Starting phenix.real_space_refine on Thu Jul 2 01:26:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yi9_33854/07_2026/7yi9_33854.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yi9_33854/07_2026/7yi9_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 { model { file = "/net/cci-nas-00/data/ceres_data/7yi9_33854/07_2026/7yi9_33854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yi9_33854/07_2026/7yi9_33854.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yi9_33854/07_2026/7yi9_33854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yi9_33854/07_2026/7yi9_33854.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yi9_33854/07_2026/7yi9_33854.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yi9_33854/07_2026/7yi9_33854.cif" } resolution = 2.6 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= 0.076 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 1.22, per 1000 atoms: 0.23 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: 0.39 Conformation dependent library (CDL) restraints added in 148.9 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: 0.14 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: 0.49 Time building geometry restraints manager: 0.54 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: 2892 17.48 - 34.95: 276 34.95 - 52.43: 53 52.43 - 69.90: 7 69.90 - 87.38: 8 Dihedral angle restraints: 3236 sinusoidal: 1381 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 3233 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.110 Find NCS groups from input model: 0.020 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:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 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= 0.168 Angle : 0.651 8.895 7149 Z= 0.340 Chirality : 0.399 11.090 781 Planarity : 0.004 0.054 909 Dihedral : 14.290 87.381 2030 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.82 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.001 0.000 ARG A 349 TYR 0.008 0.001 TYR B 258 PHE 0.014 0.002 PHE B 158 TRP 0.008 0.001 TRP D 50 HIS 0.002 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 ( 5319) covalent geometry : angle 0.65079 / 0.34 ( 7149) hydrogen bonds : bond 0.17991 / 11.98 ( 188) hydrogen bonds : angle 7.02784 / 4.71 ( 528) *********************** 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 : 0.164 Fit side-chains REVERT: B 371 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7383 (pp20) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.5852 time to fit residues: 61.3510 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 : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.191785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.148205 restraints weight = 5983.744| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.38 r_work: 0.3721 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1427 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= 0.222 Angle : 0.673 6.658 7149 Z= 0.358 Chirality : 0.045 0.159 781 Planarity : 0.005 0.060 909 Dihedral : 5.305 17.903 675 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.33), residues: 620 helix: -0.03 (0.36), residues: 212 sheet: 0.45 (0.50), residues: 103 loop : -1.47 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 359 TYR 0.012 0.002 TYR A 407 PHE 0.016 0.002 PHE B 250 TRP 0.014 0.002 TRP B 212 HIS 0.003 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 ( 5319) covalent geometry : angle 0.67252 / 0.36 ( 7149) hydrogen bonds : bond 0.05127 / 3.34 ( 188) hydrogen bonds : angle 5.73796 / 3.78 ( 528) *********************** 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 96 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.209 Fit side-chains REVERT: A 152 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7821 (tp) REVERT: A 326 GLN cc_start: 0.6579 (OUTLIER) cc_final: 0.6161 (pt0) REVERT: A 381 ARG cc_start: 0.8177 (mmm-85) cc_final: 0.7748 (mmt-90) REVERT: B 289 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7647 (mppt) REVERT: D 21 MET cc_start: 0.8181 (mmm) cc_final: 0.7945 (mmm) REVERT: D 110 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.6153 (mp0) REVERT: D 114 GLU cc_start: 0.5416 (OUTLIER) cc_final: 0.4928 (tt0) outliers start: 18 outliers final: 5 residues processed: 84 average time/residue: 0.5513 time to fit residues: 48.2423 Evaluate side-chains 82 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 260 VAL Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 332 SER 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 50 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.193392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.150126 restraints weight = 6016.875| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.38 r_work: 0.3737 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5319 Z= 0.140 Angle : 0.561 5.525 7149 Z= 0.302 Chirality : 0.041 0.140 781 Planarity : 0.004 0.055 909 Dihedral : 4.954 17.792 675 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.81 % Allowed : 14.73 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.33), residues: 620 helix: 0.19 (0.36), residues: 214 sheet: 0.70 (0.50), residues: 102 loop : -1.33 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 158 TYR 0.007 0.001 TYR B 258 PHE 0.016 0.002 PHE B 158 TRP 0.010 0.001 TRP B 212 HIS 0.002 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 5319) covalent geometry : angle 0.56118 / 0.30 ( 7149) hydrogen bonds : bond 0.04142 / 2.67 ( 188) hydrogen bonds : angle 5.38102 / 3.52 ( 528) *********************** 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 97 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.154 Fit side-chains REVERT: A 152 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7824 (tp) REVERT: A 223 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.6411 (mt0) REVERT: A 326 GLN cc_start: 0.6508 (OUTLIER) cc_final: 0.6145 (pt0) REVERT: A 381 ARG cc_start: 0.8215 (mmm-85) cc_final: 0.7871 (mmt-90) REVERT: B 289 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7679 (mppt) REVERT: B 371 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7131 (pp20) REVERT: B 372 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7303 (tt) REVERT: D 88 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.6091 (pm20) REVERT: D 110 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.6105 (mp0) REVERT: D 114 GLU cc_start: 0.5366 (OUTLIER) cc_final: 0.4787 (tt0) outliers start: 22 outliers final: 8 residues processed: 83 average time/residue: 0.5917 time to fit residues: 51.0512 Evaluate side-chains 89 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL 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 326 GLN 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 264 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 372 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 chunk 45 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 360 HIS B 348 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.191001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.143111 restraints weight = 6007.749| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.28 r_work: 0.3706 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5319 Z= 0.177 Angle : 0.591 6.261 7149 Z= 0.318 Chirality : 0.043 0.145 781 Planarity : 0.005 0.056 909 Dihedral : 5.074 17.810 675 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.68 % Allowed : 15.94 % Favored : 79.38 % 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 are not related in a simple way. whole: -0.75 (0.33), residues: 620 helix: 0.11 (0.36), residues: 214 sheet: 0.63 (0.50), residues: 103 loop : -1.35 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 359 TYR 0.013 0.001 TYR B 153 PHE 0.014 0.002 PHE B 250 TRP 0.010 0.002 TRP B 212 HIS 0.003 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 5319) covalent geometry : angle 0.59145 / 0.32 ( 7149) hydrogen bonds : bond 0.04286 / 2.76 ( 188) hydrogen bonds : angle 5.35713 / 3.51 ( 528) *********************** 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 103 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.122 Fit side-chains REVERT: A 152 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7844 (tp) REVERT: A 223 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6427 (mt0) REVERT: A 326 GLN cc_start: 0.6539 (OUTLIER) cc_final: 0.6175 (pt0) REVERT: A 381 ARG cc_start: 0.8219 (mmm-85) cc_final: 0.7824 (mmt-90) REVERT: B 160 GLU cc_start: 0.6191 (tp30) cc_final: 0.5942 (tp30) REVERT: B 171 MET cc_start: 0.5671 (pmm) cc_final: 0.5106 (pp-130) REVERT: B 289 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7614 (mppt) REVERT: B 372 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7482 (tt) REVERT: D 63 GLU cc_start: 0.6164 (pp20) cc_final: 0.5849 (tm-30) REVERT: D 84 ILE cc_start: 0.5849 (OUTLIER) cc_final: 0.5621 (tp) REVERT: D 88 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.6118 (pm20) REVERT: D 110 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.6100 (mp0) REVERT: D 114 GLU cc_start: 0.5415 (OUTLIER) cc_final: 0.4919 (tt0) outliers start: 27 outliers final: 11 residues processed: 87 average time/residue: 0.4508 time to fit residues: 40.7468 Evaluate side-chains 97 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 B residue 183 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 264 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 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 93 MET 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 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 161 GLN B 348 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 128 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.193738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.146146 restraints weight = 6122.731| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.30 r_work: 0.3743 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1934 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= 0.113 Angle : 0.519 5.080 7149 Z= 0.283 Chirality : 0.040 0.159 781 Planarity : 0.004 0.053 909 Dihedral : 4.758 16.776 675 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.16 % Allowed : 18.02 % Favored : 77.82 % 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 are not related in a simple way. whole: -0.39 (0.33), residues: 620 helix: 0.46 (0.37), residues: 208 sheet: 0.91 (0.51), residues: 97 loop : -1.13 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.009 0.001 TYR B 153 PHE 0.012 0.001 PHE B 157 TRP 0.009 0.001 TRP B 212 HIS 0.003 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 5319) covalent geometry : angle 0.51857 / 0.28 ( 7149) hydrogen bonds : bond 0.03601 / 2.31 ( 188) hydrogen bonds : angle 5.11995 / 3.36 ( 528) *********************** 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 99 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.221 Fit side-chains REVERT: A 152 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7800 (tp) REVERT: A 223 GLN cc_start: 0.6946 (OUTLIER) cc_final: 0.6383 (mt0) REVERT: A 381 ARG cc_start: 0.8110 (mmm-85) cc_final: 0.7769 (mmt-90) REVERT: B 289 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7462 (mppt) REVERT: B 372 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7337 (tt) REVERT: D 63 GLU cc_start: 0.6219 (pp20) cc_final: 0.5876 (tm-30) REVERT: D 88 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.6081 (pm20) REVERT: D 110 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.6063 (mp0) REVERT: D 114 GLU cc_start: 0.5419 (OUTLIER) cc_final: 0.4911 (tt0) outliers start: 24 outliers final: 8 residues processed: 83 average time/residue: 0.5364 time to fit residues: 46.3946 Evaluate side-chains 88 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 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 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 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 58 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 348 ASN C 163 ASN D 128 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.191885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.143991 restraints weight = 6143.081| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.31 r_work: 0.3719 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5319 Z= 0.153 Angle : 0.566 7.230 7149 Z= 0.304 Chirality : 0.042 0.155 781 Planarity : 0.004 0.053 909 Dihedral : 4.867 16.812 675 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.03 % Allowed : 17.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.33), residues: 620 helix: 0.44 (0.37), residues: 207 sheet: 0.83 (0.52), residues: 99 loop : -1.21 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.009 0.001 TYR A 207 PHE 0.013 0.002 PHE B 250 TRP 0.009 0.001 TRP B 212 HIS 0.004 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 5319) covalent geometry : angle 0.56572 / 0.30 ( 7149) hydrogen bonds : bond 0.03967 / 2.54 ( 188) hydrogen bonds : angle 5.16668 / 3.40 ( 528) *********************** 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 104 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.221 Fit side-chains REVERT: A 152 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7849 (tp) REVERT: A 180 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7107 (mmmt) REVERT: A 223 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6389 (mt0) REVERT: A 381 ARG cc_start: 0.8144 (mmm-85) cc_final: 0.7859 (mmt-90) REVERT: A 429 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.7487 (mpp) REVERT: B 171 MET cc_start: 0.5695 (pmm) cc_final: 0.5027 (pp-130) REVERT: B 289 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7573 (mppt) REVERT: B 371 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7043 (pp20) REVERT: B 372 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7379 (tt) REVERT: D 88 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.6105 (pm20) REVERT: D 110 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.6029 (mp0) REVERT: D 114 GLU cc_start: 0.5371 (OUTLIER) cc_final: 0.4854 (tt0) outliers start: 29 outliers final: 9 residues processed: 90 average time/residue: 0.5827 time to fit residues: 54.6334 Evaluate side-chains 89 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 180 LYS 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 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 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 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 52 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.193211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.145409 restraints weight = 6171.348| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.31 r_work: 0.3740 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2110 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= 0.120 Angle : 0.543 7.374 7149 Z= 0.290 Chirality : 0.041 0.149 781 Planarity : 0.004 0.052 909 Dihedral : 4.689 16.661 675 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.99 % Allowed : 18.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.34), residues: 620 helix: 0.69 (0.37), residues: 207 sheet: 1.02 (0.51), residues: 97 loop : -1.07 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.006 0.001 TYR B 153 PHE 0.014 0.001 PHE A 330 TRP 0.009 0.001 TRP B 212 HIS 0.002 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 5319) covalent geometry : angle 0.54291 / 0.29 ( 7149) hydrogen bonds : bond 0.03629 / 2.32 ( 188) hydrogen bonds : angle 5.08779 / 3.35 ( 528) *********************** 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: 23 poor density : 71 time to evaluate : 0.207 Fit side-chains REVERT: A 152 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7792 (tp) REVERT: A 223 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6413 (mt0) REVERT: A 429 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.7519 (mpp) REVERT: B 171 MET cc_start: 0.5640 (pmm) cc_final: 0.5025 (pp-130) REVERT: B 289 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7473 (mppt) REVERT: B 371 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7052 (pp20) REVERT: B 372 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7286 (tt) REVERT: D 88 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.6115 (pm20) REVERT: D 110 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.6037 (mp0) REVERT: D 114 GLU cc_start: 0.5358 (OUTLIER) cc_final: 0.4846 (tt0) outliers start: 23 outliers final: 9 residues processed: 79 average time/residue: 0.5672 time to fit residues: 46.6780 Evaluate side-chains 87 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 A residue 429 MET Chi-restraints excluded: chain B residue 183 VAL 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 88 GLU Chi-restraints excluded: chain D residue 93 MET 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 32 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 0.0170 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4330 r_free = 0.4330 target = 0.193170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.145501 restraints weight = 6114.327| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.30 r_work: 0.3739 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2195 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= 0.123 Angle : 0.539 6.786 7149 Z= 0.290 Chirality : 0.041 0.148 781 Planarity : 0.004 0.052 909 Dihedral : 4.667 17.239 675 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.99 % Allowed : 18.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.34), residues: 620 helix: 0.79 (0.38), residues: 207 sheet: 1.04 (0.51), residues: 97 loop : -1.07 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.006 0.001 TYR B 258 PHE 0.013 0.001 PHE A 330 TRP 0.008 0.001 TRP B 212 HIS 0.002 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 5319) covalent geometry : angle 0.53851 / 0.29 ( 7149) hydrogen bonds : bond 0.03591 / 2.30 ( 188) hydrogen bonds : angle 5.04375 / 3.33 ( 528) *********************** 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 93 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.136 Fit side-chains REVERT: A 152 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7775 (tp) REVERT: A 180 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7205 (mmmm) REVERT: A 223 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6429 (mt0) REVERT: A 381 ARG cc_start: 0.8104 (mmm-85) cc_final: 0.7764 (mmt-90) REVERT: A 429 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.7535 (mpp) REVERT: B 160 GLU cc_start: 0.6223 (tp30) cc_final: 0.6000 (tp30) REVERT: B 171 MET cc_start: 0.5594 (pmm) cc_final: 0.5031 (pp-130) REVERT: B 289 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7503 (mppt) REVERT: B 371 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7082 (pp20) REVERT: B 372 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7311 (tt) REVERT: D 110 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.6084 (mp0) REVERT: D 114 GLU cc_start: 0.5358 (OUTLIER) cc_final: 0.4859 (tt0) outliers start: 23 outliers final: 10 residues processed: 79 average time/residue: 0.5293 time to fit residues: 43.4275 Evaluate side-chains 89 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 180 LYS 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 A residue 429 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 264 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 93 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 6 optimal weight: 0.0370 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.0270 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 0.0470 chunk 32 optimal weight: 0.0370 chunk 57 optimal weight: 6.9990 overall best weight: 0.2292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4360 r_free = 0.4360 target = 0.196481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.158707 restraints weight = 6083.018| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.76 r_work: 0.3776 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 5319 Z= 0.097 Angle : 0.510 6.683 7149 Z= 0.275 Chirality : 0.040 0.138 781 Planarity : 0.004 0.050 909 Dihedral : 4.407 15.947 675 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.25 % Allowed : 20.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.33), residues: 620 helix: 0.57 (0.37), residues: 219 sheet: 1.15 (0.52), residues: 97 loop : -1.22 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.006 0.001 TYR B 258 PHE 0.012 0.001 PHE B 248 TRP 0.006 0.001 TRP D 70 HIS 0.003 0.000 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 5319) covalent geometry : angle 0.50957 / 0.27 ( 7149) hydrogen bonds : bond 0.03142 / 1.99 ( 188) hydrogen bonds : angle 4.87661 / 3.24 ( 528) *********************** 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 88 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 381 ARG cc_start: 0.8247 (mmm-85) cc_final: 0.7924 (mmt-90) REVERT: A 429 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7515 (mpp) REVERT: B 160 GLU cc_start: 0.6201 (tp30) cc_final: 0.5964 (tp30) REVERT: B 171 MET cc_start: 0.5518 (pmm) cc_final: 0.4937 (pp-130) REVERT: B 371 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7111 (pp20) REVERT: B 372 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.6790 (tp) REVERT: D 90 ARG cc_start: 0.6621 (mtt180) cc_final: 0.6404 (mtt180) REVERT: D 114 GLU cc_start: 0.5280 (OUTLIER) cc_final: 0.4759 (tt0) outliers start: 13 outliers final: 5 residues processed: 80 average time/residue: 0.5935 time to fit residues: 49.3488 Evaluate side-chains 80 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain D residue 95 LEU 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 45 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 41 optimal weight: 0.0060 chunk 3 optimal weight: 1.9990 overall best weight: 0.9578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4333 r_free = 0.4333 target = 0.193468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.145830 restraints weight = 6146.011| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.35 r_work: 0.3742 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5319 Z= 0.132 Angle : 0.547 6.530 7149 Z= 0.297 Chirality : 0.041 0.141 781 Planarity : 0.004 0.052 909 Dihedral : 4.571 17.053 675 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.08 % Allowed : 21.32 % Favored : 76.60 % 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 are not related in a simple way. whole: -0.34 (0.33), residues: 620 helix: 0.46 (0.37), residues: 219 sheet: 1.09 (0.50), residues: 101 loop : -1.23 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 381 TYR 0.018 0.001 TYR A 207 PHE 0.012 0.001 PHE B 250 TRP 0.007 0.001 TRP B 212 HIS 0.004 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 5319) covalent geometry : angle 0.54651 / 0.30 ( 7149) hydrogen bonds : bond 0.03592 / 2.30 ( 188) hydrogen bonds : angle 4.98656 / 3.31 ( 528) ********************** 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 80 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.217 Fit side-chains REVERT: A 376 GLU cc_start: 0.6340 (tm-30) cc_final: 0.5939 (tm-30) REVERT: A 381 ARG cc_start: 0.8222 (mmm-85) cc_final: 0.7902 (mmt-90) REVERT: A 429 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.7575 (mpp) REVERT: B 160 GLU cc_start: 0.6256 (tp30) cc_final: 0.6015 (tp30) REVERT: B 371 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7087 (pp20) REVERT: B 372 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7298 (tt) REVERT: D 63 GLU cc_start: 0.6246 (pp20) cc_final: 0.5878 (tm-30) REVERT: D 88 GLU cc_start: 0.5877 (pm20) cc_final: 0.5644 (pm20) REVERT: D 114 GLU cc_start: 0.5442 (OUTLIER) cc_final: 0.4950 (tt0) outliers start: 12 outliers final: 5 residues processed: 74 average time/residue: 0.5266 time to fit residues: 40.6053 Evaluate side-chains 74 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 368 ILE Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain D residue 95 LEU 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 22 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.0370 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4341 r_free = 0.4341 target = 0.194362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.147098 restraints weight = 6150.513| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.31 r_work: 0.3757 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2393 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= 0.116 Angle : 0.554 10.924 7149 Z= 0.298 Chirality : 0.041 0.137 781 Planarity : 0.004 0.051 909 Dihedral : 4.521 16.903 675 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.43 % Allowed : 20.62 % Favored : 76.95 % 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 are not related in a simple way. whole: -0.24 (0.34), residues: 620 helix: 0.61 (0.37), residues: 213 sheet: 1.15 (0.53), residues: 98 loop : -1.17 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 381 TYR 0.006 0.001 TYR B 258 PHE 0.021 0.001 PHE A 330 TRP 0.007 0.001 TRP B 212 HIS 0.004 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 5319) covalent geometry : angle 0.55362 / 0.30 ( 7149) hydrogen bonds : bond 0.03452 / 2.20 ( 188) hydrogen bonds : angle 4.95237 / 3.29 ( 528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2272.27 seconds wall clock time: 39 minutes 22.72 seconds (2362.72 seconds total)