Starting phenix.real_space_refine on Tue Feb 11 10:35:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yi9_33854/02_2025/7yi9_33854.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yi9_33854/02_2025/7yi9_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_33854/02_2025/7yi9_33854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yi9_33854/02_2025/7yi9_33854.map" model { file = "/net/cci-nas-00/data/ceres_data/7yi9_33854/02_2025/7yi9_33854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yi9_33854/02_2025/7yi9_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.11, per 1000 atoms: 0.79 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: 1.16 Conformation dependent library (CDL) restraints added in 580.2 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: 0.55 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: 1.30 Time building geometry restraints manager: 1.35 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: 1.370 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.020 Find NCS groups from input model: 0.070 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:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.140 ------------------------------------------------------------------------------- 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 : 0.579 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: 1.3376 time to fit residues: 140.4562 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 : 0.654 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.191282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.145661 restraints weight = 5954.714| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.55 r_work: 0.3720 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.665 Fit side-chains REVERT: A 152 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7795 (tp) REVERT: A 326 GLN cc_start: 0.6551 (OUTLIER) cc_final: 0.6137 (pt0) REVERT: A 381 ARG cc_start: 0.8154 (mmm-85) cc_final: 0.7717 (mmt-90) REVERT: B 289 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7631 (mppt) REVERT: D 21 MET cc_start: 0.8159 (mmm) cc_final: 0.7919 (mmm) REVERT: D 88 GLU cc_start: 0.6162 (OUTLIER) cc_final: 0.5916 (pm20) REVERT: D 110 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.6159 (mp0) REVERT: D 114 GLU cc_start: 0.5444 (OUTLIER) cc_final: 0.4921 (tt0) outliers start: 18 outliers final: 5 residues processed: 83 average time/residue: 1.2670 time to fit residues: 109.8100 Evaluate side-chains 83 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 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 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.194528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.145250 restraints weight = 5976.201| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.31 r_work: 0.3737 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1591 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= 0.186 Angle : 0.538 5.270 7149 Z= 0.291 Chirality : 0.041 0.136 781 Planarity : 0.004 0.054 909 Dihedral : 6.638 57.957 707 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.95 % Allowed : 15.77 % 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: -0.75 (0.33), residues: 620 helix: 0.14 (0.36), residues: 220 sheet: 0.75 (0.51), residues: 101 loop : -1.43 (0.33), 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 0.015 0.002 PHE B 158 TYR 0.007 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 90 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.694 Fit side-chains REVERT: A 223 GLN cc_start: 0.6960 (OUTLIER) cc_final: 0.6366 (mt0) REVERT: A 381 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.7855 (mmt-90) REVERT: B 289 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7530 (mppt) REVERT: B 371 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7089 (pp20) REVERT: B 372 LEU cc_start: 0.7886 (tt) cc_final: 0.7252 (tt) REVERT: D 21 MET cc_start: 0.8140 (mmm) cc_final: 0.7938 (mmm) REVERT: D 114 GLU cc_start: 0.5328 (OUTLIER) cc_final: 0.4778 (tt0) outliers start: 17 outliers final: 6 residues processed: 79 average time/residue: 1.3671 time to fit residues: 112.3036 Evaluate side-chains 80 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 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 D residue 114 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.193096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.143610 restraints weight = 6018.235| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.35 r_work: 0.3725 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 : 0.004 0.037 5319 Z= 0.228 Angle : 0.556 6.177 7149 Z= 0.300 Chirality : 0.041 0.143 781 Planarity : 0.004 0.054 909 Dihedral : 6.543 55.566 707 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.16 % Allowed : 16.81 % 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: -0.61 (0.33), residues: 620 helix: 0.24 (0.36), residues: 214 sheet: 0.76 (0.50), residues: 102 loop : -1.29 (0.34), residues: 304 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 0.010 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 100 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.589 Fit side-chains REVERT: A 152 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7784 (tp) REVERT: A 223 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.6410 (mt0) REVERT: A 381 ARG cc_start: 0.8212 (mmm-85) cc_final: 0.7904 (mmt-90) REVERT: B 171 MET cc_start: 0.5730 (pmm) cc_final: 0.5095 (pp-130) REVERT: B 289 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7577 (mppt) REVERT: B 319 ILE cc_start: 0.6709 (OUTLIER) cc_final: 0.6494 (pt) REVERT: B 372 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7467 (tt) REVERT: D 21 MET cc_start: 0.8120 (mmm) cc_final: 0.7893 (mmm) REVERT: D 63 GLU cc_start: 0.6255 (pp20) cc_final: 0.5883 (tm-30) REVERT: D 84 ILE cc_start: 0.5878 (OUTLIER) cc_final: 0.5638 (tp) REVERT: D 88 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5972 (pm20) REVERT: D 110 GLU cc_start: 0.6365 (OUTLIER) cc_final: 0.6029 (mp0) REVERT: D 114 GLU cc_start: 0.5400 (OUTLIER) cc_final: 0.4900 (tt0) outliers start: 24 outliers final: 9 residues processed: 86 average time/residue: 1.2945 time to fit residues: 115.9146 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 : 0.588 ------------------------------------------------------------------------------- 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 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 319 ILE 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 22 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 0.0470 chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 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 = 0.4329 r_free = 0.4329 target = 0.193587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.145870 restraints weight = 6073.662| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.30 r_work: 0.3746 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1835 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= 0.174 Angle : 0.512 5.035 7149 Z= 0.278 Chirality : 0.040 0.136 781 Planarity : 0.004 0.053 909 Dihedral : 6.238 49.631 707 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.16 % Allowed : 17.33 % Favored : 78.51 % 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: -0.56 (0.33), residues: 620 helix: 0.36 (0.37), residues: 214 sheet: 0.82 (0.52), residues: 99 loop : -1.31 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 212 HIS 0.003 0.001 HIS B 291 PHE 0.011 0.001 PHE B 250 TYR 0.010 0.001 TYR B 153 ARG 0.002 0.000 ARG B 314 *********************** 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 96 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.570 Fit side-chains REVERT: A 152 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7832 (tp) REVERT: A 223 GLN cc_start: 0.6917 (OUTLIER) cc_final: 0.6355 (mt0) REVERT: A 381 ARG cc_start: 0.8138 (mmm-85) cc_final: 0.7781 (mmt-90) REVERT: B 289 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7478 (mppt) REVERT: B 372 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7433 (tt) REVERT: D 21 MET cc_start: 0.8099 (mmm) cc_final: 0.7874 (mmm) REVERT: D 63 GLU cc_start: 0.6204 (pp20) cc_final: 0.5876 (tm-30) REVERT: D 84 ILE cc_start: 0.5810 (OUTLIER) cc_final: 0.5569 (tp) REVERT: D 88 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.6036 (pm20) REVERT: D 110 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.6077 (mp0) REVERT: D 114 GLU cc_start: 0.5406 (OUTLIER) cc_final: 0.4878 (tt0) outliers start: 24 outliers final: 9 residues processed: 80 average time/residue: 1.2454 time to fit residues: 104.0418 Evaluate side-chains 86 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 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 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 27 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 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 99 ASN A 360 HIS B 161 GLN B 213 GLN B 244 GLN B 348 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.189857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.141867 restraints weight = 6112.919| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.32 r_work: 0.3694 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5319 Z= 0.330 Angle : 0.634 7.824 7149 Z= 0.338 Chirality : 0.044 0.152 781 Planarity : 0.005 0.054 909 Dihedral : 6.620 50.939 707 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.68 % Allowed : 18.02 % 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: -0.76 (0.33), residues: 620 helix: 0.20 (0.36), residues: 208 sheet: 0.61 (0.54), residues: 93 loop : -1.34 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 212 HIS 0.004 0.001 HIS B 291 PHE 0.014 0.002 PHE A 330 TYR 0.011 0.002 TYR A 207 ARG 0.003 0.000 ARG A 359 *********************** 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 100 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.569 Fit side-chains REVERT: A 152 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7863 (tp) REVERT: A 223 GLN cc_start: 0.6985 (OUTLIER) cc_final: 0.6363 (mt0) REVERT: A 326 GLN cc_start: 0.6602 (OUTLIER) cc_final: 0.6314 (pt0) REVERT: A 376 GLU cc_start: 0.6299 (tm-30) cc_final: 0.5915 (tm-30) REVERT: B 171 MET cc_start: 0.5668 (pmm) cc_final: 0.4962 (pp-130) REVERT: B 372 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7225 (tp) REVERT: D 21 MET cc_start: 0.8122 (mmm) cc_final: 0.7865 (mmm) REVERT: D 84 ILE cc_start: 0.6082 (OUTLIER) cc_final: 0.5776 (tp) REVERT: D 88 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5963 (pm20) REVERT: D 110 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5984 (mp0) REVERT: D 114 GLU cc_start: 0.5422 (OUTLIER) cc_final: 0.4966 (tt0) outliers start: 27 outliers final: 8 residues processed: 87 average time/residue: 1.2707 time to fit residues: 115.2400 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 : 0.567 ------------------------------------------------------------------------------- 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 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 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 41 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 ASN C 163 ASN D 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.190610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.142592 restraints weight = 6072.200| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.31 r_work: 0.3704 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2093 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= 0.268 Angle : 0.606 7.617 7149 Z= 0.324 Chirality : 0.043 0.166 781 Planarity : 0.005 0.055 909 Dihedral : 6.441 46.155 707 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.99 % Allowed : 18.72 % 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: -0.81 (0.33), residues: 620 helix: 0.17 (0.36), residues: 214 sheet: 0.58 (0.54), residues: 93 loop : -1.41 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 212 HIS 0.002 0.001 HIS A 360 PHE 0.014 0.002 PHE B 250 TYR 0.008 0.001 TYR A 207 ARG 0.002 0.000 ARG A 359 *********************** 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 85 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.620 Fit side-chains REVERT: A 152 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7860 (tp) REVERT: A 180 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7116 (mmmt) REVERT: A 223 GLN cc_start: 0.6921 (OUTLIER) cc_final: 0.6350 (mt0) REVERT: B 171 MET cc_start: 0.5743 (pmm) cc_final: 0.5077 (pp-130) REVERT: B 372 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7173 (tp) REVERT: D 21 MET cc_start: 0.8136 (mmm) cc_final: 0.7879 (mmm) REVERT: D 84 ILE cc_start: 0.6020 (OUTLIER) cc_final: 0.5719 (tp) REVERT: D 88 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.5912 (pm20) REVERT: D 110 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5982 (mp0) REVERT: D 114 GLU cc_start: 0.5418 (OUTLIER) cc_final: 0.4949 (tt0) outliers start: 23 outliers final: 11 residues processed: 78 average time/residue: 1.3107 time to fit residues: 106.6003 Evaluate side-chains 83 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 139 LYS 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 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 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 57 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 0.0470 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 0.0060 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 0.0030 chunk 53 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 overall best weight: 0.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN B 348 ASN D 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.194585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.147036 restraints weight = 6083.542| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.32 r_work: 0.3758 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2238 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= 0.157 Angle : 0.527 7.104 7149 Z= 0.283 Chirality : 0.040 0.152 781 Planarity : 0.004 0.053 909 Dihedral : 5.919 44.759 707 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.12 % Allowed : 19.41 % 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: -0.46 (0.33), residues: 620 helix: 0.39 (0.37), residues: 220 sheet: 0.92 (0.51), residues: 98 loop : -1.26 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 70 HIS 0.002 0.001 HIS B 291 PHE 0.011 0.001 PHE A 330 TYR 0.007 0.001 TYR B 258 ARG 0.003 0.000 ARG A 381 *********************** 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 88 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.581 Fit side-chains REVERT: A 180 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7184 (mmmm) REVERT: A 381 ARG cc_start: 0.8213 (mmm-85) cc_final: 0.7929 (mmt-90) REVERT: B 171 MET cc_start: 0.5551 (pmm) cc_final: 0.4982 (pp-130) REVERT: B 372 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7357 (tt) REVERT: D 21 MET cc_start: 0.8086 (mmm) cc_final: 0.7853 (mmm) REVERT: D 84 ILE cc_start: 0.5909 (OUTLIER) cc_final: 0.5605 (tp) REVERT: D 88 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.6055 (pm20) REVERT: D 110 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5991 (mp0) REVERT: D 114 GLU cc_start: 0.5335 (OUTLIER) cc_final: 0.4838 (tt0) outliers start: 18 outliers final: 7 residues processed: 78 average time/residue: 1.2093 time to fit residues: 98.5790 Evaluate side-chains 85 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 180 LYS 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 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 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 47 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 0.0030 chunk 33 optimal weight: 0.1980 chunk 44 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.4339 r_free = 0.4339 target = 0.194375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.156278 restraints weight = 6038.184| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.72 r_work: 0.3752 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2275 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= 0.166 Angle : 0.526 6.813 7149 Z= 0.286 Chirality : 0.040 0.144 781 Planarity : 0.004 0.052 909 Dihedral : 5.804 45.075 707 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.77 % Allowed : 20.28 % 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 (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: -0.27 (0.34), residues: 620 helix: 0.61 (0.37), residues: 214 sheet: 0.96 (0.51), residues: 98 loop : -1.13 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 70 HIS 0.003 0.001 HIS B 291 PHE 0.011 0.001 PHE B 250 TYR 0.014 0.001 TYR A 207 ARG 0.002 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 90 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.669 Fit side-chains REVERT: A 180 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7193 (mmmm) REVERT: A 381 ARG cc_start: 0.8236 (mmm-85) cc_final: 0.7881 (mmt-90) REVERT: B 371 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7115 (pp20) REVERT: B 372 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7366 (tt) REVERT: D 21 MET cc_start: 0.8110 (mmm) cc_final: 0.7895 (mmm) REVERT: D 84 ILE cc_start: 0.5972 (OUTLIER) cc_final: 0.5660 (tp) REVERT: D 88 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6100 (pm20) REVERT: D 114 GLU cc_start: 0.5359 (OUTLIER) cc_final: 0.4857 (tt0) outliers start: 16 outliers final: 5 residues processed: 81 average time/residue: 1.4272 time to fit residues: 120.0053 Evaluate side-chains 77 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain B residue 183 VAL 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 84 ILE Chi-restraints excluded: chain D residue 88 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 45 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.191665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.144001 restraints weight = 6064.567| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.29 r_work: 0.3728 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5319 Z= 0.247 Angle : 0.606 11.262 7149 Z= 0.324 Chirality : 0.042 0.145 781 Planarity : 0.004 0.053 909 Dihedral : 5.998 44.492 707 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.77 % Allowed : 20.62 % 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 (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: -0.26 (0.34), residues: 620 helix: 0.66 (0.37), residues: 207 sheet: 0.80 (0.50), residues: 102 loop : -1.09 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 212 HIS 0.005 0.001 HIS B 291 PHE 0.020 0.002 PHE A 330 TYR 0.007 0.001 TYR B 339 ARG 0.002 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 78 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.601 Fit side-chains REVERT: A 180 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7177 (mmmm) REVERT: B 171 MET cc_start: 0.5564 (pmm) cc_final: 0.4862 (pp-130) REVERT: B 372 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7460 (tt) REVERT: D 21 MET cc_start: 0.8073 (mmm) cc_final: 0.7830 (mmm) REVERT: D 84 ILE cc_start: 0.6050 (OUTLIER) cc_final: 0.5784 (tp) REVERT: D 88 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6137 (pm20) REVERT: D 114 GLU cc_start: 0.5404 (OUTLIER) cc_final: 0.4890 (tt0) outliers start: 16 outliers final: 7 residues processed: 72 average time/residue: 1.2482 time to fit residues: 93.9642 Evaluate side-chains 79 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 180 LYS 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 310 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 88 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 17 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.4318 r_free = 0.4318 target = 0.192095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.144446 restraints weight = 6097.427| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.32 r_work: 0.3730 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2341 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= 0.221 Angle : 0.584 10.249 7149 Z= 0.313 Chirality : 0.042 0.141 781 Planarity : 0.004 0.052 909 Dihedral : 5.928 44.137 707 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.77 % Allowed : 20.80 % Favored : 76.43 % 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: -0.48 (0.33), residues: 620 helix: 0.39 (0.36), residues: 219 sheet: 0.93 (0.51), residues: 97 loop : -1.28 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 212 HIS 0.004 0.001 HIS B 291 PHE 0.019 0.002 PHE A 330 TYR 0.007 0.001 TYR B 339 ARG 0.004 0.000 ARG A 381 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4853.29 seconds wall clock time: 85 minutes 58.21 seconds (5158.21 seconds total)