Starting phenix.real_space_refine on Tue Jul 29 04:00:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tin_41296/07_2025/8tin_41296.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tin_41296/07_2025/8tin_41296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tin_41296/07_2025/8tin_41296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tin_41296/07_2025/8tin_41296.map" model { file = "/net/cci-nas-00/data/ceres_data/8tin_41296/07_2025/8tin_41296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tin_41296/07_2025/8tin_41296.cif" } resolution = 4.0 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= 0.022 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 21 5.16 5 C 3513 2.51 5 N 929 2.21 5 O 1050 1.98 5 H 5456 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10971 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3182 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Chain breaks: 3 Chain: "A" Number of atoms: 4565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4565 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 263} Chain breaks: 9 Chain: "L" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 3115 Classifications: {'peptide': 204} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 192} Chain breaks: 1 Chain: "R" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 109 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 6.03, per 1000 atoms: 0.55 Number of scatterers: 10971 At special positions: 0 Unit cell: (54.808, 103.292, 119.102, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 21 16.00 P 2 15.00 O 1050 8.00 N 929 7.00 C 3513 6.00 H 5456 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 215 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 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: 3.16 Conformation dependent library (CDL) restraints added in 790.8 milliseconds 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1338 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 16 sheets defined 5.0% alpha, 40.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.676A pdb=" N LEU A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.715A pdb=" N LYS A 108 " --> pdb=" O ARG A 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 Processing helix chain 'L' and resid 184 through 190 removed outlier: 3.952A pdb=" N HIS L 190 " --> pdb=" O ASP L 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 60 through 63 removed outlier: 5.324A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR H 121 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 60 through 63 removed outlier: 5.324A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 139 through 143 removed outlier: 4.667A pdb=" N ALA H 156 " --> pdb=" O VAL H 203 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL H 203 " --> pdb=" O ALA H 156 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLY H 158 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL H 201 " --> pdb=" O GLY H 158 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU H 160 " --> pdb=" O SER H 199 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N SER H 199 " --> pdb=" O LEU H 160 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS H 162 " --> pdb=" O LEU H 197 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU H 197 " --> pdb=" O LYS H 162 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N SER H 196 " --> pdb=" O ALA H 187 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ALA H 187 " --> pdb=" O SER H 196 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER H 198 " --> pdb=" O PHE H 185 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL H 200 " --> pdb=" O HIS H 183 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS H 183 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 172 through 173 Processing sheet with id=AA6, first strand: chain 'A' and resid 113 through 118 Processing sheet with id=AA7, first strand: chain 'A' and resid 28 through 29 removed outlier: 6.016A pdb=" N PHE A 28 " --> pdb=" O VAL A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 82 through 88 removed outlier: 5.846A pdb=" N ASN A 84 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU A 58 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N GLN A 86 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 56 " --> pdb=" O GLN A 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 62 through 63 removed outlier: 3.544A pdb=" N ARG A 63 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 142 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 184 through 188 removed outlier: 3.590A pdb=" N LYS A 271 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 253 through 259 removed outlier: 6.997A pdb=" N GLN A 238 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA A 255 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AB4, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.752A pdb=" N LEU L 12 " --> pdb=" O LYS L 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'L' and resid 35 through 39 removed outlier: 4.223A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 115 through 119 removed outlier: 4.302A pdb=" N ASN L 139 " --> pdb=" O TYR L 174 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 145 through 150 208 hydrogen bonds defined for protein. 537 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: 3.93 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5444 1.03 - 1.23: 27 1.23 - 1.42: 2354 1.42 - 1.62: 3240 1.62 - 1.81: 26 Bond restraints: 11091 Sorted by residual: bond pdb=" CB TPO R 352 " pdb=" HB TPO R 352 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" CG2 TPO R 352 " pdb="HG23 TPO R 352 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CG2 TPO R 352 " pdb="HG21 TPO R 352 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" CG2 TPO R 352 " pdb="HG22 TPO R 352 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" OG1 TPO R 352 " pdb=" P TPO R 352 " ideal model delta sigma weight residual 1.717 1.612 0.105 2.00e-02 2.50e+03 2.76e+01 ... (remaining 11086 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 19909 2.15 - 4.30: 91 4.30 - 6.46: 6 6.46 - 8.61: 0 8.61 - 10.76: 2 Bond angle restraints: 20008 Sorted by residual: angle pdb=" CB TPO R 352 " pdb=" OG1 TPO R 352 " pdb=" P TPO R 352 " ideal model delta sigma weight residual 119.31 108.55 10.76 3.00e+00 1.11e-01 1.29e+01 angle pdb=" OG1 TPO R 352 " pdb=" P TPO R 352 " pdb=" O1P TPO R 352 " ideal model delta sigma weight residual 100.43 110.04 -9.61 3.00e+00 1.11e-01 1.03e+01 angle pdb=" CA VAL H 203 " pdb=" C VAL H 203 " pdb=" N PRO H 204 " ideal model delta sigma weight residual 116.57 119.45 -2.88 9.80e-01 1.04e+00 8.61e+00 angle pdb=" C VAL H 203 " pdb=" CA VAL H 203 " pdb=" CB VAL H 203 " ideal model delta sigma weight residual 109.33 111.52 -2.19 9.80e-01 1.04e+00 4.99e+00 angle pdb=" N VAL H 32 " pdb=" CA VAL H 32 " pdb=" C VAL H 32 " ideal model delta sigma weight residual 112.50 109.52 2.98 1.39e+00 5.18e-01 4.59e+00 ... (remaining 20003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 4810 16.56 - 33.12: 348 33.12 - 49.68: 102 49.68 - 66.24: 29 66.24 - 82.80: 2 Dihedral angle restraints: 5291 sinusoidal: 2839 harmonic: 2452 Sorted by residual: dihedral pdb=" CA ASN A 224 " pdb=" C ASN A 224 " pdb=" N SER A 225 " pdb=" CA SER A 225 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA HIS H 106 " pdb=" C HIS H 106 " pdb=" N ARG H 107 " pdb=" CA ARG H 107 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PHE L 119 " pdb=" C PHE L 119 " pdb=" N PRO L 120 " pdb=" CA PRO L 120 " ideal model delta harmonic sigma weight residual 180.00 161.16 18.84 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 541 0.033 - 0.067: 222 0.067 - 0.100: 47 0.100 - 0.133: 63 0.133 - 0.166: 1 Chirality restraints: 874 Sorted by residual: chirality pdb=" CA ILE A 147 " pdb=" N ILE A 147 " pdb=" C ILE A 147 " pdb=" CB ILE A 147 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA VAL H 40 " pdb=" N VAL H 40 " pdb=" C VAL H 40 " pdb=" CB VAL H 40 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA VAL A 326 " pdb=" N VAL A 326 " pdb=" C VAL A 326 " pdb=" CB VAL A 326 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 871 not shown) Planarity restraints: 1586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 167 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO H 168 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO H 168 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 168 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE L 119 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO L 120 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO L 120 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 120 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 165 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO H 166 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO H 166 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 166 " 0.017 5.00e-02 4.00e+02 ... (remaining 1583 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 274 2.10 - 2.73: 19466 2.73 - 3.35: 30454 3.35 - 3.98: 39819 3.98 - 4.60: 61653 Nonbonded interactions: 151666 Sorted by model distance: nonbonded pdb=" HE1 TRP H 50 " pdb=" OG SER H 53 " model vdw 1.476 2.450 nonbonded pdb=" O ALA A 289 " pdb=" H ALA A 302 " model vdw 1.523 2.450 nonbonded pdb=" OE2 GLU H 9 " pdb=" H CYS H 99 " model vdw 1.537 2.450 nonbonded pdb="HE21 GLN H 42 " pdb=" O LYS H 46 " model vdw 1.579 2.450 nonbonded pdb=" OE1 GLN H 42 " pdb="HE22 GLN L 39 " model vdw 1.594 2.450 ... (remaining 151661 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 group one per residue 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: 3.750 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: 0.210 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 27.600 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5273 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 0.105 5639 Z= 0.197 Angle : 0.640 10.762 7653 Z= 0.348 Chirality : 0.046 0.166 874 Planarity : 0.004 0.040 954 Dihedral : 12.418 82.796 2035 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.96 % Favored : 91.89 % Rotamer: Outliers : 6.58 % Allowed : 8.35 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.33), residues: 666 helix: 0.03 (1.06), residues: 30 sheet: -0.63 (0.30), residues: 325 loop : -1.70 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.004 0.001 HIS A 346 PHE 0.015 0.002 PHE A 62 TYR 0.011 0.001 TYR H 98 ARG 0.003 0.000 ARG L 212 Details of bonding type rmsd hydrogen bonds : bond 0.14398 ( 192) hydrogen bonds : angle 7.35998 ( 537) SS BOND : bond 0.00210 ( 4) SS BOND : angle 0.85093 ( 8) covalent geometry : bond 0.00391 ( 5635) covalent geometry : angle 0.63954 ( 7645) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 167 GLU cc_start: 0.6532 (mm-30) cc_final: 0.6308 (mt-10) REVERT: H 173 TRP cc_start: 0.5007 (m100) cc_final: 0.4382 (m100) REVERT: L 88 TYR cc_start: 0.3284 (OUTLIER) cc_final: 0.2174 (m-80) outliers start: 41 outliers final: 28 residues processed: 140 average time/residue: 0.4621 time to fit residues: 81.1555 Evaluate side-chains 95 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 36 TYR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain H residue 218 ASN Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 88 TYR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain R residue 354 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 224 ASN A 281 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.233070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.223744 restraints weight = 20738.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.226914 restraints weight = 12033.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.228832 restraints weight = 7340.203| |-----------------------------------------------------------------------------| r_work (final): 0.4664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5272 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 5639 Z= 0.254 Angle : 0.721 7.364 7653 Z= 0.382 Chirality : 0.050 0.186 874 Planarity : 0.006 0.043 954 Dihedral : 10.168 58.986 809 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.51 % Favored : 89.34 % Rotamer: Outliers : 6.42 % Allowed : 13.32 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.32), residues: 666 helix: -0.16 (1.03), residues: 29 sheet: -0.86 (0.29), residues: 323 loop : -2.21 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 50 HIS 0.008 0.001 HIS A 211 PHE 0.030 0.003 PHE A 62 TYR 0.020 0.002 TYR L 37 ARG 0.004 0.001 ARG L 212 Details of bonding type rmsd hydrogen bonds : bond 0.04804 ( 192) hydrogen bonds : angle 7.19134 ( 537) SS BOND : bond 0.00575 ( 4) SS BOND : angle 1.68335 ( 8) covalent geometry : bond 0.00579 ( 5635) covalent geometry : angle 0.71911 ( 7645) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 68 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 167 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6376 (mt-10) REVERT: A 47 ASP cc_start: 0.2992 (OUTLIER) cc_final: 0.0440 (t70) REVERT: A 208 LEU cc_start: 0.3366 (OUTLIER) cc_final: 0.2813 (tt) REVERT: L 88 TYR cc_start: 0.3547 (OUTLIER) cc_final: 0.1933 (m-80) REVERT: R 354 TYR cc_start: 0.5343 (OUTLIER) cc_final: 0.3893 (m-80) outliers start: 40 outliers final: 27 residues processed: 102 average time/residue: 0.4136 time to fit residues: 54.9228 Evaluate side-chains 89 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 58 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 36 TYR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 88 TYR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain R residue 354 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.0870 chunk 10 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 216 ASN A 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.237020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.229562 restraints weight = 20655.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.232113 restraints weight = 12018.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.233770 restraints weight = 7366.560| |-----------------------------------------------------------------------------| r_work (final): 0.4702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5168 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5639 Z= 0.140 Angle : 0.592 4.812 7653 Z= 0.312 Chirality : 0.047 0.169 874 Planarity : 0.005 0.047 954 Dihedral : 9.691 58.607 799 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.06 % Favored : 92.79 % Rotamer: Outliers : 6.58 % Allowed : 15.57 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.33), residues: 666 helix: 0.17 (1.06), residues: 30 sheet: -0.71 (0.30), residues: 318 loop : -1.91 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.008 0.001 HIS A 346 PHE 0.021 0.002 PHE A 342 TYR 0.010 0.001 TYR H 213 ARG 0.004 0.001 ARG L 212 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 192) hydrogen bonds : angle 6.57337 ( 537) SS BOND : bond 0.00370 ( 4) SS BOND : angle 1.22905 ( 8) covalent geometry : bond 0.00320 ( 5635) covalent geometry : angle 0.59145 ( 7645) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 64 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 101 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6861 (ppt170) REVERT: H 167 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6189 (mt-10) REVERT: A 47 ASP cc_start: 0.2996 (OUTLIER) cc_final: 0.0673 (t70) REVERT: A 208 LEU cc_start: 0.3276 (OUTLIER) cc_final: 0.2730 (tt) REVERT: L 88 TYR cc_start: 0.3153 (OUTLIER) cc_final: 0.1773 (m-80) REVERT: R 354 TYR cc_start: 0.5425 (OUTLIER) cc_final: 0.4244 (m-80) outliers start: 41 outliers final: 28 residues processed: 99 average time/residue: 0.4017 time to fit residues: 52.8442 Evaluate side-chains 92 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 36 TYR Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 88 TYR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain R residue 354 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 50 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 62 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.239460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.222870 restraints weight = 219271.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.228468 restraints weight = 126110.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.228731 restraints weight = 97054.738| |-----------------------------------------------------------------------------| r_work (final): 0.4535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5355 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5639 Z= 0.140 Angle : 0.574 4.797 7653 Z= 0.303 Chirality : 0.047 0.165 874 Planarity : 0.005 0.045 954 Dihedral : 9.584 59.769 799 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.96 % Favored : 91.89 % Rotamer: Outliers : 5.62 % Allowed : 16.85 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.33), residues: 666 helix: 0.37 (1.08), residues: 30 sheet: -0.63 (0.30), residues: 308 loop : -1.80 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.007 0.001 HIS A 346 PHE 0.017 0.002 PHE A 342 TYR 0.014 0.001 TYR H 213 ARG 0.007 0.001 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 192) hydrogen bonds : angle 6.33803 ( 537) SS BOND : bond 0.00174 ( 4) SS BOND : angle 1.31979 ( 8) covalent geometry : bond 0.00321 ( 5635) covalent geometry : angle 0.57236 ( 7645) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 61 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 101 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6908 (ppt170) REVERT: H 167 GLU cc_start: 0.6684 (mm-30) cc_final: 0.6204 (mt-10) REVERT: H 216 ASN cc_start: 0.7003 (OUTLIER) cc_final: 0.6164 (p0) REVERT: A 47 ASP cc_start: 0.2637 (OUTLIER) cc_final: 0.0640 (t70) REVERT: A 208 LEU cc_start: 0.2871 (OUTLIER) cc_final: 0.2381 (tt) REVERT: L 88 TYR cc_start: 0.3037 (OUTLIER) cc_final: 0.1833 (m-80) REVERT: R 354 TYR cc_start: 0.5313 (OUTLIER) cc_final: 0.4196 (m-80) outliers start: 35 outliers final: 26 residues processed: 91 average time/residue: 0.3996 time to fit residues: 47.8285 Evaluate side-chains 90 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 58 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 88 TYR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain R residue 354 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 54 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 216 ASN A 220 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.236619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.219616 restraints weight = 223955.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.224923 restraints weight = 127384.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.227079 restraints weight = 94446.901| |-----------------------------------------------------------------------------| r_work (final): 0.4563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5428 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5639 Z= 0.179 Angle : 0.621 5.963 7653 Z= 0.328 Chirality : 0.047 0.174 874 Planarity : 0.005 0.045 954 Dihedral : 9.376 58.266 795 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.76 % Favored : 90.09 % Rotamer: Outliers : 6.74 % Allowed : 17.17 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.33), residues: 666 helix: 0.29 (1.05), residues: 30 sheet: -0.70 (0.30), residues: 314 loop : -2.00 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 109 HIS 0.005 0.001 HIS A 211 PHE 0.022 0.002 PHE A 62 TYR 0.014 0.002 TYR L 37 ARG 0.008 0.001 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 192) hydrogen bonds : angle 6.54326 ( 537) SS BOND : bond 0.00561 ( 4) SS BOND : angle 0.99804 ( 8) covalent geometry : bond 0.00408 ( 5635) covalent geometry : angle 0.62029 ( 7645) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 63 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 98 TYR cc_start: 0.3037 (OUTLIER) cc_final: 0.2688 (m-80) REVERT: H 101 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6957 (ppt170) REVERT: H 167 GLU cc_start: 0.6683 (mm-30) cc_final: 0.6383 (mt-10) REVERT: A 47 ASP cc_start: 0.3290 (OUTLIER) cc_final: 0.1133 (t70) REVERT: A 208 LEU cc_start: 0.3016 (OUTLIER) cc_final: 0.2471 (tt) REVERT: L 88 TYR cc_start: 0.3307 (OUTLIER) cc_final: 0.1926 (m-80) REVERT: R 354 TYR cc_start: 0.5750 (OUTLIER) cc_final: 0.4318 (m-80) outliers start: 42 outliers final: 29 residues processed: 99 average time/residue: 0.4312 time to fit residues: 57.6944 Evaluate side-chains 95 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 60 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 88 TYR Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain R residue 354 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.235059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.227166 restraints weight = 21039.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.229864 restraints weight = 12280.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.231436 restraints weight = 7609.017| |-----------------------------------------------------------------------------| r_work (final): 0.4687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5234 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5639 Z= 0.156 Angle : 0.591 5.214 7653 Z= 0.311 Chirality : 0.047 0.157 874 Planarity : 0.005 0.045 954 Dihedral : 8.849 57.077 791 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.96 % Favored : 91.89 % Rotamer: Outliers : 5.94 % Allowed : 18.14 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.33), residues: 666 helix: 0.49 (1.07), residues: 30 sheet: -0.66 (0.30), residues: 314 loop : -1.90 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 50 HIS 0.005 0.001 HIS A 346 PHE 0.017 0.002 PHE A 62 TYR 0.021 0.002 TYR L 37 ARG 0.008 0.001 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 192) hydrogen bonds : angle 6.39921 ( 537) SS BOND : bond 0.00275 ( 4) SS BOND : angle 0.96091 ( 8) covalent geometry : bond 0.00361 ( 5635) covalent geometry : angle 0.59029 ( 7645) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 59 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 101 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6913 (ppt170) REVERT: H 167 GLU cc_start: 0.6564 (mm-30) cc_final: 0.6281 (mt-10) REVERT: H 216 ASN cc_start: 0.6983 (OUTLIER) cc_final: 0.6626 (p0) REVERT: A 47 ASP cc_start: 0.3122 (OUTLIER) cc_final: 0.1045 (t70) REVERT: A 208 LEU cc_start: 0.3319 (OUTLIER) cc_final: 0.2758 (tt) REVERT: L 88 TYR cc_start: 0.3062 (OUTLIER) cc_final: 0.1865 (m-80) REVERT: R 354 TYR cc_start: 0.5780 (OUTLIER) cc_final: 0.5056 (m-80) outliers start: 37 outliers final: 26 residues processed: 91 average time/residue: 0.3575 time to fit residues: 43.4921 Evaluate side-chains 90 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 58 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 88 TYR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain R residue 354 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 7 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 34 optimal weight: 0.0010 chunk 33 optimal weight: 0.0970 chunk 17 optimal weight: 0.0170 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 4 optimal weight: 0.0170 chunk 55 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 overall best weight: 0.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 216 ASN A 220 HIS ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.241047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.233796 restraints weight = 20581.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.236292 restraints weight = 11874.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.237706 restraints weight = 7307.058| |-----------------------------------------------------------------------------| r_work (final): 0.4746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5082 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5639 Z= 0.108 Angle : 0.535 5.301 7653 Z= 0.278 Chirality : 0.046 0.153 874 Planarity : 0.005 0.045 954 Dihedral : 8.360 54.189 790 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.35 % Favored : 95.50 % Rotamer: Outliers : 5.14 % Allowed : 18.30 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.34), residues: 666 helix: 0.63 (1.07), residues: 30 sheet: -0.51 (0.30), residues: 316 loop : -1.66 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.007 0.001 HIS A 346 PHE 0.018 0.001 PHE A 342 TYR 0.017 0.001 TYR L 37 ARG 0.009 0.001 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.02814 ( 192) hydrogen bonds : angle 5.72046 ( 537) SS BOND : bond 0.00332 ( 4) SS BOND : angle 0.69987 ( 8) covalent geometry : bond 0.00233 ( 5635) covalent geometry : angle 0.53473 ( 7645) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 58 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.2539 (OUTLIER) cc_final: 0.0817 (t70) REVERT: A 208 LEU cc_start: 0.3075 (OUTLIER) cc_final: 0.2526 (tt) REVERT: L 88 TYR cc_start: 0.2922 (OUTLIER) cc_final: 0.2281 (m-80) REVERT: L 99 PHE cc_start: 0.3177 (OUTLIER) cc_final: 0.1665 (m-80) REVERT: L 101 GLN cc_start: 0.5930 (mp10) cc_final: 0.5717 (mp10) REVERT: R 354 TYR cc_start: 0.5865 (OUTLIER) cc_final: 0.5175 (m-80) outliers start: 32 outliers final: 20 residues processed: 84 average time/residue: 0.3486 time to fit residues: 39.6348 Evaluate side-chains 84 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 88 TYR Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain R residue 354 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 59 optimal weight: 0.1980 chunk 15 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.237748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.230187 restraints weight = 20871.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.232803 restraints weight = 12356.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.234275 restraints weight = 7669.913| |-----------------------------------------------------------------------------| r_work (final): 0.4727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5142 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5639 Z= 0.119 Angle : 0.535 5.150 7653 Z= 0.280 Chirality : 0.046 0.141 874 Planarity : 0.005 0.044 954 Dihedral : 7.960 53.203 787 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.61 % Favored : 93.24 % Rotamer: Outliers : 3.69 % Allowed : 19.10 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.34), residues: 666 helix: 0.67 (1.05), residues: 30 sheet: -0.44 (0.31), residues: 311 loop : -1.66 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.003 0.001 HIS A 346 PHE 0.016 0.002 PHE A 342 TYR 0.012 0.001 TYR L 37 ARG 0.007 0.000 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.03084 ( 192) hydrogen bonds : angle 5.73909 ( 537) SS BOND : bond 0.00215 ( 4) SS BOND : angle 0.84042 ( 8) covalent geometry : bond 0.00277 ( 5635) covalent geometry : angle 0.53457 ( 7645) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 101 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6812 (ppt170) REVERT: H 216 ASN cc_start: 0.6849 (OUTLIER) cc_final: 0.5971 (p0) REVERT: A 47 ASP cc_start: 0.2778 (OUTLIER) cc_final: 0.0880 (t70) REVERT: A 208 LEU cc_start: 0.3104 (OUTLIER) cc_final: 0.2715 (mp) REVERT: L 88 TYR cc_start: 0.3000 (OUTLIER) cc_final: 0.2192 (m-80) REVERT: L 99 PHE cc_start: 0.3222 (OUTLIER) cc_final: 0.1712 (m-80) outliers start: 23 outliers final: 15 residues processed: 77 average time/residue: 0.3476 time to fit residues: 35.8872 Evaluate side-chains 77 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain L residue 88 TYR Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 198 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 0.1980 chunk 54 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.236537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.228892 restraints weight = 21018.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.231384 restraints weight = 12438.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.233026 restraints weight = 7854.293| |-----------------------------------------------------------------------------| r_work (final): 0.4741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5216 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5639 Z= 0.138 Angle : 0.560 5.203 7653 Z= 0.294 Chirality : 0.046 0.137 874 Planarity : 0.005 0.044 954 Dihedral : 7.331 51.964 781 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.56 % Favored : 91.29 % Rotamer: Outliers : 3.85 % Allowed : 19.42 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.34), residues: 666 helix: 0.80 (1.07), residues: 30 sheet: -0.49 (0.30), residues: 319 loop : -1.70 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.004 0.001 HIS A 220 PHE 0.017 0.002 PHE A 342 TYR 0.013 0.001 TYR L 37 ARG 0.008 0.000 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.03153 ( 192) hydrogen bonds : angle 5.85305 ( 537) SS BOND : bond 0.00394 ( 4) SS BOND : angle 0.85120 ( 8) covalent geometry : bond 0.00320 ( 5635) covalent geometry : angle 0.56010 ( 7645) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 101 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6812 (ppt170) REVERT: A 8 ARG cc_start: 0.6408 (mtp-110) cc_final: 0.5862 (ttt180) REVERT: A 47 ASP cc_start: 0.3183 (OUTLIER) cc_final: 0.1229 (t70) REVERT: L 88 TYR cc_start: 0.3019 (OUTLIER) cc_final: 0.2133 (m-80) REVERT: L 99 PHE cc_start: 0.3176 (OUTLIER) cc_final: 0.1588 (m-80) REVERT: L 101 GLN cc_start: 0.6087 (mp10) cc_final: 0.5881 (mp10) outliers start: 24 outliers final: 18 residues processed: 76 average time/residue: 0.3314 time to fit residues: 34.0241 Evaluate side-chains 79 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain L residue 88 TYR Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 1 optimal weight: 0.0980 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 18 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.237464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.230244 restraints weight = 20791.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.232708 restraints weight = 12095.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.234049 restraints weight = 7536.406| |-----------------------------------------------------------------------------| r_work (final): 0.4723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5192 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5639 Z= 0.124 Angle : 0.543 5.362 7653 Z= 0.283 Chirality : 0.046 0.138 874 Planarity : 0.005 0.048 954 Dihedral : 7.253 52.226 781 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.21 % Favored : 92.64 % Rotamer: Outliers : 3.53 % Allowed : 19.74 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.34), residues: 666 helix: 0.95 (1.07), residues: 30 sheet: -0.52 (0.31), residues: 319 loop : -1.62 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 50 HIS 0.006 0.001 HIS A 220 PHE 0.017 0.002 PHE A 342 TYR 0.012 0.001 TYR L 37 ARG 0.006 0.000 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.03005 ( 192) hydrogen bonds : angle 5.75435 ( 537) SS BOND : bond 0.00387 ( 4) SS BOND : angle 0.85634 ( 8) covalent geometry : bond 0.00290 ( 5635) covalent geometry : angle 0.54218 ( 7645) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.6644 (mtp-110) cc_final: 0.6057 (ttt180) REVERT: A 47 ASP cc_start: 0.3065 (OUTLIER) cc_final: 0.1264 (t70) REVERT: L 88 TYR cc_start: 0.3140 (OUTLIER) cc_final: 0.2254 (m-80) REVERT: L 99 PHE cc_start: 0.3159 (OUTLIER) cc_final: 0.1589 (m-80) outliers start: 22 outliers final: 18 residues processed: 75 average time/residue: 0.3754 time to fit residues: 37.9165 Evaluate side-chains 75 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain L residue 88 TYR Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 168 ASP Chi-restraints excluded: chain L residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 13 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 0.0670 chunk 66 optimal weight: 0.0970 chunk 30 optimal weight: 0.8980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.241130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.225099 restraints weight = 217600.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.229160 restraints weight = 120892.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.231531 restraints weight = 97102.040| |-----------------------------------------------------------------------------| r_work (final): 0.4604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5348 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5639 Z= 0.112 Angle : 0.528 5.327 7653 Z= 0.275 Chirality : 0.045 0.138 874 Planarity : 0.005 0.048 954 Dihedral : 7.112 52.316 781 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.81 % Favored : 92.04 % Rotamer: Outliers : 3.69 % Allowed : 19.58 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.35), residues: 666 helix: 1.02 (1.05), residues: 30 sheet: -0.51 (0.30), residues: 324 loop : -1.59 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 50 HIS 0.005 0.001 HIS A 220 PHE 0.016 0.001 PHE A 342 TYR 0.012 0.001 TYR L 37 ARG 0.006 0.000 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.02890 ( 192) hydrogen bonds : angle 5.61166 ( 537) SS BOND : bond 0.00373 ( 4) SS BOND : angle 0.76904 ( 8) covalent geometry : bond 0.00261 ( 5635) covalent geometry : angle 0.52786 ( 7645) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4635.38 seconds wall clock time: 81 minutes 16.57 seconds (4876.57 seconds total)