Starting phenix.real_space_refine on Thu Sep 10 19:48:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8acc_15346/09_2026/8acc_15346.cif Found real_map, /net/cci-nas-00/data/ceres_data/8acc_15346/09_2026/8acc_15346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8acc_15346/09_2026/8acc_15346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8acc_15346/09_2026/8acc_15346.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8acc_15346/09_2026/8acc_15346.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8acc_15346/09_2026/8acc_15346.cif" model { file = "/net/cci-nas-00/data/ceres_data/8acc_15346/09_2026/8acc_15346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8acc_15346/09_2026/8acc_15346.cif" } resolution = 2.9 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= 0.012 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 10 5.16 5 C 1104 2.51 5 N 309 2.21 5 O 351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1779 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1680 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 10, 'TRANS': 220} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ASP:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Classifications: {'RNAv2': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 3} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.47, per 1000 atoms: 0.26 Number of scatterers: 1779 At special positions: 0 Unit cell: (85.2, 73.485, 123.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 5 15.00 O 351 8.00 N 309 7.00 C 1104 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: 0.11 Conformation dependent library (CDL) restraints added in 40.4 milliseconds 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 438 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 1 sheets defined 49.4% alpha, 4.8% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.518A pdb=" N ARG A 85 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.624A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 128 Processing helix chain 'A' and resid 130 through 137 Processing helix chain 'A' and resid 137 through 149 removed outlier: 3.882A pdb=" N ALA A 141 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 removed outlier: 3.861A pdb=" N ASN A 157 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 189 through 194 removed outlier: 3.544A pdb=" N VAL A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.531A pdb=" N ALA A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.992A pdb=" N GLU A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.502A pdb=" N ARG A 262 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 166 removed outlier: 4.034A pdb=" N GLU A 173 " --> pdb=" O ILE A 165 " (cutoff:3.500A) 64 hydrogen bonds defined for protein. 171 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 0.13 Time building geometry restraints manager: 0.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 538 1.34 - 1.45: 271 1.45 - 1.57: 984 1.57 - 1.69: 9 1.69 - 1.80: 18 Bond restraints: 1820 Sorted by residual: bond pdb=" N PRO A 273 " pdb=" CA PRO A 273 " ideal model delta sigma weight residual 1.468 1.456 0.012 1.20e-02 6.94e+03 9.83e-01 bond pdb=" CA VAL A 286 " pdb=" CB VAL A 286 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.36e-02 5.41e+03 7.88e-01 bond pdb=" CA VAL A 289 " pdb=" CB VAL A 289 " ideal model delta sigma weight residual 1.536 1.526 0.010 1.17e-02 7.31e+03 7.02e-01 bond pdb=" CA VAL A 65 " pdb=" CB VAL A 65 " ideal model delta sigma weight residual 1.540 1.519 0.021 2.70e-02 1.37e+03 6.26e-01 bond pdb=" N GLY A 276 " pdb=" CA GLY A 276 " ideal model delta sigma weight residual 1.449 1.460 -0.011 1.45e-02 4.76e+03 5.73e-01 ... (remaining 1815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 2452 2.06 - 4.11: 42 4.11 - 6.17: 4 6.17 - 8.22: 5 8.22 - 10.28: 2 Bond angle restraints: 2505 Sorted by residual: angle pdb=" N PRO A 273 " pdb=" CA PRO A 273 " pdb=" CB PRO A 273 " ideal model delta sigma weight residual 103.27 110.20 -6.93 9.00e-01 1.23e+00 5.93e+01 angle pdb=" N PRO A 69 " pdb=" CA PRO A 69 " pdb=" CB PRO A 69 " ideal model delta sigma weight residual 103.08 110.52 -7.44 9.70e-01 1.06e+00 5.89e+01 angle pdb=" N PRO A 70 " pdb=" CA PRO A 70 " pdb=" CB PRO A 70 " ideal model delta sigma weight residual 103.25 110.45 -7.20 1.05e+00 9.07e-01 4.70e+01 angle pdb=" OP1 U B 6 " pdb=" P U B 6 " pdb=" OP2 U B 6 " ideal model delta sigma weight residual 119.60 109.32 10.28 3.00e+00 1.11e-01 1.17e+01 angle pdb=" OP1 U B 4 " pdb=" P U B 4 " pdb=" OP2 U B 4 " ideal model delta sigma weight residual 119.60 109.53 10.07 3.00e+00 1.11e-01 1.13e+01 ... (remaining 2500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.33: 966 15.33 - 30.66: 74 30.66 - 45.99: 23 45.99 - 61.32: 6 61.32 - 76.65: 2 Dihedral angle restraints: 1071 sinusoidal: 395 harmonic: 676 Sorted by residual: dihedral pdb=" C4' U B 5 " pdb=" C3' U B 5 " pdb=" C2' U B 5 " pdb=" C1' U B 5 " ideal model delta sinusoidal sigma weight residual 36.34 -34.45 70.79 1 3.10e+00 1.04e-01 6.70e+02 dihedral pdb=" O4' U B 5 " pdb=" C4' U B 5 " pdb=" C3' U B 5 " pdb=" C2' U B 5 " ideal model delta sinusoidal sigma weight residual -35.15 23.18 -58.33 1 4.00e+00 6.25e-02 2.85e+02 dihedral pdb=" O4' U B 5 " pdb=" C2' U B 5 " pdb=" C1' U B 5 " pdb=" C3' U B 5 " ideal model delta sinusoidal sigma weight residual -94.41 -34.77 -59.64 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 1068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 286 0.100 - 0.200: 5 0.200 - 0.300: 7 0.300 - 0.399: 0 0.399 - 0.499: 2 Chirality restraints: 300 Sorted by residual: chirality pdb=" P U B 6 " pdb=" OP1 U B 6 " pdb=" OP2 U B 6 " pdb=" O5' U B 6 " both_signs ideal model delta sigma weight residual True 2.17 -2.67 -0.50 2.00e-01 2.50e+01 6.23e+00 chirality pdb=" P U B 4 " pdb=" OP1 U B 4 " pdb=" OP2 U B 4 " pdb=" O5' U B 4 " both_signs ideal model delta sigma weight residual True 2.17 -2.64 -0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" CA PRO A 70 " pdb=" N PRO A 70 " pdb=" C PRO A 70 " pdb=" CB PRO A 70 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 297 not shown) Planarity restraints: 309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 256 " 0.005 2.00e-02 2.50e+03 1.02e-02 1.04e+00 pdb=" C ILE A 256 " -0.018 2.00e-02 2.50e+03 pdb=" O ILE A 256 " 0.007 2.00e-02 2.50e+03 pdb=" N ALA A 257 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 180 " 0.016 5.00e-02 4.00e+02 2.41e-02 9.33e-01 pdb=" N PRO A 181 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 159 " 0.004 2.00e-02 2.50e+03 7.32e-03 5.37e-01 pdb=" C HIS A 159 " -0.013 2.00e-02 2.50e+03 pdb=" O HIS A 159 " 0.005 2.00e-02 2.50e+03 pdb=" N THR A 160 " 0.004 2.00e-02 2.50e+03 ... (remaining 306 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 143 2.74 - 3.28: 1856 3.28 - 3.82: 2587 3.82 - 4.36: 3178 4.36 - 4.90: 5043 Nonbonded interactions: 12807 Sorted by model distance: nonbonded pdb=" O ALA A 258 " pdb=" OG1 THR A 261 " model vdw 2.200 3.040 nonbonded pdb=" O PRO A 181 " pdb=" ND2 ASN A 185 " model vdw 2.265 3.120 nonbonded pdb=" O VAL A 260 " pdb=" NH2 ARG A 263 " model vdw 2.273 3.120 nonbonded pdb=" O PRO A 188 " pdb=" OG1 THR A 189 " model vdw 2.307 3.040 nonbonded pdb=" OE2 GLU A 154 " pdb=" NZ LYS A 264 " model vdw 2.307 3.120 ... (remaining 12802 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: 0.460 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.990 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.000 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:5.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.002 0.021 1820 Z= 0.127 Angle : 0.721 10.278 2505 Z= 0.419 Chirality : 0.068 0.499 300 Planarity : 0.002 0.024 309 Dihedral : 13.199 76.647 633 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 2.18 % Allowed : 11.35 % Favored : 86.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.55), residues: 229 helix: -1.18 (0.53), residues: 100 sheet: 1.20 (1.45), residues: 12 loop : -2.40 (0.56), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 82 TYR 0.007 0.001 TYR A 205 PHE 0.007 0.001 PHE A 237 TRP 0.005 0.001 TRP A 161 HIS 0.001 0.000 HIS A 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.13 ( 1820) covalent geometry : angle 0.72138 / 0.42 ( 2505) hydrogen bonds : bond 0.25066 / 17.22 ( 64) hydrogen bonds : angle 6.96312 / 4.84 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.038 Fit side-chains REVERT: A 97 LYS cc_start: 0.8956 (mttp) cc_final: 0.7965 (tptt) REVERT: A 132 ASP cc_start: 0.7999 (t0) cc_final: 0.7764 (t0) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.3770 time to fit residues: 21.8081 Evaluate side-chains 49 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.0770 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 0.1980 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN A 104 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** 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 = 0.3675 r_free = 0.3675 target = 0.141870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.126535 restraints weight = 2834.862| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.08 r_work: 0.3409 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1820 Z= 0.107 Angle : 0.630 6.958 2505 Z= 0.307 Chirality : 0.050 0.258 300 Planarity : 0.003 0.021 309 Dihedral : 10.740 141.237 304 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.48 % Favored : 89.08 % Rotamer: Outliers : 1.97 % Allowed : 15.79 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.55), residues: 229 helix: -0.80 (0.53), residues: 101 sheet: 1.23 (1.37), residues: 12 loop : -2.16 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 263 TYR 0.008 0.001 TYR A 92 PHE 0.005 0.001 PHE A 237 TRP 0.010 0.001 TRP A 161 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.11 ( 1820) covalent geometry : angle 0.63003 / 0.31 ( 2505) hydrogen bonds : bond 0.03295 / 2.38 ( 64) hydrogen bonds : angle 4.72524 / 3.23 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.120 Fit side-chains REVERT: A 92 TYR cc_start: 0.8848 (t80) cc_final: 0.8638 (t80) REVERT: A 97 LYS cc_start: 0.8894 (mttp) cc_final: 0.7859 (tptt) REVERT: A 245 THR cc_start: 0.9299 (p) cc_final: 0.9089 (t) outliers start: 3 outliers final: 2 residues processed: 54 average time/residue: 0.6093 time to fit residues: 33.4000 Evaluate side-chains 52 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 8 optimal weight: 10.0000 chunk 6 optimal weight: 0.0070 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 chunk 19 optimal weight: 0.0040 chunk 22 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 overall best weight: 2.5614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** 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 = 0.3606 r_free = 0.3606 target = 0.136453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120985 restraints weight = 2827.846| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.06 r_work: 0.3351 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1820 Z= 0.131 Angle : 0.625 6.034 2505 Z= 0.308 Chirality : 0.052 0.249 300 Planarity : 0.003 0.018 309 Dihedral : 10.800 140.835 304 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.44 % Allowed : 12.23 % Favored : 87.34 % Rotamer: Outliers : 4.61 % Allowed : 19.08 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.55), residues: 229 helix: -0.46 (0.53), residues: 95 sheet: -0.33 (1.37), residues: 16 loop : -2.29 (0.57), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 263 TYR 0.010 0.001 TYR A 92 PHE 0.010 0.002 PHE A 237 TRP 0.010 0.001 TRP A 161 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 1820) covalent geometry : angle 0.62487 / 0.31 ( 2505) hydrogen bonds : bond 0.03121 / 2.25 ( 64) hydrogen bonds : angle 4.33453 / 2.98 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.072 Fit side-chains REVERT: A 97 LYS cc_start: 0.8910 (mttp) cc_final: 0.7911 (tptt) REVERT: A 262 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7854 (ptp-110) outliers start: 7 outliers final: 4 residues processed: 54 average time/residue: 0.5804 time to fit residues: 31.8428 Evaluate side-chains 53 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 264 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 20 optimal weight: 0.0570 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 11 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.1980 chunk 4 optimal weight: 6.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.138159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122426 restraints weight = 2826.324| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.16 r_work: 0.3353 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1820 Z= 0.105 Angle : 0.582 6.280 2505 Z= 0.289 Chirality : 0.049 0.252 300 Planarity : 0.003 0.018 309 Dihedral : 10.608 137.882 304 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.04 % Favored : 89.08 % Rotamer: Outliers : 3.29 % Allowed : 23.03 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.56), residues: 229 helix: -0.21 (0.54), residues: 95 sheet: -0.50 (1.36), residues: 14 loop : -2.23 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 155 TYR 0.009 0.001 TYR A 92 PHE 0.007 0.001 PHE A 237 TRP 0.009 0.001 TRP A 161 HIS 0.005 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 ( 1820) covalent geometry : angle 0.58235 / 0.29 ( 2505) hydrogen bonds : bond 0.02629 / 1.93 ( 64) hydrogen bonds : angle 4.15820 / 2.85 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.070 Fit side-chains REVERT: A 92 TYR cc_start: 0.9000 (t80) cc_final: 0.8758 (t80) REVERT: A 97 LYS cc_start: 0.8880 (mttp) cc_final: 0.7867 (tptt) REVERT: A 262 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7532 (ptp-110) outliers start: 5 outliers final: 3 residues processed: 50 average time/residue: 0.6107 time to fit residues: 30.9973 Evaluate side-chains 51 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 264 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 14 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 0.0060 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 115 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 = 0.3595 r_free = 0.3595 target = 0.137078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.121244 restraints weight = 2860.005| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.16 r_work: 0.3316 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1820 Z= 0.111 Angle : 0.584 5.679 2505 Z= 0.289 Chirality : 0.049 0.233 300 Planarity : 0.003 0.017 309 Dihedral : 10.604 138.937 304 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.04 % Favored : 89.08 % Rotamer: Outliers : 4.61 % Allowed : 21.71 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.56), residues: 229 helix: -0.08 (0.54), residues: 95 sheet: -0.69 (1.37), residues: 14 loop : -2.23 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 263 TYR 0.011 0.001 TYR A 87 PHE 0.008 0.001 PHE A 237 TRP 0.010 0.001 TRP A 161 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 1820) covalent geometry : angle 0.58420 / 0.29 ( 2505) hydrogen bonds : bond 0.02646 / 1.93 ( 64) hydrogen bonds : angle 4.07911 / 2.79 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.071 Fit side-chains REVERT: A 92 TYR cc_start: 0.9008 (t80) cc_final: 0.8761 (t80) REVERT: A 97 LYS cc_start: 0.8897 (mttp) cc_final: 0.7907 (tptt) REVERT: A 256 ILE cc_start: 0.9218 (mm) cc_final: 0.8990 (mt) REVERT: A 262 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7567 (ptp-110) outliers start: 7 outliers final: 4 residues processed: 51 average time/residue: 0.5459 time to fit residues: 28.2776 Evaluate side-chains 51 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 2 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 20.0000 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 40.0000 chunk 3 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 115 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 = 0.3649 r_free = 0.3649 target = 0.141463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.125607 restraints weight = 2835.603| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.19 r_work: 0.3378 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1820 Z= 0.099 Angle : 0.571 6.043 2505 Z= 0.282 Chirality : 0.049 0.237 300 Planarity : 0.002 0.016 309 Dihedral : 10.438 136.738 304 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.17 % Favored : 89.96 % Rotamer: Outliers : 3.29 % Allowed : 23.68 % Favored : 73.03 % 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 are not related in a simple way. whole: -1.51 (0.56), residues: 229 helix: 0.53 (0.56), residues: 89 sheet: -1.03 (1.35), residues: 14 loop : -2.26 (0.55), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 82 TYR 0.009 0.001 TYR A 92 PHE 0.006 0.001 PHE A 237 TRP 0.009 0.001 TRP A 161 HIS 0.002 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 ( 1820) covalent geometry : angle 0.57076 / 0.28 ( 2505) hydrogen bonds : bond 0.02387 / 1.76 ( 64) hydrogen bonds : angle 3.83273 / 2.65 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.057 Fit side-chains REVERT: A 92 TYR cc_start: 0.8977 (t80) cc_final: 0.8666 (t80) REVERT: A 97 LYS cc_start: 0.8827 (mttp) cc_final: 0.7865 (tptt) REVERT: A 194 MET cc_start: 0.9229 (mmm) cc_final: 0.8986 (mmp) REVERT: A 256 ILE cc_start: 0.9176 (mm) cc_final: 0.8951 (mt) REVERT: A 262 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7242 (ptp-110) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 0.4905 time to fit residues: 26.8905 Evaluate side-chains 53 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 3 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 115 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 = 0.3586 r_free = 0.3586 target = 0.136141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.120153 restraints weight = 2814.424| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.13 r_work: 0.3303 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1820 Z= 0.126 Angle : 0.603 5.328 2505 Z= 0.298 Chirality : 0.050 0.238 300 Planarity : 0.003 0.026 309 Dihedral : 10.602 139.260 304 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.04 % Favored : 89.08 % Rotamer: Outliers : 2.63 % Allowed : 26.32 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.56), residues: 229 helix: 0.23 (0.54), residues: 95 sheet: -1.34 (1.34), residues: 14 loop : -2.13 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 82 TYR 0.010 0.001 TYR A 87 PHE 0.010 0.001 PHE A 237 TRP 0.009 0.001 TRP A 161 HIS 0.002 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 1820) covalent geometry : angle 0.60332 / 0.30 ( 2505) hydrogen bonds : bond 0.02645 / 1.90 ( 64) hydrogen bonds : angle 3.94352 / 2.73 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.066 Fit side-chains REVERT: A 92 TYR cc_start: 0.8987 (t80) cc_final: 0.8670 (t80) REVERT: A 97 LYS cc_start: 0.8890 (mttp) cc_final: 0.7936 (tptt) REVERT: A 256 ILE cc_start: 0.9211 (mm) cc_final: 0.8991 (mt) REVERT: A 262 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7557 (ptp-110) outliers start: 4 outliers final: 4 residues processed: 54 average time/residue: 0.5274 time to fit residues: 28.8981 Evaluate side-chains 52 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 20 optimal weight: 0.0770 chunk 14 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 16 optimal weight: 0.0170 chunk 0 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 overall best weight: 2.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 115 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 = 0.3579 r_free = 0.3579 target = 0.135794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.119939 restraints weight = 2864.079| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.11 r_work: 0.3300 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1820 Z= 0.122 Angle : 0.608 5.757 2505 Z= 0.299 Chirality : 0.050 0.246 300 Planarity : 0.003 0.027 309 Dihedral : 10.522 137.494 304 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.61 % Favored : 89.52 % Rotamer: Outliers : 3.95 % Allowed : 28.29 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.57), residues: 229 helix: 0.38 (0.56), residues: 95 sheet: -1.45 (1.34), residues: 14 loop : -2.10 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 82 TYR 0.008 0.001 TYR A 92 PHE 0.008 0.001 PHE A 237 TRP 0.009 0.001 TRP A 161 HIS 0.002 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 1820) covalent geometry : angle 0.60755 / 0.30 ( 2505) hydrogen bonds : bond 0.02529 / 1.84 ( 64) hydrogen bonds : angle 3.84661 / 2.68 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.070 Fit side-chains REVERT: A 92 TYR cc_start: 0.9028 (t80) cc_final: 0.8708 (t80) REVERT: A 97 LYS cc_start: 0.8879 (mttp) cc_final: 0.7867 (tptt) REVERT: A 250 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7474 (pm20) REVERT: A 256 ILE cc_start: 0.9229 (mm) cc_final: 0.9013 (mt) REVERT: A 262 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7589 (ptp-110) outliers start: 6 outliers final: 5 residues processed: 56 average time/residue: 0.4955 time to fit residues: 28.2169 Evaluate side-chains 57 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 1 optimal weight: 0.0570 chunk 12 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 overall best weight: 1.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.121455 restraints weight = 2859.625| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.12 r_work: 0.3335 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1820 Z= 0.108 Angle : 0.590 5.711 2505 Z= 0.290 Chirality : 0.049 0.233 300 Planarity : 0.003 0.029 309 Dihedral : 10.435 136.647 304 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.17 % Favored : 89.96 % Rotamer: Outliers : 4.61 % Allowed : 28.29 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.57), residues: 229 helix: 0.90 (0.57), residues: 89 sheet: -1.58 (1.34), residues: 14 loop : -2.10 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 82 TYR 0.011 0.001 TYR A 87 PHE 0.007 0.001 PHE A 237 TRP 0.010 0.001 TRP A 161 HIS 0.002 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 1820) covalent geometry : angle 0.58995 / 0.29 ( 2505) hydrogen bonds : bond 0.02382 / 1.73 ( 64) hydrogen bonds : angle 3.75540 / 2.62 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.039 Fit side-chains REVERT: A 92 TYR cc_start: 0.9037 (t80) cc_final: 0.8777 (t80) REVERT: A 97 LYS cc_start: 0.8872 (mttp) cc_final: 0.7855 (tptt) REVERT: A 250 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7449 (pm20) REVERT: A 256 ILE cc_start: 0.9195 (mm) cc_final: 0.8975 (mt) REVERT: A 262 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7377 (ptp-110) outliers start: 7 outliers final: 5 residues processed: 55 average time/residue: 0.4221 time to fit residues: 23.5871 Evaluate side-chains 55 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 ASN A 168 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.115665 restraints weight = 2845.496| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.10 r_work: 0.3235 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1820 Z= 0.158 Angle : 0.669 6.146 2505 Z= 0.327 Chirality : 0.053 0.278 300 Planarity : 0.003 0.032 309 Dihedral : 10.696 139.540 304 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.87 % Allowed : 10.48 % Favored : 88.65 % Rotamer: Outliers : 3.95 % Allowed : 29.61 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.57), residues: 229 helix: 0.31 (0.55), residues: 95 sheet: -1.67 (1.37), residues: 14 loop : -2.04 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 82 TYR 0.008 0.001 TYR A 92 PHE 0.011 0.002 PHE A 237 TRP 0.008 0.001 TRP A 161 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 1820) covalent geometry : angle 0.66944 / 0.33 ( 2505) hydrogen bonds : bond 0.02853 / 2.04 ( 64) hydrogen bonds : angle 3.97697 / 2.78 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 458 Ramachandran restraints generated. 229 Oldfield, 0 Emsley, 229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.040 Fit side-chains REVERT: A 92 TYR cc_start: 0.8997 (t80) cc_final: 0.8752 (t80) REVERT: A 97 LYS cc_start: 0.8905 (mttp) cc_final: 0.7873 (tptt) REVERT: A 236 ASP cc_start: 0.7888 (t0) cc_final: 0.7562 (t0) REVERT: A 247 LYS cc_start: 0.8631 (mmmm) cc_final: 0.7934 (mppt) REVERT: A 250 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7506 (pm20) REVERT: A 256 ILE cc_start: 0.9221 (mm) cc_final: 0.9013 (mt) REVERT: A 262 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7755 (ptp-110) outliers start: 6 outliers final: 4 residues processed: 57 average time/residue: 0.4348 time to fit residues: 25.1643 Evaluate side-chains 59 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 263 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 22 optimal weight: 20.0000 chunk 3 optimal weight: 0.0970 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.0010 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 overall best weight: 2.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN A 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118207 restraints weight = 2908.170| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.15 r_work: 0.3297 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1820 Z= 0.121 Angle : 0.625 6.109 2505 Z= 0.307 Chirality : 0.050 0.261 300 Planarity : 0.003 0.032 309 Dihedral : 10.533 137.431 304 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.61 % Favored : 89.52 % Rotamer: Outliers : 3.95 % Allowed : 29.61 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.58), residues: 229 helix: 0.39 (0.56), residues: 95 sheet: -1.71 (1.35), residues: 14 loop : -2.02 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 82 TYR 0.011 0.001 TYR A 87 PHE 0.008 0.001 PHE A 237 TRP 0.009 0.001 TRP A 161 HIS 0.002 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 1820) covalent geometry : angle 0.62514 / 0.31 ( 2505) hydrogen bonds : bond 0.02523 / 1.83 ( 64) hydrogen bonds : angle 3.87708 / 2.72 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1065.09 seconds wall clock time: 18 minutes 46.12 seconds (1126.12 seconds total)