Starting phenix.real_space_refine on Fri Aug 22 18:21:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c0j_45086/08_2025/9c0j_45086.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c0j_45086/08_2025/9c0j_45086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c0j_45086/08_2025/9c0j_45086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c0j_45086/08_2025/9c0j_45086.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c0j_45086/08_2025/9c0j_45086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c0j_45086/08_2025/9c0j_45086.map" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians K 1 8.98 5 P 167 5.49 5 Mg 1 5.21 5 S 13 5.16 5 C 3809 2.51 5 N 1240 2.21 5 O 1779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7010 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3481 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 13, 'TRANS': 411} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "R" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3313 Classifications: {'RNA': 155} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 10, 'rna3p_pur': 67, 'rna3p_pyr': 61} Link IDs: {'rna2p': 26, 'rna3p': 128} Chain breaks: 4 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.93, per 1000 atoms: 0.28 Number of scatterers: 7010 At special positions: 0 Unit cell: (131.716, 110.5, 79.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 S 13 16.00 P 167 15.00 Mg 1 11.99 O 1779 8.00 N 1240 7.00 C 3809 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 250.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 814 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 53.4% alpha, 13.6% beta 58 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 removed outlier: 3.603A pdb=" N LYS A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 removed outlier: 3.630A pdb=" N ILE A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 38 " --> pdb=" O GLU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 101 removed outlier: 4.132A pdb=" N GLY A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS A 93 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 149 through 162 Processing helix chain 'A' and resid 167 through 179 Processing helix chain 'A' and resid 185 through 193 Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 237 through 246 removed outlier: 3.731A pdb=" N MET A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 260 removed outlier: 3.728A pdb=" N ARG A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.772A pdb=" N ALA A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 336 through 368 removed outlier: 3.865A pdb=" N LEU A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 385 Processing helix chain 'A' and resid 391 through 403 Processing helix chain 'A' and resid 405 through 413 removed outlier: 3.937A pdb=" N LYS A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 425 Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 74 removed outlier: 3.780A pdb=" N ARG A 70 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 49 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE A 44 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 267 removed outlier: 3.645A pdb=" N CYS A 134 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 314 " --> pdb=" O LYS A 311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 323 181 hydrogen bonds defined for protein. 516 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 140 hydrogen bonds 236 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 816 1.32 - 1.44: 2984 1.44 - 1.56: 3337 1.56 - 1.68: 334 1.68 - 1.81: 22 Bond restraints: 7493 Sorted by residual: bond pdb=" C LYS A 205 " pdb=" O LYS A 205 " ideal model delta sigma weight residual 1.234 1.193 0.041 1.28e-02 6.10e+03 1.04e+01 bond pdb=" CB ASP A 329 " pdb=" CG ASP A 329 " ideal model delta sigma weight residual 1.516 1.582 -0.066 2.50e-02 1.60e+03 6.99e+00 bond pdb=" C1' DT P 8 " pdb=" N1 DT P 8 " ideal model delta sigma weight residual 1.490 1.568 -0.078 3.00e-02 1.11e+03 6.77e+00 bond pdb=" C1' DT P 5 " pdb=" N1 DT P 5 " ideal model delta sigma weight residual 1.490 1.567 -0.077 3.00e-02 1.11e+03 6.51e+00 bond pdb=" N CYS A 207 " pdb=" CA CYS A 207 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.23e-02 6.61e+03 4.24e+00 ... (remaining 7488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 10341 2.04 - 4.08: 449 4.08 - 6.13: 81 6.13 - 8.17: 18 8.17 - 10.21: 8 Bond angle restraints: 10897 Sorted by residual: angle pdb=" C LYS A 311 " pdb=" N ASP A 312 " pdb=" CA ASP A 312 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.86e+01 angle pdb=" O3' A R 210 " pdb=" C3' A R 210 " pdb=" C2' A R 210 " ideal model delta sigma weight residual 113.70 121.37 -7.67 1.50e+00 4.44e-01 2.62e+01 angle pdb=" CA ARG A 390 " pdb=" CB ARG A 390 " pdb=" CG ARG A 390 " ideal model delta sigma weight residual 114.10 123.91 -9.81 2.00e+00 2.50e-01 2.41e+01 angle pdb=" N LYS A 205 " pdb=" CA LYS A 205 " pdb=" C LYS A 205 " ideal model delta sigma weight residual 110.14 102.94 7.20 1.55e+00 4.16e-01 2.16e+01 angle pdb=" CA ASP A 329 " pdb=" CB ASP A 329 " pdb=" CG ASP A 329 " ideal model delta sigma weight residual 112.60 117.06 -4.46 1.00e+00 1.00e+00 1.98e+01 ... (remaining 10892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.66: 4126 28.66 - 57.32: 345 57.32 - 85.98: 202 85.98 - 114.63: 7 114.63 - 143.29: 6 Dihedral angle restraints: 4686 sinusoidal: 3423 harmonic: 1263 Sorted by residual: dihedral pdb=" O4' U R 134 " pdb=" C1' U R 134 " pdb=" N1 U R 134 " pdb=" C2 U R 134 " ideal model delta sinusoidal sigma weight residual -160.00 -67.13 -92.87 1 1.50e+01 4.44e-03 4.48e+01 dihedral pdb=" C2 TTP A 502 " pdb=" C1' TTP A 502 " pdb=" N1 TTP A 502 " pdb=" O4' TTP A 502 " ideal model delta sinusoidal sigma weight residual 301.68 158.39 143.29 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" O2G TTP A 502 " pdb=" O3B TTP A 502 " pdb=" PG TTP A 502 " pdb=" PB TTP A 502 " ideal model delta sinusoidal sigma weight residual 180.00 49.01 130.99 1 2.00e+01 2.50e-03 3.97e+01 ... (remaining 4683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1162 0.073 - 0.145: 138 0.145 - 0.218: 19 0.218 - 0.291: 4 0.291 - 0.363: 1 Chirality restraints: 1324 Sorted by residual: chirality pdb=" C3' A R 210 " pdb=" C4' A R 210 " pdb=" O3' A R 210 " pdb=" C2' A R 210 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" C1' U R 173 " pdb=" O4' U R 173 " pdb=" C2' U R 173 " pdb=" N1 U R 173 " both_signs ideal model delta sigma weight residual False 2.47 2.18 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C1' U R 224 " pdb=" O4' U R 224 " pdb=" C2' U R 224 " pdb=" N1 U R 224 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1321 not shown) Planarity restraints: 771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 254 " -0.226 9.50e-02 1.11e+02 1.02e-01 7.97e+00 pdb=" NE ARG A 254 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 254 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG A 254 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 254 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 302 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C LYS A 302 " 0.046 2.00e-02 2.50e+03 pdb=" O LYS A 302 " -0.017 2.00e-02 2.50e+03 pdb=" N THR A 303 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 204 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C ARG A 204 " 0.046 2.00e-02 2.50e+03 pdb=" O ARG A 204 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS A 205 " -0.016 2.00e-02 2.50e+03 ... (remaining 768 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.71: 374 2.71 - 3.32: 6416 3.32 - 3.92: 15484 3.92 - 4.53: 20134 4.53 - 5.14: 27208 Nonbonded interactions: 69616 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O1B TTP A 502 " model vdw 2.099 2.170 nonbonded pdb=" OD2 ASP A 269 " pdb="MG MG A 501 " model vdw 2.119 2.170 nonbonded pdb=" O LEU A 141 " pdb="MG MG A 501 " model vdw 2.307 2.170 nonbonded pdb=" O TYR A 381 " pdb=" OG SER A 385 " model vdw 2.365 3.040 nonbonded pdb=" OH TYR A 86 " pdb=" OD2 ASP A 169 " model vdw 2.385 3.040 ... (remaining 69611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.450 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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 : 0.005 0.078 7493 Z= 0.253 Angle : 1.022 10.208 10897 Z= 0.539 Chirality : 0.051 0.363 1324 Planarity : 0.009 0.102 771 Dihedral : 22.014 143.293 3872 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 0.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.80 % Allowed : 4.29 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.36), residues: 423 helix: -0.83 (0.29), residues: 209 sheet: 1.28 (0.67), residues: 55 loop : 0.07 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG A 254 TYR 0.021 0.003 TYR A 89 PHE 0.021 0.003 PHE A 212 TRP 0.013 0.002 TRP A 8 HIS 0.006 0.002 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 7493) covalent geometry : angle 1.02186 (10897) hydrogen bonds : bond 0.15167 ( 321) hydrogen bonds : angle 5.62385 ( 752) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.184 Fit side-chains REVERT: A 198 ASN cc_start: 0.8565 (t0) cc_final: 0.8306 (t0) REVERT: A 205 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8059 (mtpp) REVERT: A 246 MET cc_start: 0.8827 (mmm) cc_final: 0.8616 (mmt) REVERT: A 259 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7290 (mt-10) REVERT: A 319 MET cc_start: 0.8333 (mtm) cc_final: 0.7991 (mtp) REVERT: A 329 ASP cc_start: 0.8330 (p0) cc_final: 0.8073 (p0) outliers start: 3 outliers final: 1 residues processed: 59 average time/residue: 0.1816 time to fit residues: 12.6157 Evaluate side-chains 42 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 296 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 30.0000 chunk 56 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.0970 chunk 32 optimal weight: 0.0170 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 overall best weight: 2.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.163603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.110362 restraints weight = 7040.811| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 0.79 r_work: 0.2719 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7493 Z= 0.192 Angle : 0.637 6.491 10897 Z= 0.334 Chirality : 0.039 0.243 1324 Planarity : 0.005 0.036 771 Dihedral : 22.909 148.251 2990 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.34 % Allowed : 5.63 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.39), residues: 423 helix: 0.73 (0.34), residues: 212 sheet: 1.08 (0.63), residues: 64 loop : -0.16 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 70 TYR 0.016 0.002 TYR A 245 PHE 0.010 0.002 PHE A 328 TRP 0.011 0.002 TRP A 157 HIS 0.005 0.002 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 7493) covalent geometry : angle 0.63697 (10897) hydrogen bonds : bond 0.06266 ( 321) hydrogen bonds : angle 3.63556 ( 752) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.196 Fit side-chains REVERT: A 205 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8045 (mtpp) REVERT: A 329 ASP cc_start: 0.8634 (p0) cc_final: 0.8382 (p0) REVERT: A 352 ARG cc_start: 0.8528 (ttm-80) cc_final: 0.7996 (mtt90) outliers start: 5 outliers final: 4 residues processed: 51 average time/residue: 0.1696 time to fit residues: 10.4112 Evaluate side-chains 51 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 4 optimal weight: 0.0970 chunk 10 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.165102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.114171 restraints weight = 7048.544| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 0.78 r_work: 0.2736 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7493 Z= 0.146 Angle : 0.583 6.808 10897 Z= 0.304 Chirality : 0.036 0.239 1324 Planarity : 0.004 0.034 771 Dihedral : 22.794 147.038 2990 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.41 % Allowed : 7.51 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.40), residues: 423 helix: 1.42 (0.35), residues: 212 sheet: 1.11 (0.63), residues: 64 loop : -0.21 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 254 TYR 0.012 0.001 TYR A 245 PHE 0.007 0.001 PHE A 328 TRP 0.007 0.001 TRP A 157 HIS 0.003 0.001 HIS A 16 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 7493) covalent geometry : angle 0.58270 (10897) hydrogen bonds : bond 0.05375 ( 321) hydrogen bonds : angle 3.39287 ( 752) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.7889 (mtpp) REVERT: A 352 ARG cc_start: 0.8536 (ttm-80) cc_final: 0.7958 (mtt90) outliers start: 9 outliers final: 5 residues processed: 52 average time/residue: 0.1530 time to fit residues: 9.6703 Evaluate side-chains 49 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 0.2980 chunk 42 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.162713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.111647 restraints weight = 7153.180| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 0.77 r_work: 0.2715 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7493 Z= 0.197 Angle : 0.626 6.718 10897 Z= 0.322 Chirality : 0.038 0.235 1324 Planarity : 0.005 0.036 771 Dihedral : 22.772 149.255 2990 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.95 % Allowed : 8.31 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.40), residues: 423 helix: 1.45 (0.36), residues: 211 sheet: 1.03 (0.64), residues: 64 loop : -0.43 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 352 TYR 0.015 0.002 TYR A 245 PHE 0.010 0.002 PHE A 328 TRP 0.009 0.002 TRP A 157 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 7493) covalent geometry : angle 0.62646 (10897) hydrogen bonds : bond 0.06085 ( 321) hydrogen bonds : angle 3.46600 ( 752) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: A 259 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7619 (mt-10) REVERT: A 352 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.7946 (mtt90) outliers start: 11 outliers final: 8 residues processed: 52 average time/residue: 0.1512 time to fit residues: 9.6176 Evaluate side-chains 52 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 28 optimal weight: 0.0470 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.162752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.110613 restraints weight = 7082.433| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 0.72 r_work: 0.2671 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7493 Z= 0.183 Angle : 0.611 6.698 10897 Z= 0.315 Chirality : 0.037 0.235 1324 Planarity : 0.004 0.036 771 Dihedral : 22.755 149.276 2990 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.41 % Allowed : 9.38 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.40), residues: 423 helix: 1.46 (0.36), residues: 211 sheet: 1.06 (0.64), residues: 64 loop : -0.53 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 254 TYR 0.014 0.002 TYR A 245 PHE 0.010 0.002 PHE A 47 TRP 0.008 0.001 TRP A 157 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 7493) covalent geometry : angle 0.61131 (10897) hydrogen bonds : bond 0.05979 ( 321) hydrogen bonds : angle 3.46194 ( 752) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: A 259 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7730 (mt-10) REVERT: A 352 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8009 (mtt90) outliers start: 9 outliers final: 7 residues processed: 49 average time/residue: 0.1436 time to fit residues: 8.5957 Evaluate side-chains 50 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.166705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.113678 restraints weight = 7087.681| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 0.77 r_work: 0.2705 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7493 Z= 0.147 Angle : 0.595 6.683 10897 Z= 0.307 Chirality : 0.036 0.233 1324 Planarity : 0.004 0.036 771 Dihedral : 22.748 149.061 2990 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.14 % Allowed : 9.92 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.40), residues: 423 helix: 1.61 (0.36), residues: 211 sheet: 1.08 (0.64), residues: 64 loop : -0.52 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 213 TYR 0.012 0.001 TYR A 245 PHE 0.009 0.001 PHE A 47 TRP 0.006 0.001 TRP A 157 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 7493) covalent geometry : angle 0.59469 (10897) hydrogen bonds : bond 0.05731 ( 321) hydrogen bonds : angle 3.42758 ( 752) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: A 259 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7653 (mt-10) REVERT: A 352 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.7976 (mtt90) outliers start: 8 outliers final: 7 residues processed: 49 average time/residue: 0.1573 time to fit residues: 9.4268 Evaluate side-chains 49 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 30 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.161086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.110908 restraints weight = 7107.591| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 0.72 r_work: 0.2694 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 7493 Z= 0.241 Angle : 0.661 6.890 10897 Z= 0.337 Chirality : 0.039 0.234 1324 Planarity : 0.005 0.038 771 Dihedral : 22.772 149.374 2990 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.95 % Allowed : 9.65 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.40), residues: 423 helix: 1.32 (0.36), residues: 211 sheet: 1.00 (0.64), residues: 64 loop : -0.73 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 123 TYR 0.014 0.002 TYR A 245 PHE 0.011 0.002 PHE A 328 TRP 0.010 0.002 TRP A 157 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00551 ( 7493) covalent geometry : angle 0.66073 (10897) hydrogen bonds : bond 0.06639 ( 321) hydrogen bonds : angle 3.56061 ( 752) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7249 (pttt) cc_final: 0.6717 (mmtm) REVERT: A 119 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: A 259 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7607 (mt-10) REVERT: A 352 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.7931 (mtt90) outliers start: 11 outliers final: 7 residues processed: 53 average time/residue: 0.1521 time to fit residues: 9.8008 Evaluate side-chains 51 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 43 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.162857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.112632 restraints weight = 7114.356| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 0.75 r_work: 0.2719 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7493 Z= 0.146 Angle : 0.604 6.587 10897 Z= 0.311 Chirality : 0.036 0.234 1324 Planarity : 0.004 0.039 771 Dihedral : 22.770 149.243 2990 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.14 % Allowed : 11.26 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.41), residues: 423 helix: 1.52 (0.36), residues: 211 sheet: 1.15 (0.65), residues: 64 loop : -0.72 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 260 TYR 0.014 0.001 TYR A 245 PHE 0.011 0.001 PHE A 52 TRP 0.006 0.001 TRP A 157 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7493) covalent geometry : angle 0.60397 (10897) hydrogen bonds : bond 0.05997 ( 321) hydrogen bonds : angle 3.46882 ( 752) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.197 Fit side-chains REVERT: A 53 LYS cc_start: 0.7192 (pttt) cc_final: 0.6674 (mmtm) REVERT: A 119 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: A 259 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7630 (mt-10) REVERT: A 352 ARG cc_start: 0.8502 (ttm-80) cc_final: 0.7950 (mtt90) outliers start: 8 outliers final: 7 residues processed: 48 average time/residue: 0.1563 time to fit residues: 9.2399 Evaluate side-chains 49 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 0.0370 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.164533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.113268 restraints weight = 7058.848| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 0.73 r_work: 0.2744 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7493 Z= 0.127 Angle : 0.575 6.399 10897 Z= 0.297 Chirality : 0.035 0.227 1324 Planarity : 0.004 0.038 771 Dihedral : 22.720 147.881 2990 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.34 % Allowed : 12.06 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.41), residues: 423 helix: 1.74 (0.36), residues: 211 sheet: 1.32 (0.64), residues: 66 loop : -0.65 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 254 TYR 0.012 0.001 TYR A 14 PHE 0.020 0.001 PHE A 52 TRP 0.007 0.001 TRP A 157 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7493) covalent geometry : angle 0.57509 (10897) hydrogen bonds : bond 0.05565 ( 321) hydrogen bonds : angle 3.39442 ( 752) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.189 Fit side-chains REVERT: A 53 LYS cc_start: 0.7391 (pttt) cc_final: 0.6725 (mmtm) REVERT: A 119 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: A 259 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7635 (mt-10) REVERT: A 352 ARG cc_start: 0.8494 (ttm-80) cc_final: 0.8017 (mtt180) outliers start: 5 outliers final: 3 residues processed: 46 average time/residue: 0.1495 time to fit residues: 8.3570 Evaluate side-chains 46 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 30.0000 chunk 36 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.165705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.114054 restraints weight = 7075.359| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 0.72 r_work: 0.2731 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7493 Z= 0.178 Angle : 0.599 6.628 10897 Z= 0.307 Chirality : 0.036 0.230 1324 Planarity : 0.004 0.039 771 Dihedral : 22.687 149.126 2990 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.34 % Allowed : 12.06 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.41), residues: 423 helix: 1.64 (0.36), residues: 211 sheet: 0.90 (0.63), residues: 68 loop : -0.57 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 352 TYR 0.013 0.002 TYR A 245 PHE 0.013 0.002 PHE A 52 TRP 0.007 0.001 TRP A 157 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 7493) covalent geometry : angle 0.59890 (10897) hydrogen bonds : bond 0.06027 ( 321) hydrogen bonds : angle 3.42503 ( 752) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.194 Fit side-chains REVERT: A 53 LYS cc_start: 0.7363 (pttt) cc_final: 0.6727 (mmtm) REVERT: A 119 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: A 259 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7605 (mt-10) REVERT: A 352 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.7946 (mtt90) outliers start: 5 outliers final: 4 residues processed: 47 average time/residue: 0.1668 time to fit residues: 9.4300 Evaluate side-chains 48 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 48 optimal weight: 30.0000 chunk 16 optimal weight: 0.0980 chunk 50 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.167207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.116859 restraints weight = 7008.993| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 0.74 r_work: 0.2738 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7493 Z= 0.127 Angle : 0.577 6.619 10897 Z= 0.297 Chirality : 0.034 0.229 1324 Planarity : 0.004 0.039 771 Dihedral : 22.690 148.730 2990 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.34 % Allowed : 12.33 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.41), residues: 423 helix: 1.75 (0.36), residues: 211 sheet: 0.94 (0.63), residues: 68 loop : -0.56 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 254 TYR 0.012 0.001 TYR A 245 PHE 0.013 0.001 PHE A 52 TRP 0.004 0.001 TRP A 157 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7493) covalent geometry : angle 0.57714 (10897) hydrogen bonds : bond 0.05688 ( 321) hydrogen bonds : angle 3.38561 ( 752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1723.26 seconds wall clock time: 30 minutes 22.27 seconds (1822.27 seconds total)