Starting phenix.real_space_refine on Wed Feb 12 12:56:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xdg_38277/02_2025/8xdg_38277_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xdg_38277/02_2025/8xdg_38277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xdg_38277/02_2025/8xdg_38277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xdg_38277/02_2025/8xdg_38277.map" model { file = "/net/cci-nas-00/data/ceres_data/8xdg_38277/02_2025/8xdg_38277_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xdg_38277/02_2025/8xdg_38277_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.084 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 69 5.16 5 C 5286 2.51 5 N 1272 2.21 5 O 1311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7938 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2646 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 14, 'TRANS': 335} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'TRP:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Restraints were copied for chains: C, B Time building chain proxies: 4.87, per 1000 atoms: 0.61 Number of scatterers: 7938 At special positions: 0 Unit cell: (97.06, 101.28, 70.685, 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 69 16.00 O 1311 8.00 N 1272 7.00 C 5286 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: 1.94 Conformation dependent library (CDL) restraints added in 1.1 seconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 77.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 41 through 51 removed outlier: 3.734A pdb=" N GLY A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN A 51 " --> pdb=" O TRP A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 66 removed outlier: 3.626A pdb=" N GLY A 64 " --> pdb=" O TRP A 60 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 70 Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 88 through 109 Processing helix chain 'A' and resid 122 through 135 Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 145 through 168 Proline residue: A 157 - end of helix Processing helix chain 'A' and resid 176 through 191 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 217 through 231 removed outlier: 4.615A pdb=" N ILE A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Proline residue: A 226 - end of helix Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 237 through 252 Processing helix chain 'A' and resid 252 through 273 Processing helix chain 'A' and resid 276 through 283 Processing helix chain 'A' and resid 286 through 299 removed outlier: 3.568A pdb=" N GLY A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 330 Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.642A pdb=" N VAL A 366 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 380 Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 41 through 51 removed outlier: 3.734A pdb=" N GLY B 50 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN B 51 " --> pdb=" O TRP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 66 removed outlier: 3.626A pdb=" N GLY B 64 " --> pdb=" O TRP B 60 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 70 Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 88 through 109 Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 145 through 168 Proline residue: B 157 - end of helix Processing helix chain 'B' and resid 176 through 191 Processing helix chain 'B' and resid 212 through 216 Processing helix chain 'B' and resid 217 through 231 removed outlier: 4.616A pdb=" N ILE B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Proline residue: B 226 - end of helix Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 237 through 252 Processing helix chain 'B' and resid 252 through 273 Processing helix chain 'B' and resid 276 through 283 Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.568A pdb=" N GLY B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 330 Processing helix chain 'B' and resid 338 through 349 Processing helix chain 'B' and resid 362 through 366 removed outlier: 3.642A pdb=" N VAL B 366 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 380 Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 41 through 51 removed outlier: 3.735A pdb=" N GLY C 50 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN C 51 " --> pdb=" O TRP C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 66 removed outlier: 3.626A pdb=" N GLY C 64 " --> pdb=" O TRP C 60 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 70 Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 88 through 109 Processing helix chain 'C' and resid 122 through 135 Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 145 through 168 Proline residue: C 157 - end of helix Processing helix chain 'C' and resid 176 through 191 Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 217 through 231 removed outlier: 4.615A pdb=" N ILE C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Proline residue: C 226 - end of helix Processing helix chain 'C' and resid 232 through 234 No H-bonds generated for 'chain 'C' and resid 232 through 234' Processing helix chain 'C' and resid 237 through 252 Processing helix chain 'C' and resid 252 through 273 Processing helix chain 'C' and resid 276 through 283 Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.569A pdb=" N GLY C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 330 Processing helix chain 'C' and resid 338 through 349 Processing helix chain 'C' and resid 362 through 366 removed outlier: 3.641A pdb=" N VAL C 366 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 380 541 hydrogen bonds defined for protein. 1587 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: 2.29 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1158 1.29 - 1.42: 2430 1.42 - 1.55: 4491 1.55 - 1.68: 0 1.68 - 1.81: 108 Bond restraints: 8187 Sorted by residual: bond pdb=" CA ALA C 189 " pdb=" C ALA C 189 " ideal model delta sigma weight residual 1.524 1.413 0.111 1.28e-02 6.10e+03 7.53e+01 bond pdb=" CA ALA A 189 " pdb=" C ALA A 189 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.28e-02 6.10e+03 7.42e+01 bond pdb=" CA ALA B 189 " pdb=" C ALA B 189 " ideal model delta sigma weight residual 1.524 1.415 0.110 1.28e-02 6.10e+03 7.38e+01 bond pdb=" CA PHE C 44 " pdb=" C PHE C 44 " ideal model delta sigma weight residual 1.523 1.440 0.084 1.30e-02 5.92e+03 4.14e+01 bond pdb=" CA PHE A 44 " pdb=" C PHE A 44 " ideal model delta sigma weight residual 1.523 1.440 0.084 1.30e-02 5.92e+03 4.14e+01 ... (remaining 8182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 10760 2.28 - 4.57: 349 4.57 - 6.85: 78 6.85 - 9.13: 18 9.13 - 11.42: 9 Bond angle restraints: 11214 Sorted by residual: angle pdb=" N ALA C 42 " pdb=" CA ALA C 42 " pdb=" C ALA C 42 " ideal model delta sigma weight residual 111.28 122.70 -11.42 1.09e+00 8.42e-01 1.10e+02 angle pdb=" N ALA A 42 " pdb=" CA ALA A 42 " pdb=" C ALA A 42 " ideal model delta sigma weight residual 111.28 122.63 -11.35 1.09e+00 8.42e-01 1.08e+02 angle pdb=" N ALA B 42 " pdb=" CA ALA B 42 " pdb=" C ALA B 42 " ideal model delta sigma weight residual 111.28 122.61 -11.33 1.09e+00 8.42e-01 1.08e+02 angle pdb=" N PHE A 44 " pdb=" CA PHE A 44 " pdb=" C PHE A 44 " ideal model delta sigma weight residual 111.28 100.94 10.34 1.09e+00 8.42e-01 8.99e+01 angle pdb=" N PHE B 44 " pdb=" CA PHE B 44 " pdb=" C PHE B 44 " ideal model delta sigma weight residual 111.28 100.96 10.32 1.09e+00 8.42e-01 8.96e+01 ... (remaining 11209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.00: 4044 14.00 - 28.00: 369 28.00 - 42.01: 129 42.01 - 56.01: 24 56.01 - 70.01: 3 Dihedral angle restraints: 4569 sinusoidal: 1560 harmonic: 3009 Sorted by residual: dihedral pdb=" C VAL B 188 " pdb=" N VAL B 188 " pdb=" CA VAL B 188 " pdb=" CB VAL B 188 " ideal model delta harmonic sigma weight residual -122.00 -132.29 10.29 0 2.50e+00 1.60e-01 1.69e+01 dihedral pdb=" C VAL A 188 " pdb=" N VAL A 188 " pdb=" CA VAL A 188 " pdb=" CB VAL A 188 " ideal model delta harmonic sigma weight residual -122.00 -132.24 10.24 0 2.50e+00 1.60e-01 1.68e+01 dihedral pdb=" C VAL C 188 " pdb=" N VAL C 188 " pdb=" CA VAL C 188 " pdb=" CB VAL C 188 " ideal model delta harmonic sigma weight residual -122.00 -132.21 10.21 0 2.50e+00 1.60e-01 1.67e+01 ... (remaining 4566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1171 0.112 - 0.224: 68 0.224 - 0.336: 27 0.336 - 0.448: 12 0.448 - 0.560: 3 Chirality restraints: 1281 Sorted by residual: chirality pdb=" CA MET A 187 " pdb=" N MET A 187 " pdb=" C MET A 187 " pdb=" CB MET A 187 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.83e+00 chirality pdb=" CA MET C 187 " pdb=" N MET C 187 " pdb=" C MET C 187 " pdb=" CB MET C 187 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.82e+00 chirality pdb=" CA MET B 187 " pdb=" N MET B 187 " pdb=" C MET B 187 " pdb=" CB MET B 187 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.80e+00 ... (remaining 1278 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 40 " -0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C ASP C 40 " 0.068 2.00e-02 2.50e+03 pdb=" O ASP C 40 " -0.025 2.00e-02 2.50e+03 pdb=" N MET C 41 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 40 " -0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C ASP A 40 " 0.068 2.00e-02 2.50e+03 pdb=" O ASP A 40 " -0.025 2.00e-02 2.50e+03 pdb=" N MET A 41 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 40 " -0.020 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C ASP B 40 " 0.067 2.00e-02 2.50e+03 pdb=" O ASP B 40 " -0.025 2.00e-02 2.50e+03 pdb=" N MET B 41 " -0.023 2.00e-02 2.50e+03 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 3776 2.96 - 3.44: 8669 3.44 - 3.93: 13400 3.93 - 4.41: 16085 4.41 - 4.90: 24807 Nonbonded interactions: 66737 Sorted by model distance: nonbonded pdb=" OG SER C 105 " pdb=" O MET C 154 " model vdw 2.471 3.040 nonbonded pdb=" OG SER A 105 " pdb=" O MET A 154 " model vdw 2.472 3.040 nonbonded pdb=" OG SER B 105 " pdb=" O MET B 154 " model vdw 2.472 3.040 nonbonded pdb=" ND1 HIS A 186 " pdb=" OH TYR B 320 " model vdw 2.515 3.120 nonbonded pdb=" N PHE A 44 " pdb=" N GLY A 45 " model vdw 2.516 2.560 ... (remaining 66732 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: 0.05 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 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.030 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 0.111 8187 Z= 0.643 Angle : 1.009 11.417 11214 Z= 0.692 Chirality : 0.080 0.560 1281 Planarity : 0.005 0.039 1371 Dihedral : 12.827 70.008 2649 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.76 % Allowed : 2.67 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.26), residues: 1044 helix: 1.51 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -0.46 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 170 HIS 0.004 0.001 HIS B 186 PHE 0.048 0.002 PHE C 36 TYR 0.022 0.002 TYR C 320 ARG 0.001 0.000 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 178 time to evaluate : 0.872 Fit side-chains REVERT: A 38 SER cc_start: 0.8387 (t) cc_final: 0.8174 (p) REVERT: A 104 ILE cc_start: 0.8011 (mm) cc_final: 0.7782 (mt) REVERT: B 89 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6972 (mmm160) REVERT: B 267 MET cc_start: 0.8049 (ptm) cc_final: 0.7848 (ptt) REVERT: C 38 SER cc_start: 0.8484 (t) cc_final: 0.8201 (p) REVERT: C 89 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.7037 (mmm160) outliers start: 6 outliers final: 2 residues processed: 179 average time/residue: 0.2398 time to fit residues: 55.7927 Evaluate side-chains 134 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 89 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.116000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.102849 restraints weight = 11218.748| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.41 r_work: 0.3059 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8187 Z= 0.283 Angle : 0.549 5.820 11214 Z= 0.294 Chirality : 0.041 0.127 1281 Planarity : 0.004 0.036 1371 Dihedral : 5.678 58.429 1121 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.04 % Allowed : 10.56 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1044 helix: 1.61 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -0.53 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 170 HIS 0.004 0.001 HIS A 359 PHE 0.018 0.001 PHE A 101 TYR 0.012 0.002 TYR A 123 ARG 0.003 0.000 ARG C 223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.799 Fit side-chains REVERT: A 38 SER cc_start: 0.8369 (t) cc_final: 0.8098 (p) REVERT: A 104 ILE cc_start: 0.8060 (mm) cc_final: 0.7811 (mt) REVERT: A 171 ASP cc_start: 0.8884 (t0) cc_final: 0.8652 (t0) REVERT: B 47 TRP cc_start: 0.7220 (t60) cc_final: 0.6988 (t60) REVERT: B 67 GLN cc_start: 0.8616 (tt0) cc_final: 0.8181 (tt0) REVERT: B 89 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.6731 (mmm160) REVERT: B 201 LEU cc_start: 0.8141 (tp) cc_final: 0.7841 (tp) REVERT: B 203 GLN cc_start: 0.8619 (mm110) cc_final: 0.8185 (mt0) REVERT: B 267 MET cc_start: 0.8388 (ptm) cc_final: 0.8075 (ptt) REVERT: C 38 SER cc_start: 0.8391 (t) cc_final: 0.8147 (p) REVERT: C 48 MET cc_start: 0.8420 (mmm) cc_final: 0.8123 (tpt) REVERT: C 150 ILE cc_start: 0.8918 (mm) cc_final: 0.8700 (mt) REVERT: C 224 SER cc_start: 0.8471 (t) cc_final: 0.8175 (p) outliers start: 16 outliers final: 1 residues processed: 148 average time/residue: 0.2349 time to fit residues: 45.0213 Evaluate side-chains 136 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain C residue 267 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 18 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 43 optimal weight: 7.9990 chunk 12 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: A 67 GLN B 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.102606 restraints weight = 11289.067| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.35 r_work: 0.3073 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8187 Z= 0.244 Angle : 0.521 5.818 11214 Z= 0.275 Chirality : 0.040 0.128 1281 Planarity : 0.004 0.037 1371 Dihedral : 4.413 57.224 1111 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.91 % Allowed : 12.85 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.26), residues: 1044 helix: 1.69 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -0.64 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 90 HIS 0.003 0.001 HIS A 359 PHE 0.013 0.001 PHE A 101 TYR 0.011 0.001 TYR C 287 ARG 0.003 0.001 ARG C 223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.806 Fit side-chains REVERT: A 38 SER cc_start: 0.8342 (t) cc_final: 0.8125 (p) REVERT: A 89 ARG cc_start: 0.7159 (mmm160) cc_final: 0.6725 (mpt180) REVERT: A 320 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.7756 (t80) REVERT: A 329 MET cc_start: 0.8682 (mmm) cc_final: 0.8455 (mtt) REVERT: B 47 TRP cc_start: 0.7143 (t60) cc_final: 0.6791 (t60) REVERT: B 89 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6854 (mmt90) REVERT: B 320 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.8056 (t80) REVERT: B 329 MET cc_start: 0.8715 (mmm) cc_final: 0.8485 (mtt) REVERT: C 150 ILE cc_start: 0.8976 (mm) cc_final: 0.8759 (mt) REVERT: C 224 SER cc_start: 0.8473 (t) cc_final: 0.8160 (p) REVERT: C 329 MET cc_start: 0.8773 (mmm) cc_final: 0.8450 (mtt) outliers start: 15 outliers final: 1 residues processed: 141 average time/residue: 0.2350 time to fit residues: 43.5410 Evaluate side-chains 131 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 320 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 18 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN C 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.102199 restraints weight = 11336.533| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.34 r_work: 0.3055 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8187 Z= 0.262 Angle : 0.523 5.777 11214 Z= 0.274 Chirality : 0.040 0.130 1281 Planarity : 0.004 0.035 1371 Dihedral : 4.373 54.189 1111 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.54 % Allowed : 13.87 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.26), residues: 1044 helix: 1.90 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -0.65 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 90 HIS 0.003 0.001 HIS B 258 PHE 0.013 0.001 PHE A 101 TYR 0.011 0.001 TYR C 287 ARG 0.003 0.000 ARG C 223 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.906 Fit side-chains REVERT: A 89 ARG cc_start: 0.7151 (mmm160) cc_final: 0.6708 (mpt180) REVERT: A 171 ASP cc_start: 0.8860 (t0) cc_final: 0.8620 (t0) REVERT: A 320 TYR cc_start: 0.9073 (OUTLIER) cc_final: 0.7723 (t80) REVERT: A 329 MET cc_start: 0.8670 (mmm) cc_final: 0.8420 (mtt) REVERT: B 89 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.6829 (mmt90) REVERT: B 187 MET cc_start: 0.8780 (mtm) cc_final: 0.8521 (mtp) REVERT: B 320 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.8051 (t80) REVERT: C 150 ILE cc_start: 0.8984 (mm) cc_final: 0.8767 (mt) REVERT: C 224 SER cc_start: 0.8472 (t) cc_final: 0.8188 (p) REVERT: C 329 MET cc_start: 0.8760 (mmm) cc_final: 0.8523 (mtt) outliers start: 20 outliers final: 8 residues processed: 142 average time/residue: 0.2309 time to fit residues: 43.2533 Evaluate side-chains 134 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 320 TYR Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 304 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 58 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 7 optimal weight: 0.0040 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN C 56 GLN C 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.104646 restraints weight = 11217.796| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.34 r_work: 0.3084 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8187 Z= 0.201 Angle : 0.501 5.724 11214 Z= 0.263 Chirality : 0.038 0.131 1281 Planarity : 0.004 0.035 1371 Dihedral : 4.245 51.422 1111 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.16 % Allowed : 13.36 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.26), residues: 1044 helix: 2.04 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -0.57 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 90 HIS 0.002 0.001 HIS B 258 PHE 0.011 0.001 PHE A 249 TYR 0.009 0.001 TYR A 287 ARG 0.004 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.890 Fit side-chains REVERT: A 89 ARG cc_start: 0.7126 (mmm160) cc_final: 0.6704 (mpt180) REVERT: A 320 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.7797 (t80) REVERT: B 89 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.6759 (mmt90) REVERT: B 320 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8029 (t80) REVERT: C 187 MET cc_start: 0.8843 (mtm) cc_final: 0.8636 (mtp) REVERT: C 224 SER cc_start: 0.8418 (t) cc_final: 0.8100 (p) outliers start: 17 outliers final: 10 residues processed: 138 average time/residue: 0.2351 time to fit residues: 42.7156 Evaluate side-chains 139 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 320 TYR Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 304 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 67 GLN C 56 GLN C 67 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.099119 restraints weight = 11454.475| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.41 r_work: 0.3005 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8187 Z= 0.365 Angle : 0.577 6.416 11214 Z= 0.302 Chirality : 0.042 0.166 1281 Planarity : 0.004 0.036 1371 Dihedral : 4.439 50.194 1111 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.54 % Allowed : 13.10 % Favored : 84.35 % 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: 1.67 (0.26), residues: 1044 helix: 1.80 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -0.60 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 47 HIS 0.005 0.001 HIS B 258 PHE 0.012 0.001 PHE B 348 TYR 0.014 0.002 TYR A 287 ARG 0.004 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.782 Fit side-chains REVERT: A 89 ARG cc_start: 0.7030 (mmm160) cc_final: 0.6668 (mpt180) REVERT: A 320 TYR cc_start: 0.9119 (OUTLIER) cc_final: 0.7504 (t80) REVERT: B 89 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.6824 (mmt90) REVERT: B 187 MET cc_start: 0.8985 (mtm) cc_final: 0.8740 (mtp) REVERT: B 320 TYR cc_start: 0.9073 (OUTLIER) cc_final: 0.8028 (t80) REVERT: C 224 SER cc_start: 0.8517 (t) cc_final: 0.8222 (p) REVERT: C 357 PHE cc_start: 0.8050 (m-10) cc_final: 0.7817 (m-10) outliers start: 20 outliers final: 13 residues processed: 132 average time/residue: 0.2360 time to fit residues: 40.6984 Evaluate side-chains 131 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 320 TYR Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 307 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 67 GLN C 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.100924 restraints weight = 11447.328| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.35 r_work: 0.3048 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8187 Z= 0.243 Angle : 0.525 5.750 11214 Z= 0.274 Chirality : 0.039 0.131 1281 Planarity : 0.004 0.035 1371 Dihedral : 4.317 48.067 1111 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.16 % Allowed : 14.25 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.26), residues: 1044 helix: 1.93 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -0.54 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.003 0.001 HIS B 258 PHE 0.012 0.001 PHE C 249 TYR 0.010 0.001 TYR C 287 ARG 0.004 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.932 Fit side-chains REVERT: A 89 ARG cc_start: 0.7170 (mmm160) cc_final: 0.6722 (mpt180) REVERT: A 320 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.7578 (t80) REVERT: A 374 ARG cc_start: 0.7950 (mtm-85) cc_final: 0.7596 (mtm-85) REVERT: B 89 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.6758 (mmt90) REVERT: B 320 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.8059 (t80) REVERT: C 224 SER cc_start: 0.8474 (t) cc_final: 0.8190 (p) REVERT: C 357 PHE cc_start: 0.8025 (m-10) cc_final: 0.7808 (m-10) outliers start: 17 outliers final: 10 residues processed: 132 average time/residue: 0.2388 time to fit residues: 41.3433 Evaluate side-chains 131 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 320 TYR Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 304 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 75 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 81 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 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 67 GLN B 51 GLN C 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.101846 restraints weight = 11449.599| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.35 r_work: 0.3058 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8187 Z= 0.225 Angle : 0.515 5.730 11214 Z= 0.269 Chirality : 0.039 0.131 1281 Planarity : 0.004 0.034 1371 Dihedral : 4.258 48.377 1111 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.78 % Allowed : 15.01 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.26), residues: 1044 helix: 2.02 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -0.50 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.003 0.001 HIS B 258 PHE 0.008 0.001 PHE B 249 TYR 0.010 0.001 TYR C 287 ARG 0.004 0.001 ARG C 223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.886 Fit side-chains REVERT: A 48 MET cc_start: 0.8136 (tpt) cc_final: 0.7797 (mmm) REVERT: A 89 ARG cc_start: 0.7237 (mmm160) cc_final: 0.6660 (mpt180) REVERT: A 320 TYR cc_start: 0.9069 (OUTLIER) cc_final: 0.7642 (t80) REVERT: A 374 ARG cc_start: 0.7921 (mtm-85) cc_final: 0.7577 (mtm-85) REVERT: B 89 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.6727 (mmt90) REVERT: B 320 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.8119 (t80) REVERT: C 223 ARG cc_start: 0.7593 (ttt-90) cc_final: 0.7372 (ttt-90) REVERT: C 224 SER cc_start: 0.8460 (t) cc_final: 0.8168 (p) REVERT: C 357 PHE cc_start: 0.8048 (m-10) cc_final: 0.7835 (m-10) outliers start: 14 outliers final: 9 residues processed: 131 average time/residue: 0.2323 time to fit residues: 39.8764 Evaluate side-chains 130 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 320 TYR Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 309 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 21 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 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 67 GLN C 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.102232 restraints weight = 11607.459| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.36 r_work: 0.3063 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8187 Z= 0.224 Angle : 0.518 5.786 11214 Z= 0.270 Chirality : 0.039 0.137 1281 Planarity : 0.004 0.037 1371 Dihedral : 4.231 48.379 1111 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.78 % Allowed : 15.65 % Favored : 82.57 % 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: 2.02 (0.26), residues: 1044 helix: 2.05 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -0.46 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.002 0.001 HIS B 258 PHE 0.014 0.001 PHE C 249 TYR 0.010 0.001 TYR C 287 ARG 0.004 0.000 ARG C 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.822 Fit side-chains REVERT: A 48 MET cc_start: 0.8181 (tpt) cc_final: 0.7830 (mmm) REVERT: A 89 ARG cc_start: 0.7279 (mmm160) cc_final: 0.6664 (mpt180) REVERT: A 320 TYR cc_start: 0.9067 (OUTLIER) cc_final: 0.7638 (t80) REVERT: A 374 ARG cc_start: 0.7951 (mtm-85) cc_final: 0.7622 (mtm-85) REVERT: B 89 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6773 (mmt90) REVERT: B 320 TYR cc_start: 0.8990 (OUTLIER) cc_final: 0.8105 (t80) REVERT: C 223 ARG cc_start: 0.7589 (ttt-90) cc_final: 0.7367 (ttt-90) REVERT: C 224 SER cc_start: 0.8458 (t) cc_final: 0.8157 (p) REVERT: C 249 PHE cc_start: 0.8357 (t80) cc_final: 0.8106 (t80) REVERT: C 357 PHE cc_start: 0.8052 (m-10) cc_final: 0.7845 (m-10) outliers start: 14 outliers final: 9 residues processed: 131 average time/residue: 0.2370 time to fit residues: 40.8197 Evaluate side-chains 132 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 320 TYR Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 309 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 95 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 chunk 65 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN C 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.103243 restraints weight = 11436.431| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.35 r_work: 0.3060 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8187 Z= 0.226 Angle : 0.519 6.150 11214 Z= 0.270 Chirality : 0.039 0.134 1281 Planarity : 0.004 0.035 1371 Dihedral : 4.211 48.158 1111 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.65 % Allowed : 16.28 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.26), residues: 1044 helix: 2.06 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -0.45 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.002 0.001 HIS B 258 PHE 0.014 0.001 PHE C 249 TYR 0.010 0.001 TYR C 287 ARG 0.004 0.000 ARG B 223 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.857 Fit side-chains REVERT: A 48 MET cc_start: 0.8192 (tpt) cc_final: 0.7847 (mmm) REVERT: A 89 ARG cc_start: 0.7265 (mmm160) cc_final: 0.6656 (mpt180) REVERT: A 320 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.7629 (t80) REVERT: A 374 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7627 (mtm-85) REVERT: B 89 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6769 (mmt90) REVERT: B 320 TYR cc_start: 0.8984 (OUTLIER) cc_final: 0.8094 (t80) REVERT: C 224 SER cc_start: 0.8461 (t) cc_final: 0.8160 (p) REVERT: C 249 PHE cc_start: 0.8384 (t80) cc_final: 0.8164 (t80) REVERT: C 357 PHE cc_start: 0.8062 (m-10) cc_final: 0.7859 (m-10) outliers start: 13 outliers final: 9 residues processed: 133 average time/residue: 0.2450 time to fit residues: 42.4330 Evaluate side-chains 134 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 320 TYR Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 309 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 42 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 46 optimal weight: 0.0040 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 83 optimal weight: 0.1980 chunk 74 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN C 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.103103 restraints weight = 11503.525| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.37 r_work: 0.3073 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8187 Z= 0.207 Angle : 0.509 6.084 11214 Z= 0.265 Chirality : 0.039 0.134 1281 Planarity : 0.004 0.035 1371 Dihedral : 4.175 47.700 1111 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.53 % Allowed : 16.41 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.26), residues: 1044 helix: 2.09 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -0.44 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 90 HIS 0.002 0.001 HIS B 258 PHE 0.013 0.001 PHE C 249 TYR 0.009 0.001 TYR C 287 ARG 0.004 0.000 ARG B 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3658.85 seconds wall clock time: 65 minutes 48.75 seconds (3948.75 seconds total)