Starting phenix.real_space_refine on Fri Dec 27 14:14:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yi9_33854/12_2024/7yi9_33854.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yi9_33854/12_2024/7yi9_33854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yi9_33854/12_2024/7yi9_33854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yi9_33854/12_2024/7yi9_33854.map" model { file = "/net/cci-nas-00/data/ceres_data/7yi9_33854/12_2024/7yi9_33854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yi9_33854/12_2024/7yi9_33854.cif" } resolution = 2.6 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= 0.076 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 27 5.16 5 C 3335 2.51 5 N 892 2.21 5 O 972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5226 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2117 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain breaks: 2 Chain: "B" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1819 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain breaks: 1 Chain: "C" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 269 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "D" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 994 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Time building chain proxies: 3.59, per 1000 atoms: 0.69 Number of scatterers: 5226 At special positions: 0 Unit cell: (80.75, 68, 122.4, 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 27 16.00 O 972 8.00 N 892 7.00 C 3335 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: 1.23 Conformation dependent library (CDL) restraints added in 668.2 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1206 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 39.9% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 106 through 109 Processing helix chain 'A' and resid 165 through 170 removed outlier: 3.707A pdb=" N SER A 170 " --> pdb=" O ASN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 218 through 227 Processing helix chain 'A' and resid 320 through 334 Processing helix chain 'A' and resid 337 through 341 removed outlier: 4.321A pdb=" N SER A 340 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 402 through 414 Processing helix chain 'B' and resid 141 through 167 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 231 through 237 Processing helix chain 'B' and resid 239 through 244 removed outlier: 3.655A pdb=" N GLN B 244 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 257 through 268 Processing helix chain 'B' and resid 336 through 346 removed outlier: 3.701A pdb=" N GLN B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 removed outlier: 3.614A pdb=" N LEU B 361 " --> pdb=" O ARG B 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 removed outlier: 3.743A pdb=" N ASN C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 159' Processing helix chain 'C' and resid 169 through 183 removed outlier: 4.420A pdb=" N ALA C 175 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 26 Processing helix chain 'D' and resid 38 through 43 removed outlier: 3.750A pdb=" N PHE D 42 " --> pdb=" O ASN D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 66 Processing helix chain 'D' and resid 70 through 76 Processing helix chain 'D' and resid 83 through 96 removed outlier: 4.639A pdb=" N CYS D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 removed outlier: 3.744A pdb=" N TYR D 104 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 125 through 129 removed outlier: 4.037A pdb=" N ASN D 128 " --> pdb=" O LYS D 125 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 129 removed outlier: 6.227A pdb=" N ALA A 146 " --> pdb=" O MET A 430 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU A 432 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE A 148 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TRP A 187 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 182 " --> pdb=" O ARG A 367 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR A 361 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A 364 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 209 " --> pdb=" O MET A 364 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ARG A 366 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N TYR A 207 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 177 through 180 removed outlier: 6.520A pdb=" N TYR B 351 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE B 368 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU B 353 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL B 205 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE B 354 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N MET B 207 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER B 301 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 306 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU B 272 " --> pdb=" O VAL B 306 " (cutoff:3.500A) 188 hydrogen bonds defined for protein. 528 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: 1.27 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1686 1.34 - 1.46: 761 1.46 - 1.57: 2824 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 5319 Sorted by residual: bond pdb=" C2 SAM B 401 " pdb=" N3 SAM B 401 " ideal model delta sigma weight residual 1.322 1.378 -0.056 2.00e-02 2.50e+03 7.88e+00 bond pdb=" C8 SAM B 401 " pdb=" N7 SAM B 401 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 7.10e+00 bond pdb=" C2 SAM B 401 " pdb=" N1 SAM B 401 " ideal model delta sigma weight residual 1.329 1.378 -0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" C6 SAM B 401 " pdb=" N1 SAM B 401 " ideal model delta sigma weight residual 1.337 1.377 -0.040 2.00e-02 2.50e+03 4.06e+00 bond pdb=" C1' SAM B 401 " pdb=" N9 SAM B 401 " ideal model delta sigma weight residual 1.452 1.478 -0.026 2.00e-02 2.50e+03 1.67e+00 ... (remaining 5314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 6987 1.78 - 3.56: 133 3.56 - 5.34: 17 5.34 - 7.12: 9 7.12 - 8.90: 3 Bond angle restraints: 7149 Sorted by residual: angle pdb=" N ILE A 337 " pdb=" CA ILE A 337 " pdb=" C ILE A 337 " ideal model delta sigma weight residual 111.90 107.94 3.96 8.10e-01 1.52e+00 2.38e+01 angle pdb=" C LEU D 87 " pdb=" N GLU D 88 " pdb=" CA GLU D 88 " ideal model delta sigma weight residual 122.38 115.48 6.90 1.81e+00 3.05e-01 1.45e+01 angle pdb=" CA GLU D 88 " pdb=" CB GLU D 88 " pdb=" CG GLU D 88 " ideal model delta sigma weight residual 114.10 120.20 -6.10 2.00e+00 2.50e-01 9.30e+00 angle pdb=" O SAM B 401 " pdb=" C SAM B 401 " pdb=" OXT SAM B 401 " ideal model delta sigma weight residual 126.77 117.87 8.90 3.00e+00 1.11e-01 8.79e+00 angle pdb=" N1 SAM B 401 " pdb=" C2 SAM B 401 " pdb=" N3 SAM B 401 " ideal model delta sigma weight residual 128.51 120.01 8.50 3.00e+00 1.11e-01 8.02e+00 ... (remaining 7144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 2898 17.48 - 34.95: 294 34.95 - 52.43: 61 52.43 - 69.90: 7 69.90 - 87.38: 8 Dihedral angle restraints: 3268 sinusoidal: 1413 harmonic: 1855 Sorted by residual: dihedral pdb=" CA LEU A 178 " pdb=" C LEU A 178 " pdb=" N MET A 179 " pdb=" CA MET A 179 " ideal model delta harmonic sigma weight residual -180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA MET A 402 " pdb=" C MET A 402 " pdb=" N LYS A 403 " pdb=" CA LYS A 403 " ideal model delta harmonic sigma weight residual 180.00 162.43 17.57 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA HIS A 379 " pdb=" C HIS A 379 " pdb=" N GLN A 380 " pdb=" CA GLN A 380 " ideal model delta harmonic sigma weight residual -180.00 -163.47 -16.53 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 2.218: 780 2.218 - 4.436: 0 4.436 - 6.654: 0 6.654 - 8.872: 0 8.872 - 11.090: 1 Chirality restraints: 781 Sorted by residual: chirality pdb=" SD SAM B 401 " pdb=" CG SAM B 401 " pdb=" CE SAM B 401 " pdb=" C5' SAM B 401 " both_signs ideal model delta sigma weight residual False 5.50 -5.59 11.09 2.00e-01 2.50e+01 3.07e+03 chirality pdb=" CA GLN B 161 " pdb=" N GLN B 161 " pdb=" C GLN B 161 " pdb=" CB GLN B 161 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" C2' SAM B 401 " pdb=" C1' SAM B 401 " pdb=" C3' SAM B 401 " pdb=" O2' SAM B 401 " both_signs ideal model delta sigma weight residual False -2.76 -2.59 -0.17 2.00e-01 2.50e+01 7.07e-01 ... (remaining 778 not shown) Planarity restraints: 909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 112 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO A 113 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 352 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO A 353 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 353 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 353 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 174 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO A 175 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " -0.020 5.00e-02 4.00e+02 ... (remaining 906 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 67 2.67 - 3.23: 4830 3.23 - 3.79: 7715 3.79 - 4.34: 11199 4.34 - 4.90: 17983 Nonbonded interactions: 41794 Sorted by model distance: nonbonded pdb=" O LEU C 164 " pdb=" OH TYR C 171 " model vdw 2.115 3.040 nonbonded pdb=" NE2 GLN A 380 " pdb=" O GLY B 292 " model vdw 2.193 3.120 nonbonded pdb=" OD1 ASN A 210 " pdb=" OG1 THR A 361 " model vdw 2.237 3.040 nonbonded pdb=" NE1 TRP A 153 " pdb=" O TRP A 187 " model vdw 2.255 3.120 nonbonded pdb=" OD2 ASP B 204 " pdb=" NH1 ARG B 314 " model vdw 2.260 3.120 ... (remaining 41789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.810 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 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 : 0.004 0.056 5319 Z= 0.232 Angle : 0.651 8.895 7149 Z= 0.340 Chirality : 0.399 11.090 781 Planarity : 0.004 0.054 909 Dihedral : 14.607 87.381 2062 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: -0.81 (0.33), residues: 620 helix: -0.03 (0.36), residues: 204 sheet: 0.53 (0.52), residues: 102 loop : -1.23 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 50 HIS 0.002 0.001 HIS C 169 PHE 0.014 0.002 PHE B 158 TYR 0.008 0.001 TYR B 258 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.622 Fit side-chains REVERT: B 371 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7381 (pp20) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 1.3917 time to fit residues: 146.2612 Evaluate side-chains 79 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 334 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 128 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5319 Z= 0.340 Angle : 0.675 6.697 7149 Z= 0.360 Chirality : 0.045 0.155 781 Planarity : 0.005 0.063 909 Dihedral : 7.286 58.431 707 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.12 % Allowed : 11.79 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.33), residues: 620 helix: -0.03 (0.36), residues: 212 sheet: 0.46 (0.50), residues: 103 loop : -1.47 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 212 HIS 0.003 0.001 HIS B 291 PHE 0.016 0.002 PHE B 250 TYR 0.011 0.002 TYR A 407 ARG 0.004 0.001 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.666 Fit side-chains REVERT: A 152 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7688 (tp) REVERT: A 326 GLN cc_start: 0.6515 (OUTLIER) cc_final: 0.5983 (pt0) REVERT: A 381 ARG cc_start: 0.7795 (mmm-85) cc_final: 0.7465 (mmt-90) REVERT: B 207 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7645 (ttp) REVERT: B 289 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7690 (mppt) REVERT: D 21 MET cc_start: 0.7970 (mmm) cc_final: 0.7764 (mmm) REVERT: D 88 GLU cc_start: 0.6154 (OUTLIER) cc_final: 0.5914 (pm20) REVERT: D 110 GLU cc_start: 0.6314 (OUTLIER) cc_final: 0.6042 (mp0) REVERT: D 114 GLU cc_start: 0.5474 (OUTLIER) cc_final: 0.4959 (tt0) outliers start: 18 outliers final: 5 residues processed: 83 average time/residue: 1.5368 time to fit residues: 133.1038 Evaluate side-chains 84 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 114 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 128 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5319 Z= 0.178 Angle : 0.533 5.257 7149 Z= 0.289 Chirality : 0.041 0.136 781 Planarity : 0.004 0.054 909 Dihedral : 6.618 57.814 707 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.12 % Allowed : 15.60 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.33), residues: 620 helix: 0.17 (0.36), residues: 219 sheet: 0.77 (0.50), residues: 103 loop : -1.44 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 212 HIS 0.002 0.001 HIS B 291 PHE 0.016 0.002 PHE B 158 TYR 0.008 0.001 TYR A 207 ARG 0.001 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.586 Fit side-chains REVERT: A 223 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.6476 (mt0) REVERT: A 381 ARG cc_start: 0.7830 (mmm-85) cc_final: 0.7582 (mmt-90) REVERT: B 207 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7562 (ttp) REVERT: B 289 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7548 (mppt) REVERT: B 371 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7351 (pp20) REVERT: B 372 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.6994 (tt) REVERT: D 114 GLU cc_start: 0.5360 (OUTLIER) cc_final: 0.4806 (tt0) outliers start: 18 outliers final: 6 residues processed: 81 average time/residue: 1.5298 time to fit residues: 129.0054 Evaluate side-chains 81 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain D residue 114 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5319 Z= 0.212 Angle : 0.544 6.452 7149 Z= 0.293 Chirality : 0.041 0.141 781 Planarity : 0.004 0.054 909 Dihedral : 6.481 55.194 707 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.33 % Allowed : 16.64 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.33), residues: 620 helix: 0.29 (0.36), residues: 214 sheet: 0.86 (0.51), residues: 98 loop : -1.26 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 212 HIS 0.003 0.001 HIS B 291 PHE 0.014 0.002 PHE B 250 TYR 0.008 0.001 TYR B 153 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.513 Fit side-chains REVERT: A 152 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7761 (tp) REVERT: A 223 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6482 (mt0) REVERT: B 171 MET cc_start: 0.5435 (pmm) cc_final: 0.4842 (pp-130) REVERT: B 207 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7635 (ttp) REVERT: B 289 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7629 (mppt) REVERT: B 372 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7147 (tt) REVERT: D 63 GLU cc_start: 0.6191 (pp20) cc_final: 0.5940 (tm-30) REVERT: D 84 ILE cc_start: 0.5808 (OUTLIER) cc_final: 0.5569 (tp) REVERT: D 88 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.5980 (pm20) REVERT: D 110 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5940 (mp0) REVERT: D 114 GLU cc_start: 0.5423 (OUTLIER) cc_final: 0.4915 (tt0) outliers start: 25 outliers final: 9 residues processed: 85 average time/residue: 1.3256 time to fit residues: 117.3613 Evaluate side-chains 92 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 114 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 360 HIS B 161 GLN B 213 GLN B 244 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 128 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 5319 Z= 0.335 Angle : 0.634 6.085 7149 Z= 0.341 Chirality : 0.044 0.157 781 Planarity : 0.005 0.056 909 Dihedral : 6.780 54.100 707 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.85 % Allowed : 16.81 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.33), residues: 620 helix: 0.01 (0.36), residues: 213 sheet: 0.49 (0.54), residues: 95 loop : -1.47 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 212 HIS 0.003 0.001 HIS B 291 PHE 0.014 0.002 PHE B 250 TYR 0.011 0.002 TYR B 153 ARG 0.005 0.001 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.610 Fit side-chains REVERT: A 152 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7744 (tp) REVERT: A 223 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6426 (mt0) REVERT: A 326 GLN cc_start: 0.6596 (OUTLIER) cc_final: 0.6242 (pt0) REVERT: A 376 GLU cc_start: 0.6144 (tm-30) cc_final: 0.5844 (tm-30) REVERT: A 429 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7125 (mtp) REVERT: B 371 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7381 (pp20) REVERT: B 372 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.6953 (tp) REVERT: D 63 GLU cc_start: 0.6245 (pp20) cc_final: 0.5912 (tm-30) REVERT: D 84 ILE cc_start: 0.6110 (OUTLIER) cc_final: 0.5711 (tp) REVERT: D 88 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5945 (pm20) REVERT: D 110 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.5902 (mp0) REVERT: D 114 GLU cc_start: 0.5464 (OUTLIER) cc_final: 0.5007 (tt0) outliers start: 28 outliers final: 10 residues processed: 91 average time/residue: 1.2853 time to fit residues: 121.9234 Evaluate side-chains 93 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 114 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5319 Z= 0.177 Angle : 0.527 6.940 7149 Z= 0.284 Chirality : 0.040 0.134 781 Planarity : 0.004 0.053 909 Dihedral : 6.153 44.543 707 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.16 % Allowed : 17.68 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.33), residues: 620 helix: 0.35 (0.37), residues: 213 sheet: 0.75 (0.52), residues: 98 loop : -1.35 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 212 HIS 0.002 0.001 HIS B 291 PHE 0.011 0.001 PHE B 250 TYR 0.007 0.001 TYR B 153 ARG 0.003 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.557 Fit side-chains REVERT: A 223 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6540 (mt0) REVERT: A 378 ARG cc_start: 0.5585 (OUTLIER) cc_final: 0.5015 (mmt-90) REVERT: B 171 MET cc_start: 0.5351 (pmm) cc_final: 0.4772 (pp-130) REVERT: B 372 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7075 (tt) REVERT: D 84 ILE cc_start: 0.5929 (OUTLIER) cc_final: 0.5643 (tp) REVERT: D 88 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.5946 (pm20) REVERT: D 110 GLU cc_start: 0.6177 (OUTLIER) cc_final: 0.5811 (mp0) REVERT: D 114 GLU cc_start: 0.5387 (OUTLIER) cc_final: 0.4865 (tt0) outliers start: 24 outliers final: 8 residues processed: 82 average time/residue: 1.2043 time to fit residues: 103.2214 Evaluate side-chains 84 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 114 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5319 Z= 0.215 Angle : 0.560 7.447 7149 Z= 0.300 Chirality : 0.041 0.144 781 Planarity : 0.004 0.052 909 Dihedral : 6.158 44.508 707 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.81 % Allowed : 18.54 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.33), residues: 620 helix: 0.60 (0.37), residues: 207 sheet: 0.70 (0.50), residues: 103 loop : -1.23 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 212 HIS 0.002 0.001 HIS B 291 PHE 0.016 0.002 PHE A 330 TYR 0.010 0.001 TYR A 207 ARG 0.003 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.620 Fit side-chains REVERT: A 152 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7743 (tp) REVERT: A 223 GLN cc_start: 0.7051 (OUTLIER) cc_final: 0.6493 (mt0) REVERT: A 376 GLU cc_start: 0.6111 (tm-30) cc_final: 0.5792 (tm-30) REVERT: A 378 ARG cc_start: 0.5602 (OUTLIER) cc_final: 0.5031 (mmt-90) REVERT: B 371 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7367 (pp20) REVERT: B 372 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7132 (tt) REVERT: D 84 ILE cc_start: 0.6048 (OUTLIER) cc_final: 0.5731 (tp) REVERT: D 88 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.6118 (pm20) REVERT: D 110 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.5834 (mp0) REVERT: D 114 GLU cc_start: 0.5397 (OUTLIER) cc_final: 0.4868 (tt0) outliers start: 22 outliers final: 8 residues processed: 82 average time/residue: 1.4162 time to fit residues: 120.6733 Evaluate side-chains 85 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 114 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 ASN D 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5319 Z= 0.311 Angle : 0.653 9.288 7149 Z= 0.345 Chirality : 0.043 0.151 781 Planarity : 0.005 0.054 909 Dihedral : 6.410 44.105 707 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.99 % Allowed : 18.02 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.33), residues: 620 helix: 0.23 (0.36), residues: 219 sheet: 0.59 (0.54), residues: 93 loop : -1.46 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 212 HIS 0.003 0.001 HIS B 291 PHE 0.014 0.002 PHE A 330 TYR 0.008 0.001 TYR B 339 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.563 Fit side-chains REVERT: A 152 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7765 (tp) REVERT: A 180 LYS cc_start: 0.7435 (mmmm) cc_final: 0.7037 (mmmt) REVERT: A 223 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6461 (mt0) REVERT: A 376 GLU cc_start: 0.6177 (tm-30) cc_final: 0.5875 (tm-30) REVERT: A 378 ARG cc_start: 0.5655 (OUTLIER) cc_final: 0.5076 (mmt-90) REVERT: A 429 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7207 (mtp) REVERT: B 171 MET cc_start: 0.5267 (pmm) cc_final: 0.4583 (pp-130) REVERT: B 371 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7359 (pp20) REVERT: B 372 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.6947 (tp) REVERT: D 84 ILE cc_start: 0.6129 (OUTLIER) cc_final: 0.5817 (tp) REVERT: D 88 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6189 (pm20) REVERT: D 110 GLU cc_start: 0.6180 (OUTLIER) cc_final: 0.5838 (mp0) REVERT: D 114 GLU cc_start: 0.5461 (OUTLIER) cc_final: 0.5002 (tt0) outliers start: 23 outliers final: 10 residues processed: 82 average time/residue: 1.3136 time to fit residues: 112.3645 Evaluate side-chains 87 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 114 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 GLN D 38 ASN D 128 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5319 Z= 0.201 Angle : 0.575 8.270 7149 Z= 0.304 Chirality : 0.041 0.137 781 Planarity : 0.004 0.052 909 Dihedral : 6.024 44.036 707 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.16 % Allowed : 18.37 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.33), residues: 620 helix: 0.37 (0.36), residues: 219 sheet: 0.81 (0.50), residues: 102 loop : -1.39 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 212 HIS 0.002 0.001 HIS B 291 PHE 0.013 0.001 PHE A 330 TYR 0.007 0.001 TYR B 258 ARG 0.003 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.662 Fit side-chains REVERT: A 152 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7769 (tp) REVERT: A 180 LYS cc_start: 0.7389 (mmmm) cc_final: 0.7048 (mmmt) REVERT: A 223 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.6481 (mt0) REVERT: A 376 GLU cc_start: 0.6192 (tm-30) cc_final: 0.5900 (tm-30) REVERT: A 378 ARG cc_start: 0.5683 (OUTLIER) cc_final: 0.5089 (mmt-90) REVERT: A 429 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7103 (mtp) REVERT: B 171 MET cc_start: 0.5318 (pmm) cc_final: 0.4707 (pp-130) REVERT: B 371 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7344 (pp20) REVERT: B 372 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7094 (tt) REVERT: D 84 ILE cc_start: 0.6083 (OUTLIER) cc_final: 0.5785 (tp) REVERT: D 88 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.6177 (pm20) REVERT: D 110 GLU cc_start: 0.6162 (OUTLIER) cc_final: 0.5834 (mp0) REVERT: D 114 GLU cc_start: 0.5394 (OUTLIER) cc_final: 0.4895 (tt0) outliers start: 24 outliers final: 11 residues processed: 83 average time/residue: 1.2813 time to fit residues: 110.9096 Evaluate side-chains 86 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 114 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 ASN D 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5319 Z= 0.216 Angle : 0.598 7.896 7149 Z= 0.317 Chirality : 0.041 0.141 781 Planarity : 0.004 0.053 909 Dihedral : 5.942 44.201 707 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.81 % Allowed : 19.06 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.33), residues: 620 helix: 0.49 (0.37), residues: 213 sheet: 0.73 (0.49), residues: 103 loop : -1.33 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 50 HIS 0.003 0.001 HIS B 291 PHE 0.013 0.001 PHE B 250 TYR 0.007 0.001 TYR B 258 ARG 0.003 0.000 ARG A 381 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.612 Fit side-chains REVERT: A 152 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7758 (tp) REVERT: A 180 LYS cc_start: 0.7510 (mmmm) cc_final: 0.7147 (mmmt) REVERT: A 223 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.6471 (mt0) REVERT: A 376 GLU cc_start: 0.6197 (tm-30) cc_final: 0.5917 (tm-30) REVERT: A 378 ARG cc_start: 0.5598 (OUTLIER) cc_final: 0.5032 (mmt-90) REVERT: A 429 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7088 (mtp) REVERT: B 171 MET cc_start: 0.5447 (pmm) cc_final: 0.4830 (pp-130) REVERT: B 371 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7347 (pp20) REVERT: B 372 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7109 (tt) REVERT: D 84 ILE cc_start: 0.6123 (OUTLIER) cc_final: 0.5802 (tp) REVERT: D 88 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.6151 (pm20) REVERT: D 110 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5810 (mp0) REVERT: D 114 GLU cc_start: 0.5412 (OUTLIER) cc_final: 0.4934 (tt0) outliers start: 22 outliers final: 11 residues processed: 79 average time/residue: 1.2947 time to fit residues: 106.7661 Evaluate side-chains 85 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 114 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 6 optimal weight: 0.0970 chunk 9 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 ASN D 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.193258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.145997 restraints weight = 6022.921| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.28 r_work: 0.3742 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5319 Z= 0.193 Angle : 0.582 7.438 7149 Z= 0.311 Chirality : 0.041 0.169 781 Planarity : 0.004 0.052 909 Dihedral : 5.791 44.199 707 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.81 % Allowed : 18.89 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.33), residues: 620 helix: 0.52 (0.37), residues: 213 sheet: 0.78 (0.49), residues: 102 loop : -1.22 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 212 HIS 0.003 0.001 HIS B 291 PHE 0.011 0.001 PHE B 250 TYR 0.007 0.001 TYR B 258 ARG 0.003 0.000 ARG A 381 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2437.68 seconds wall clock time: 45 minutes 23.34 seconds (2723.34 seconds total)