_data/8ur7_42486/06_2025/8ur7_42486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ur7_42486/06_2025/8ur7_42486.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.115 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 18 5.16 5 C 3795 2.51 5 N 999 2.21 5 O 960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 5772 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1882 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 14, 'TRANS': 248} Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 21, 'ASN:plan1': 9, 'ARG:plan': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 154 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: C, B Time building chain proxies: 3.74, per 1000 atoms: 0.65 Number of scatterers: 5772 At special positions: 0 Unit cell: (82.8298, 85.686, 119.96, 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 18 16.00 O 960 8.00 N 999 7.00 C 3795 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.10 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.02 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 271 " distance=2.18 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.10 Simple disulfide: pdb=" SG CYS B 59 " - pdb=" SG CYS B 71 " distance=2.10 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.02 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 139 " distance=2.02 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 271 " distance=2.18 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 271 " distance=2.18 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 58 " " NAG A 502 " - " ASN A 163 " " NAG A 503 " - " ASN A 129 " " NAG B 501 " - " ASN B 58 " " NAG B 502 " - " ASN B 163 " " NAG B 503 " - " ASN B 129 " " NAG C 501 " - " ASN C 58 " " NAG C 502 " - " ASN C 163 " " NAG C 503 " - " ASN C 129 " Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 881.0 milliseconds 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1470 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 12 sheets defined 27.0% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 270 through 313 Processing helix chain 'B' and resid 60 through 67 Processing helix chain 'B' and resid 101 through 109 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 270 through 313 Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 101 through 109 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 270 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 119 removed outlier: 6.478A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 119 removed outlier: 6.478A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.469A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER A 146 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AA5, first strand: chain 'B' and resid 115 through 119 removed outlier: 6.478A pdb=" N TYR B 256 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 115 through 119 removed outlier: 6.478A pdb=" N TYR B 256 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 136 through 141 removed outlier: 4.470A pdb=" N CYS B 139 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER B 146 " --> pdb=" O CYS B 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AA9, first strand: chain 'C' and resid 115 through 119 removed outlier: 6.479A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 115 through 119 removed outlier: 6.479A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.470A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER C 146 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 164 through 169 309 hydrogen bonds defined for protein. 864 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: 2.10 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1182 1.33 - 1.45: 1482 1.45 - 1.57: 3267 1.57 - 1.69: 3 1.69 - 1.81: 18 Bond restraints: 5952 Sorted by residual: bond pdb=" C ALA C 52 " pdb=" N PRO C 53 " ideal model delta sigma weight residual 1.335 1.361 -0.026 9.40e-03 1.13e+04 7.48e+00 bond pdb=" C5 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.33e+00 bond pdb=" C5 NAG C 501 " pdb=" O5 NAG C 501 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" C ALA A 52 " pdb=" N PRO A 53 " ideal model delta sigma weight residual 1.335 1.360 -0.025 9.40e-03 1.13e+04 7.28e+00 bond pdb=" C5 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.28e+00 ... (remaining 5947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 6974 1.63 - 3.25: 1014 3.25 - 4.88: 106 4.88 - 6.50: 66 6.50 - 8.13: 27 Bond angle restraints: 8187 Sorted by residual: angle pdb=" C HIS A 184 " pdb=" N PRO A 185 " pdb=" CA PRO A 185 " ideal model delta sigma weight residual 119.66 126.50 -6.84 7.30e-01 1.88e+00 8.79e+01 angle pdb=" C HIS B 184 " pdb=" N PRO B 185 " pdb=" CA PRO B 185 " ideal model delta sigma weight residual 119.66 126.48 -6.82 7.30e-01 1.88e+00 8.73e+01 angle pdb=" C HIS C 184 " pdb=" N PRO C 185 " pdb=" CA PRO C 185 " ideal model delta sigma weight residual 119.66 126.44 -6.78 7.30e-01 1.88e+00 8.63e+01 angle pdb=" C ASN B 88 " pdb=" N PRO B 89 " pdb=" CA PRO B 89 " ideal model delta sigma weight residual 120.31 127.70 -7.39 9.80e-01 1.04e+00 5.69e+01 angle pdb=" C ASN A 88 " pdb=" N PRO A 89 " pdb=" CA PRO A 89 " ideal model delta sigma weight residual 120.31 127.67 -7.36 9.80e-01 1.04e+00 5.63e+01 ... (remaining 8182 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 3396 17.27 - 34.53: 87 34.53 - 51.80: 18 51.80 - 69.07: 0 69.07 - 86.33: 9 Dihedral angle restraints: 3510 sinusoidal: 1212 harmonic: 2298 Sorted by residual: dihedral pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " pdb=" SG CYS C 139 " pdb=" CB CYS C 139 " ideal model delta sinusoidal sigma weight residual 93.00 173.12 -80.12 1 1.00e+01 1.00e-02 7.95e+01 dihedral pdb=" CB CYS B 94 " pdb=" SG CYS B 94 " pdb=" SG CYS B 139 " pdb=" CB CYS B 139 " ideal model delta sinusoidal sigma weight residual 93.00 173.11 -80.11 1 1.00e+01 1.00e-02 7.95e+01 dihedral pdb=" CB CYS A 94 " pdb=" SG CYS A 94 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual 93.00 173.10 -80.10 1 1.00e+01 1.00e-02 7.95e+01 ... (remaining 3507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 659 0.065 - 0.130: 210 0.130 - 0.194: 52 0.194 - 0.259: 18 0.259 - 0.324: 9 Chirality restraints: 948 Sorted by residual: chirality pdb=" C2 NAG C 502 " pdb=" C1 NAG C 502 " pdb=" C3 NAG C 502 " pdb=" N2 NAG C 502 " both_signs ideal model delta sigma weight residual False -2.49 -2.82 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C2 NAG B 502 " pdb=" C1 NAG B 502 " pdb=" C3 NAG B 502 " pdb=" N2 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.49 -2.81 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C2 NAG A 502 " pdb=" C1 NAG A 502 " pdb=" C3 NAG A 502 " pdb=" N2 NAG A 502 " both_signs ideal model delta sigma weight residual False -2.49 -2.81 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 945 not shown) Planarity restraints: 1041 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 232 " 0.025 2.00e-02 2.50e+03 1.36e-02 3.72e+00 pdb=" CG TYR C 232 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR C 232 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR C 232 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR C 232 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 232 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 232 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 232 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 232 " 0.025 2.00e-02 2.50e+03 1.36e-02 3.71e+00 pdb=" CG TYR B 232 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR B 232 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 232 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 232 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 232 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 232 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 232 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 232 " 0.025 2.00e-02 2.50e+03 1.36e-02 3.68e+00 pdb=" CG TYR A 232 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 232 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 232 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 232 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 232 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 232 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 232 " 0.020 2.00e-02 2.50e+03 ... (remaining 1038 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 529 2.75 - 3.28: 5585 3.28 - 3.82: 9305 3.82 - 4.36: 10789 4.36 - 4.90: 17958 Nonbonded interactions: 44166 Sorted by model distance: nonbonded pdb=" CB PRO A 53 " pdb=" CE1 TYR A 82 " model vdw 2.207 3.740 nonbonded pdb=" CB PRO B 53 " pdb=" CE1 TYR B 82 " model vdw 2.207 3.740 nonbonded pdb=" CB PRO C 53 " pdb=" CE1 TYR C 82 " model vdw 2.207 3.740 nonbonded pdb=" O GLU A 309 " pdb=" N ASN A 312 " model vdw 2.399 3.120 nonbonded pdb=" O GLU C 309 " pdb=" N ASN C 312 " model vdw 2.399 3.120 ... (remaining 44161 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.360 Find NCS groups from input model: 0.170 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:3.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 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 : 0.010 0.151 5970 Z= 0.577 Angle : 1.291 8.129 8232 Z= 0.894 Chirality : 0.075 0.324 948 Planarity : 0.005 0.018 1032 Dihedral : 9.351 86.333 2013 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.66 % Allowed : 3.31 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.27), residues: 783 helix: 0.32 (0.34), residues: 201 sheet: 1.20 (0.31), residues: 198 loop : -1.30 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 80 HIS 0.003 0.001 HIS A 130 PHE 0.013 0.003 PHE B 115 TYR 0.025 0.005 TYR B 232 ARG 0.002 0.000 ARG C 117 Details of bonding type rmsd link_NAG-ASN : bond 0.05673 ( 9) link_NAG-ASN : angle 1.97272 ( 27) hydrogen bonds : bond 0.18673 ( 285) hydrogen bonds : angle 8.48611 ( 864) SS BOND : bond 0.09473 ( 9) SS BOND : angle 3.80456 ( 18) covalent geometry : bond 0.00917 ( 5952) covalent geometry : angle 1.27745 ( 8187) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 158 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 TYR cc_start: 0.9012 (t80) cc_final: 0.8386 (t80) REVERT: B 172 LYS cc_start: 0.8808 (mmtt) cc_final: 0.8595 (mmtt) REVERT: B 223 VAL cc_start: 0.9057 (t) cc_final: 0.8570 (p) REVERT: B 229 ARG cc_start: 0.8526 (mmt-90) cc_final: 0.8225 (mmt90) REVERT: B 295 HIS cc_start: 0.8473 (t70) cc_final: 0.7975 (t-170) REVERT: C 102 TYR cc_start: 0.9060 (t80) cc_final: 0.8738 (t80) REVERT: C 147 PHE cc_start: 0.6582 (t80) cc_final: 0.6143 (t80) REVERT: C 172 LYS cc_start: 0.8734 (mmtt) cc_final: 0.8519 (mmmt) outliers start: 3 outliers final: 0 residues processed: 161 average time/residue: 0.2484 time to fit residues: 49.5224 Evaluate side-chains 92 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS B 108 GLN C 130 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.184371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.153057 restraints weight = 8068.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.150886 restraints weight = 12531.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.152224 restraints weight = 9189.899| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5970 Z= 0.165 Angle : 0.645 7.816 8232 Z= 0.341 Chirality : 0.046 0.198 948 Planarity : 0.004 0.026 1032 Dihedral : 7.263 97.385 1038 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.65 % Allowed : 13.69 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.28), residues: 783 helix: 1.53 (0.36), residues: 210 sheet: 1.21 (0.33), residues: 204 loop : -1.19 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 153 HIS 0.004 0.001 HIS C 183 PHE 0.027 0.002 PHE A 115 TYR 0.014 0.002 TYR C 195 ARG 0.004 0.001 ARG A 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 9) link_NAG-ASN : angle 2.70384 ( 27) hydrogen bonds : bond 0.07183 ( 285) hydrogen bonds : angle 6.27343 ( 864) SS BOND : bond 0.00220 ( 9) SS BOND : angle 1.23311 ( 18) covalent geometry : bond 0.00365 ( 5952) covalent geometry : angle 0.62490 ( 8187) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 256 TYR cc_start: 0.8588 (m-80) cc_final: 0.8382 (m-80) REVERT: C 172 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8562 (mmtt) outliers start: 12 outliers final: 10 residues processed: 115 average time/residue: 0.2127 time to fit residues: 31.4733 Evaluate side-chains 99 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 302 HIS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 55 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 33 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 58 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 170 ASN A 191 GLN A 250 ASN B 191 GLN B 250 ASN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN C 250 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.186162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.155528 restraints weight = 8202.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.154488 restraints weight = 10013.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.154949 restraints weight = 8352.636| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5970 Z= 0.123 Angle : 0.570 8.240 8232 Z= 0.300 Chirality : 0.044 0.207 948 Planarity : 0.004 0.026 1032 Dihedral : 7.012 99.146 1038 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.09 % Allowed : 13.47 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.29), residues: 783 helix: 1.94 (0.36), residues: 210 sheet: 1.09 (0.34), residues: 195 loop : -1.15 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 153 HIS 0.010 0.001 HIS B 295 PHE 0.028 0.002 PHE A 115 TYR 0.017 0.002 TYR A 195 ARG 0.004 0.001 ARG C 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 9) link_NAG-ASN : angle 2.04202 ( 27) hydrogen bonds : bond 0.05811 ( 285) hydrogen bonds : angle 5.63123 ( 864) SS BOND : bond 0.00170 ( 9) SS BOND : angle 1.14330 ( 18) covalent geometry : bond 0.00253 ( 5952) covalent geometry : angle 0.55695 ( 8187) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8610 (mp) cc_final: 0.8365 (mp) REVERT: B 82 TYR cc_start: 0.7140 (p90) cc_final: 0.6649 (p90) REVERT: C 168 TYR cc_start: 0.7772 (t80) cc_final: 0.7460 (t80) outliers start: 14 outliers final: 8 residues processed: 103 average time/residue: 0.2230 time to fit residues: 29.7170 Evaluate side-chains 81 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 0.0970 chunk 21 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.183108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.151141 restraints weight = 8316.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.151141 restraints weight = 12893.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.151141 restraints weight = 12893.180| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 5970 Z= 0.139 Angle : 0.565 8.475 8232 Z= 0.297 Chirality : 0.044 0.257 948 Planarity : 0.004 0.029 1032 Dihedral : 6.826 96.230 1038 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.09 % Allowed : 15.89 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.29), residues: 783 helix: 1.90 (0.37), residues: 210 sheet: 0.91 (0.36), residues: 189 loop : -1.11 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 64 HIS 0.006 0.001 HIS B 295 PHE 0.025 0.002 PHE B 115 TYR 0.018 0.001 TYR C 195 ARG 0.009 0.001 ARG B 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 9) link_NAG-ASN : angle 1.86402 ( 27) hydrogen bonds : bond 0.05415 ( 285) hydrogen bonds : angle 5.56336 ( 864) SS BOND : bond 0.00534 ( 9) SS BOND : angle 1.88763 ( 18) covalent geometry : bond 0.00316 ( 5952) covalent geometry : angle 0.54924 ( 8187) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 93 average time/residue: 0.1928 time to fit residues: 24.0751 Evaluate side-chains 80 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN C 130 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.183141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.151539 restraints weight = 8236.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.149852 restraints weight = 11714.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.151615 restraints weight = 8723.867| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 5970 Z= 0.139 Angle : 0.621 11.437 8232 Z= 0.321 Chirality : 0.046 0.295 948 Planarity : 0.004 0.024 1032 Dihedral : 6.813 94.214 1038 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.43 % Allowed : 15.23 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.30), residues: 783 helix: 2.09 (0.38), residues: 204 sheet: 0.80 (0.37), residues: 189 loop : -1.06 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 127 HIS 0.006 0.001 HIS B 295 PHE 0.026 0.002 PHE A 115 TYR 0.021 0.001 TYR C 195 ARG 0.004 0.001 ARG C 305 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 9) link_NAG-ASN : angle 1.78540 ( 27) hydrogen bonds : bond 0.05225 ( 285) hydrogen bonds : angle 5.62861 ( 864) SS BOND : bond 0.00526 ( 9) SS BOND : angle 3.67362 ( 18) covalent geometry : bond 0.00320 ( 5952) covalent geometry : angle 0.58906 ( 8187) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8865 (ttp-110) cc_final: 0.8451 (tmm-80) REVERT: B 82 TYR cc_start: 0.7088 (p90) cc_final: 0.6602 (p90) REVERT: C 168 TYR cc_start: 0.7370 (t80) cc_final: 0.7092 (t80) REVERT: C 305 ARG cc_start: 0.7601 (mmt90) cc_final: 0.7253 (tpp-160) outliers start: 11 outliers final: 10 residues processed: 86 average time/residue: 0.2293 time to fit residues: 25.3122 Evaluate side-chains 79 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 75 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 HIS C 130 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.180697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.149538 restraints weight = 8274.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.148128 restraints weight = 11598.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.149955 restraints weight = 9123.621| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5970 Z= 0.145 Angle : 0.584 8.473 8232 Z= 0.308 Chirality : 0.044 0.197 948 Planarity : 0.004 0.024 1032 Dihedral : 6.572 89.302 1038 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.31 % Allowed : 14.35 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.30), residues: 783 helix: 1.92 (0.39), residues: 207 sheet: 0.73 (0.37), residues: 189 loop : -1.01 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 180 HIS 0.006 0.001 HIS B 295 PHE 0.027 0.002 PHE A 115 TYR 0.024 0.002 TYR A 195 ARG 0.004 0.001 ARG C 305 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 9) link_NAG-ASN : angle 1.67487 ( 27) hydrogen bonds : bond 0.04878 ( 285) hydrogen bonds : angle 5.52801 ( 864) SS BOND : bond 0.00437 ( 9) SS BOND : angle 2.49776 ( 18) covalent geometry : bond 0.00335 ( 5952) covalent geometry : angle 0.56553 ( 8187) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8809 (ttp-110) cc_final: 0.8024 (tmm-80) REVERT: B 82 TYR cc_start: 0.7083 (p90) cc_final: 0.6647 (p90) REVERT: B 102 TYR cc_start: 0.9302 (t80) cc_final: 0.8843 (t80) REVERT: C 168 TYR cc_start: 0.7456 (t80) cc_final: 0.7236 (t80) outliers start: 15 outliers final: 12 residues processed: 93 average time/residue: 0.1905 time to fit residues: 22.9597 Evaluate side-chains 83 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 26 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 65 optimal weight: 0.0970 chunk 14 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.182356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.151179 restraints weight = 8298.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.149485 restraints weight = 11890.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.151352 restraints weight = 8836.998| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5970 Z= 0.121 Angle : 0.565 8.569 8232 Z= 0.293 Chirality : 0.044 0.189 948 Planarity : 0.003 0.027 1032 Dihedral : 6.418 86.453 1038 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.99 % Allowed : 16.56 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.30), residues: 783 helix: 2.01 (0.39), residues: 207 sheet: 0.77 (0.38), residues: 189 loop : -0.98 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 180 HIS 0.004 0.001 HIS C 295 PHE 0.027 0.002 PHE A 115 TYR 0.023 0.001 TYR A 195 ARG 0.006 0.001 ARG A 305 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 9) link_NAG-ASN : angle 1.65770 ( 27) hydrogen bonds : bond 0.04574 ( 285) hydrogen bonds : angle 5.45155 ( 864) SS BOND : bond 0.00329 ( 9) SS BOND : angle 2.11412 ( 18) covalent geometry : bond 0.00272 ( 5952) covalent geometry : angle 0.54947 ( 8187) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8817 (ttp-110) cc_final: 0.8069 (tmm-80) REVERT: A 208 HIS cc_start: 0.6954 (m90) cc_final: 0.6687 (m90) REVERT: B 66 LEU cc_start: 0.8659 (mp) cc_final: 0.8454 (mt) REVERT: B 82 TYR cc_start: 0.7224 (p90) cc_final: 0.6847 (p90) REVERT: B 102 TYR cc_start: 0.9301 (t80) cc_final: 0.8825 (t80) REVERT: B 168 TYR cc_start: 0.7175 (t80) cc_final: 0.6893 (t80) REVERT: C 106 ARG cc_start: 0.8540 (ttp-110) cc_final: 0.8152 (ttp-170) REVERT: C 168 TYR cc_start: 0.7586 (t80) cc_final: 0.7171 (t80) outliers start: 9 outliers final: 8 residues processed: 86 average time/residue: 0.1936 time to fit residues: 21.5439 Evaluate side-chains 80 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.180059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.149863 restraints weight = 8245.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.148219 restraints weight = 11852.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.148697 restraints weight = 10060.383| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5970 Z= 0.134 Angle : 0.574 8.445 8232 Z= 0.298 Chirality : 0.044 0.196 948 Planarity : 0.003 0.025 1032 Dihedral : 6.287 82.729 1038 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.94 % Favored : 96.93 % Rotamer: Outliers : 1.77 % Allowed : 17.66 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.30), residues: 783 helix: 1.96 (0.39), residues: 207 sheet: 0.78 (0.39), residues: 189 loop : -1.03 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 180 HIS 0.004 0.001 HIS C 295 PHE 0.027 0.002 PHE A 115 TYR 0.021 0.002 TYR A 195 ARG 0.004 0.001 ARG B 305 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 9) link_NAG-ASN : angle 1.65754 ( 27) hydrogen bonds : bond 0.04532 ( 285) hydrogen bonds : angle 5.41417 ( 864) SS BOND : bond 0.00395 ( 9) SS BOND : angle 2.26027 ( 18) covalent geometry : bond 0.00314 ( 5952) covalent geometry : angle 0.55761 ( 8187) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.9331 (t80) cc_final: 0.8748 (t80) REVERT: A 106 ARG cc_start: 0.8771 (ttp-110) cc_final: 0.7909 (tmm-80) REVERT: A 208 HIS cc_start: 0.6842 (m90) cc_final: 0.6604 (m90) REVERT: A 304 GLU cc_start: 0.7788 (tt0) cc_final: 0.7581 (tp30) REVERT: B 82 TYR cc_start: 0.7163 (p90) cc_final: 0.6820 (p90) REVERT: B 102 TYR cc_start: 0.9342 (t80) cc_final: 0.8874 (t80) REVERT: B 106 ARG cc_start: 0.8884 (tmm-80) cc_final: 0.8469 (ttp-110) REVERT: C 168 TYR cc_start: 0.7435 (t80) cc_final: 0.6996 (t80) REVERT: C 304 GLU cc_start: 0.8172 (tp30) cc_final: 0.7539 (tp30) outliers start: 8 outliers final: 8 residues processed: 91 average time/residue: 0.1878 time to fit residues: 22.2542 Evaluate side-chains 84 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 0.0470 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.180093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.149749 restraints weight = 8340.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.147673 restraints weight = 12046.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.148466 restraints weight = 10027.057| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5970 Z= 0.115 Angle : 0.555 8.514 8232 Z= 0.289 Chirality : 0.044 0.179 948 Planarity : 0.003 0.026 1032 Dihedral : 6.159 79.621 1038 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.43 % Favored : 97.32 % Rotamer: Outliers : 1.77 % Allowed : 17.66 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.30), residues: 783 helix: 2.02 (0.39), residues: 207 sheet: 0.86 (0.39), residues: 189 loop : -1.03 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 180 HIS 0.004 0.001 HIS C 295 PHE 0.028 0.002 PHE A 115 TYR 0.040 0.001 TYR B 168 ARG 0.003 0.000 ARG C 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 9) link_NAG-ASN : angle 1.67523 ( 27) hydrogen bonds : bond 0.04429 ( 285) hydrogen bonds : angle 5.35781 ( 864) SS BOND : bond 0.00321 ( 9) SS BOND : angle 2.09122 ( 18) covalent geometry : bond 0.00261 ( 5952) covalent geometry : angle 0.53946 ( 8187) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.9281 (t80) cc_final: 0.8679 (t80) REVERT: A 106 ARG cc_start: 0.8787 (ttp-110) cc_final: 0.7954 (tmm-80) REVERT: A 208 HIS cc_start: 0.6859 (m90) cc_final: 0.6639 (m90) REVERT: A 304 GLU cc_start: 0.7934 (tt0) cc_final: 0.7709 (tp30) REVERT: B 82 TYR cc_start: 0.7151 (p90) cc_final: 0.6810 (p90) REVERT: B 102 TYR cc_start: 0.9340 (t80) cc_final: 0.8903 (t80) REVERT: B 106 ARG cc_start: 0.8881 (tmm-80) cc_final: 0.8459 (ttp-110) REVERT: C 168 TYR cc_start: 0.7585 (t80) cc_final: 0.7248 (t80) REVERT: C 304 GLU cc_start: 0.8010 (tp30) cc_final: 0.7559 (tp30) outliers start: 8 outliers final: 8 residues processed: 87 average time/residue: 0.1828 time to fit residues: 21.3041 Evaluate side-chains 82 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 26 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.181889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.151665 restraints weight = 8390.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.149875 restraints weight = 11351.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.150816 restraints weight = 9319.003| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5970 Z= 0.118 Angle : 0.558 8.448 8232 Z= 0.290 Chirality : 0.044 0.185 948 Planarity : 0.003 0.027 1032 Dihedral : 6.031 76.330 1038 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.30 % Favored : 97.32 % Rotamer: Outliers : 1.77 % Allowed : 17.88 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.30), residues: 783 helix: 2.05 (0.39), residues: 207 sheet: 0.84 (0.39), residues: 189 loop : -1.06 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 180 HIS 0.004 0.001 HIS C 295 PHE 0.028 0.002 PHE A 115 TYR 0.018 0.001 TYR C 195 ARG 0.003 0.000 ARG C 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 9) link_NAG-ASN : angle 1.71014 ( 27) hydrogen bonds : bond 0.04335 ( 285) hydrogen bonds : angle 5.30888 ( 864) SS BOND : bond 0.00364 ( 9) SS BOND : angle 2.03825 ( 18) covalent geometry : bond 0.00269 ( 5952) covalent geometry : angle 0.54198 ( 8187) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.9260 (t80) cc_final: 0.8664 (t80) REVERT: A 106 ARG cc_start: 0.8774 (ttp-110) cc_final: 0.7954 (tmm-80) REVERT: A 208 HIS cc_start: 0.6890 (m90) cc_final: 0.6687 (m90) REVERT: A 304 GLU cc_start: 0.7822 (tt0) cc_final: 0.7601 (tp30) REVERT: B 82 TYR cc_start: 0.7142 (p90) cc_final: 0.6786 (p90) REVERT: B 102 TYR cc_start: 0.9316 (t80) cc_final: 0.8861 (t80) REVERT: B 106 ARG cc_start: 0.8853 (tmm-80) cc_final: 0.8437 (ttp-110) REVERT: B 255 TRP cc_start: 0.8406 (t60) cc_final: 0.8134 (t60) REVERT: C 168 TYR cc_start: 0.7571 (t80) cc_final: 0.7240 (t80) outliers start: 8 outliers final: 8 residues processed: 89 average time/residue: 0.1565 time to fit residues: 18.9168 Evaluate side-chains 87 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.178621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.148446 restraints weight = 8420.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.147051 restraints weight = 11010.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.147766 restraints weight = 9165.198| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5970 Z= 0.123 Angle : 0.555 8.296 8232 Z= 0.289 Chirality : 0.044 0.177 948 Planarity : 0.003 0.027 1032 Dihedral : 5.913 72.307 1038 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.04 % Favored : 97.57 % Rotamer: Outliers : 1.77 % Allowed : 17.66 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.30), residues: 783 helix: 2.06 (0.39), residues: 207 sheet: 0.75 (0.39), residues: 189 loop : -1.09 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 180 HIS 0.004 0.001 HIS C 295 PHE 0.028 0.002 PHE A 115 TYR 0.017 0.001 TYR C 195 ARG 0.003 0.000 ARG C 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 9) link_NAG-ASN : angle 1.75437 ( 27) hydrogen bonds : bond 0.04317 ( 285) hydrogen bonds : angle 5.32658 ( 864) SS BOND : bond 0.00320 ( 9) SS BOND : angle 2.10573 ( 18) covalent geometry : bond 0.00285 ( 5952) covalent geometry : angle 0.53849 ( 8187) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2095.30 seconds wall clock time: 37 minutes 48.56 seconds (2268.56 seconds total)