Starting phenix.real_space_refine on Wed Sep 17 10:02:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xdg_38277/09_2025/8xdg_38277_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xdg_38277/09_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_38277/09_2025/8xdg_38277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xdg_38277/09_2025/8xdg_38277.map" model { file = "/net/cci-nas-00/data/ceres_data/8xdg_38277/09_2025/8xdg_38277_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xdg_38277/09_2025/8xdg_38277_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.084 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 4, 'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 45 Restraints were copied for chains: B, C Time building chain proxies: 1.83, per 1000 atoms: 0.23 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: 0.65 Conformation dependent library (CDL) restraints added in 434.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.28 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: 1.23 Time building geometry restraints manager: 0.88 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.670 Find NCS groups from input model: 0.070 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.620 ------------------------------------------------------------------------------- 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= 0.674 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (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 ARG 0.001 0.000 ARG C 169 TYR 0.022 0.002 TYR C 320 PHE 0.048 0.002 PHE C 36 TRP 0.009 0.001 TRP A 170 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00983 ( 8187) covalent geometry : angle 1.00854 (11214) hydrogen bonds : bond 0.15888 ( 541) hydrogen bonds : angle 5.82943 ( 1587) *********************** 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 : 0.305 Fit side-chains REVERT: A 38 SER cc_start: 0.8387 (t) cc_final: 0.8170 (p) REVERT: A 104 ILE cc_start: 0.8011 (mm) cc_final: 0.7781 (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: 0.7849 (ptt) REVERT: C 38 SER cc_start: 0.8484 (t) cc_final: 0.8202 (p) REVERT: C 89 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.7036 (mmm160) outliers start: 6 outliers final: 2 residues processed: 179 average time/residue: 0.1122 time to fit residues: 26.2040 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 : 0.292 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.117870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.105070 restraints weight = 11210.521| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.36 r_work: 0.3099 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8187 Z= 0.143 Angle : 0.527 5.749 11214 Z= 0.282 Chirality : 0.040 0.128 1281 Planarity : 0.004 0.036 1371 Dihedral : 5.649 59.648 1121 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.91 % Allowed : 10.81 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.26), residues: 1044 helix: 1.67 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -0.50 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 223 TYR 0.011 0.001 TYR A 123 PHE 0.018 0.001 PHE A 101 TRP 0.008 0.001 TRP C 90 HIS 0.004 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8187) covalent geometry : angle 0.52681 (11214) hydrogen bonds : bond 0.04449 ( 541) hydrogen bonds : angle 4.09248 ( 1587) *********************** 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 158 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.280 Fit side-chains REVERT: A 38 SER cc_start: 0.8434 (t) cc_final: 0.8199 (p) REVERT: A 104 ILE cc_start: 0.8195 (mm) cc_final: 0.7974 (mt) REVERT: A 171 ASP cc_start: 0.8850 (t0) cc_final: 0.8639 (t0) REVERT: B 47 TRP cc_start: 0.7282 (t60) cc_final: 0.7019 (t60) REVERT: B 67 GLN cc_start: 0.8529 (tt0) cc_final: 0.8173 (tt0) REVERT: B 89 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.6791 (mmm160) REVERT: B 267 MET cc_start: 0.8329 (ptm) cc_final: 0.8036 (ptt) REVERT: C 48 MET cc_start: 0.8406 (mmm) cc_final: 0.8105 (tpt) REVERT: C 150 ILE cc_start: 0.8963 (mm) cc_final: 0.8754 (mt) REVERT: C 224 SER cc_start: 0.8476 (t) cc_final: 0.8176 (p) outliers start: 15 outliers final: 0 residues processed: 150 average time/residue: 0.1155 time to fit residues: 22.5531 Evaluate side-chains 137 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 37 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3294 r_free = 0.3294 target = 0.113701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.101069 restraints weight = 11263.362| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.33 r_work: 0.3036 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8187 Z= 0.199 Angle : 0.561 5.871 11214 Z= 0.297 Chirality : 0.042 0.133 1281 Planarity : 0.004 0.036 1371 Dihedral : 4.542 57.730 1111 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.53 % Allowed : 13.49 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.26), residues: 1044 helix: 1.52 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -0.64 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 223 TYR 0.013 0.002 TYR C 287 PHE 0.014 0.001 PHE A 101 TRP 0.009 0.001 TRP B 170 HIS 0.004 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 8187) covalent geometry : angle 0.56096 (11214) hydrogen bonds : bond 0.04789 ( 541) hydrogen bonds : angle 4.10075 ( 1587) *********************** 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 138 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.307 Fit side-chains REVERT: A 38 SER cc_start: 0.8368 (t) cc_final: 0.8158 (p) REVERT: A 89 ARG cc_start: 0.7018 (mmm160) cc_final: 0.6797 (mpt180) REVERT: A 104 ILE cc_start: 0.8123 (mm) cc_final: 0.7899 (mt) REVERT: A 171 ASP cc_start: 0.8870 (t0) cc_final: 0.8634 (t0) REVERT: A 320 TYR cc_start: 0.9086 (OUTLIER) cc_final: 0.7675 (t80) REVERT: A 329 MET cc_start: 0.8689 (mmm) cc_final: 0.8424 (mtt) REVERT: B 47 TRP cc_start: 0.7144 (t60) cc_final: 0.6853 (t60) REVERT: B 67 GLN cc_start: 0.8588 (tt0) cc_final: 0.8258 (tt0) REVERT: B 89 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.6908 (mmt90) REVERT: B 320 TYR cc_start: 0.8949 (OUTLIER) cc_final: 0.7991 (t80) REVERT: B 329 MET cc_start: 0.8757 (mmm) cc_final: 0.8521 (mtt) REVERT: C 150 ILE cc_start: 0.8995 (mm) cc_final: 0.8775 (mt) REVERT: C 224 SER cc_start: 0.8470 (t) cc_final: 0.8208 (p) REVERT: C 329 MET cc_start: 0.8806 (mmm) cc_final: 0.8418 (mtt) outliers start: 12 outliers final: 3 residues processed: 134 average time/residue: 0.1057 time to fit residues: 18.6543 Evaluate side-chains 130 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 120 LEU Chi-restraints excluded: chain B residue 320 TYR Chi-restraints excluded: chain C residue 307 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 102 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 95 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.115089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.102584 restraints weight = 11489.871| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.35 r_work: 0.3055 rms_B_bonded: 1.81 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: 0.8410 moved from start: 0.2660 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= 0.149 Angle : 0.516 5.832 11214 Z= 0.271 Chirality : 0.039 0.132 1281 Planarity : 0.004 0.036 1371 Dihedral : 4.400 54.739 1111 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.54 % Allowed : 13.74 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.26), residues: 1044 helix: 1.88 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -0.66 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 223 TYR 0.010 0.001 TYR C 287 PHE 0.012 0.001 PHE A 101 TRP 0.007 0.001 TRP C 90 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8187) covalent geometry : angle 0.51618 (11214) hydrogen bonds : bond 0.04239 ( 541) hydrogen bonds : angle 3.95466 ( 1587) *********************** 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 149 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.182 Fit side-chains REVERT: A 38 SER cc_start: 0.8333 (t) cc_final: 0.8077 (p) REVERT: A 89 ARG cc_start: 0.7143 (mmm160) cc_final: 0.6700 (mpt180) REVERT: A 171 ASP cc_start: 0.8852 (t0) cc_final: 0.8610 (t0) REVERT: A 320 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.7718 (t80) REVERT: A 329 MET cc_start: 0.8679 (mmm) cc_final: 0.8436 (mtt) REVERT: B 89 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.6848 (mmt90) REVERT: B 320 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.7997 (t80) REVERT: C 150 ILE cc_start: 0.8978 (mm) cc_final: 0.8764 (mt) REVERT: C 224 SER cc_start: 0.8459 (t) cc_final: 0.8175 (p) REVERT: C 329 MET cc_start: 0.8744 (mmm) cc_final: 0.8500 (mtt) outliers start: 20 outliers final: 7 residues processed: 144 average time/residue: 0.0949 time to fit residues: 18.1177 Evaluate side-chains 138 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 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 91 optimal weight: 0.5980 chunk 41 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 72 ASN C 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.103101 restraints weight = 11344.472| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.34 r_work: 0.3075 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2820 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= 0.133 Angle : 0.511 6.095 11214 Z= 0.267 Chirality : 0.039 0.132 1281 Planarity : 0.004 0.033 1371 Dihedral : 4.302 52.882 1111 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.16 % Allowed : 13.23 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.26), residues: 1044 helix: 1.99 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -0.60 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 223 TYR 0.009 0.001 TYR C 287 PHE 0.011 0.001 PHE A 101 TRP 0.006 0.001 TRP B 90 HIS 0.002 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8187) covalent geometry : angle 0.51138 (11214) hydrogen bonds : bond 0.04049 ( 541) hydrogen bonds : angle 3.88306 ( 1587) *********************** 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 141 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.220 Fit side-chains REVERT: A 38 SER cc_start: 0.8356 (t) cc_final: 0.8129 (p) REVERT: A 89 ARG cc_start: 0.7248 (mmm160) cc_final: 0.6679 (mpt180) REVERT: A 320 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.7753 (t80) REVERT: A 329 MET cc_start: 0.8690 (mmm) cc_final: 0.8481 (mtt) REVERT: B 89 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.6766 (mmt90) REVERT: B 320 TYR cc_start: 0.8944 (OUTLIER) cc_final: 0.8060 (t80) REVERT: C 224 SER cc_start: 0.8438 (t) cc_final: 0.8146 (p) REVERT: C 249 PHE cc_start: 0.8310 (t80) cc_final: 0.8096 (t80) outliers start: 17 outliers final: 10 residues processed: 138 average time/residue: 0.1084 time to fit residues: 19.8078 Evaluate side-chains 137 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 72 ASN 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 64 optimal weight: 0.8980 chunk 54 optimal weight: 0.0270 chunk 86 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 87 optimal weight: 0.0370 chunk 27 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.118571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.106304 restraints weight = 11302.977| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.35 r_work: 0.3106 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8187 Z= 0.113 Angle : 0.493 5.734 11214 Z= 0.256 Chirality : 0.038 0.131 1281 Planarity : 0.003 0.033 1371 Dihedral : 4.189 51.283 1111 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.53 % Allowed : 13.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.26), residues: 1044 helix: 2.15 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -0.53 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 223 TYR 0.008 0.001 TYR B 123 PHE 0.008 0.001 PHE C 249 TRP 0.006 0.001 TRP B 90 HIS 0.003 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8187) covalent geometry : angle 0.49326 (11214) hydrogen bonds : bond 0.03761 ( 541) hydrogen bonds : angle 3.78612 ( 1587) *********************** 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 143 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.281 Fit side-chains REVERT: A 38 SER cc_start: 0.8354 (t) cc_final: 0.8114 (p) REVERT: A 89 ARG cc_start: 0.7254 (mmm160) cc_final: 0.6656 (mpt180) REVERT: A 320 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.7762 (t80) REVERT: A 374 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7572 (mtm-85) REVERT: B 89 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.6711 (mmt90) REVERT: B 320 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8115 (t80) REVERT: C 223 ARG cc_start: 0.7487 (ttt-90) cc_final: 0.7281 (ttt-90) REVERT: C 224 SER cc_start: 0.8369 (t) cc_final: 0.8028 (p) REVERT: C 249 PHE cc_start: 0.8298 (t80) cc_final: 0.8087 (t80) outliers start: 12 outliers final: 7 residues processed: 140 average time/residue: 0.1042 time to fit residues: 19.3738 Evaluate side-chains 137 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 304 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 19 optimal weight: 0.9990 chunk 46 optimal weight: 0.0980 chunk 11 optimal weight: 0.0020 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.3342 r_free = 0.3342 target = 0.117633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.105011 restraints weight = 11281.927| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.42 r_work: 0.3086 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8187 Z= 0.126 Angle : 0.503 5.895 11214 Z= 0.259 Chirality : 0.038 0.132 1281 Planarity : 0.003 0.032 1371 Dihedral : 4.156 50.372 1111 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.65 % Allowed : 15.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.26), residues: 1044 helix: 2.14 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -0.42 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 223 TYR 0.009 0.001 TYR C 287 PHE 0.007 0.001 PHE C 249 TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8187) covalent geometry : angle 0.50288 (11214) hydrogen bonds : bond 0.03861 ( 541) hydrogen bonds : angle 3.80337 ( 1587) *********************** 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 137 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.286 Fit side-chains REVERT: A 38 SER cc_start: 0.8436 (t) cc_final: 0.8137 (p) REVERT: A 89 ARG cc_start: 0.7241 (mmm160) cc_final: 0.6541 (mpt180) REVERT: A 320 TYR cc_start: 0.9001 (OUTLIER) cc_final: 0.7770 (t80) REVERT: A 374 ARG cc_start: 0.7903 (mtm-85) cc_final: 0.7548 (mtm-85) REVERT: B 89 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.6717 (mmt90) REVERT: B 320 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.8122 (t80) REVERT: C 223 ARG cc_start: 0.7484 (ttt-90) cc_final: 0.7250 (ttt-90) REVERT: C 224 SER cc_start: 0.8405 (t) cc_final: 0.8012 (p) outliers start: 13 outliers final: 8 residues processed: 135 average time/residue: 0.1045 time to fit residues: 18.8148 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 : 0.287 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 8 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.100007 restraints weight = 11471.416| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.41 r_work: 0.3017 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8187 Z= 0.212 Angle : 0.577 6.671 11214 Z= 0.299 Chirality : 0.042 0.139 1281 Planarity : 0.004 0.034 1371 Dihedral : 4.380 50.840 1111 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.78 % Allowed : 15.27 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.26), residues: 1044 helix: 1.90 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -0.51 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 223 TYR 0.013 0.002 TYR A 287 PHE 0.011 0.001 PHE B 348 TRP 0.008 0.001 TRP A 47 HIS 0.005 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 8187) covalent geometry : angle 0.57748 (11214) hydrogen bonds : bond 0.04629 ( 541) hydrogen bonds : angle 4.07831 ( 1587) *********************** 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 134 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.275 Fit side-chains REVERT: A 38 SER cc_start: 0.8462 (t) cc_final: 0.8246 (p) REVERT: A 89 ARG cc_start: 0.7065 (mmm160) cc_final: 0.6655 (mpt180) REVERT: A 320 TYR cc_start: 0.9075 (OUTLIER) cc_final: 0.7538 (t80) REVERT: B 89 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.6763 (mmt90) REVERT: B 320 TYR cc_start: 0.9038 (OUTLIER) cc_final: 0.8006 (t80) REVERT: C 224 SER cc_start: 0.8493 (t) cc_final: 0.8187 (p) outliers start: 14 outliers final: 9 residues processed: 133 average time/residue: 0.1079 time to fit residues: 18.9293 Evaluate side-chains 131 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 309 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 102 optimal weight: 0.0470 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.114467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.102116 restraints weight = 11322.036| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.35 r_work: 0.3062 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3019 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= 0.142 Angle : 0.525 5.778 11214 Z= 0.271 Chirality : 0.039 0.139 1281 Planarity : 0.004 0.036 1371 Dihedral : 4.265 49.112 1111 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.40 % Allowed : 15.78 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.26), residues: 1044 helix: 1.86 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -0.46 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 223 TYR 0.010 0.001 TYR C 287 PHE 0.017 0.001 PHE C 249 TRP 0.009 0.001 TRP A 47 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8187) covalent geometry : angle 0.52519 (11214) hydrogen bonds : bond 0.04058 ( 541) hydrogen bonds : angle 3.92458 ( 1587) *********************** 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 130 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.289 Fit side-chains REVERT: A 38 SER cc_start: 0.8436 (t) cc_final: 0.8225 (p) REVERT: A 89 ARG cc_start: 0.6954 (mmm160) cc_final: 0.6713 (mpt180) REVERT: A 187 MET cc_start: 0.8573 (mtp) cc_final: 0.8369 (mtp) REVERT: A 320 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.7643 (t80) REVERT: A 374 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7621 (mtm-85) REVERT: B 89 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6768 (mmt90) REVERT: B 320 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.8078 (t80) REVERT: C 224 SER cc_start: 0.8462 (t) cc_final: 0.8176 (p) REVERT: C 249 PHE cc_start: 0.8392 (t80) cc_final: 0.8165 (t80) REVERT: C 371 GLN cc_start: 0.8401 (tm-30) cc_final: 0.8197 (tp40) outliers start: 11 outliers final: 8 residues processed: 129 average time/residue: 0.1123 time to fit residues: 18.8997 Evaluate side-chains 130 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.0870 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 102 optimal weight: 0.4980 chunk 50 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.116427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.104039 restraints weight = 11265.354| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.40 r_work: 0.3088 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8187 Z= 0.118 Angle : 0.512 5.885 11214 Z= 0.263 Chirality : 0.038 0.135 1281 Planarity : 0.004 0.036 1371 Dihedral : 4.171 47.997 1111 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.53 % Allowed : 16.16 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.26), residues: 1044 helix: 2.00 (0.19), residues: 759 sheet: None (None), residues: 0 loop : -0.48 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 223 TYR 0.008 0.001 TYR B 368 PHE 0.015 0.001 PHE C 249 TRP 0.007 0.001 TRP B 90 HIS 0.002 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8187) covalent geometry : angle 0.51154 (11214) hydrogen bonds : bond 0.03791 ( 541) hydrogen bonds : angle 3.83150 ( 1587) ********************** 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 133 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.345 Fit side-chains REVERT: A 38 SER cc_start: 0.8429 (t) cc_final: 0.8166 (p) REVERT: A 89 ARG cc_start: 0.7117 (mmm160) cc_final: 0.6569 (mpt180) REVERT: A 320 TYR cc_start: 0.9026 (OUTLIER) cc_final: 0.7684 (t80) REVERT: A 374 ARG cc_start: 0.7930 (mtm-85) cc_final: 0.7596 (mtm-85) REVERT: B 89 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.6728 (mmt90) REVERT: B 320 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.8123 (t80) REVERT: C 223 ARG cc_start: 0.7500 (ttt-90) cc_final: 0.7292 (ttt-90) REVERT: C 224 SER cc_start: 0.8385 (t) cc_final: 0.8010 (p) outliers start: 12 outliers final: 8 residues processed: 131 average time/residue: 0.0892 time to fit residues: 15.5630 Evaluate side-chains 131 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 66 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3296 r_free = 0.3296 target = 0.113934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.101407 restraints weight = 11467.325| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.42 r_work: 0.3034 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8187 Z= 0.175 Angle : 0.553 6.320 11214 Z= 0.287 Chirality : 0.040 0.135 1281 Planarity : 0.004 0.035 1371 Dihedral : 4.270 48.909 1111 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.65 % Allowed : 16.41 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.26), residues: 1044 helix: 1.84 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -0.48 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 223 TYR 0.012 0.001 TYR A 287 PHE 0.024 0.001 PHE C 249 TRP 0.008 0.001 TRP A 47 HIS 0.004 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 8187) covalent geometry : angle 0.55288 (11214) hydrogen bonds : bond 0.04300 ( 541) hydrogen bonds : angle 3.97668 ( 1587) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1809.86 seconds wall clock time: 31 minutes 48.92 seconds (1908.92 seconds total)