Starting phenix.real_space_refine on Fri Aug 22 14:25:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hbv_34644/08_2025/8hbv_34644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hbv_34644/08_2025/8hbv_34644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hbv_34644/08_2025/8hbv_34644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hbv_34644/08_2025/8hbv_34644.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hbv_34644/08_2025/8hbv_34644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hbv_34644/08_2025/8hbv_34644.map" } resolution = 2.51 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= 0.005 sd= 0.118 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 4 5.49 5 S 18 5.16 5 C 2100 2.51 5 N 543 2.21 5 O 614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 3279 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2180 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 274} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 997 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 102 Unusual residues: {'CDL': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 102 Time building chain proxies: 0.93, per 1000 atoms: 0.28 Number of scatterers: 3279 At special positions: 0 Unit cell: (69.222, 68.388, 110.922, 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 18 16.00 P 4 15.00 O 614 8.00 N 543 7.00 C 2100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.02 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: 0.35 Conformation dependent library (CDL) restraints added in 124.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 3 sheets defined 60.4% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 11 through 42 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 56 through 69 Processing helix chain 'A' and resid 76 through 105 removed outlier: 4.567A pdb=" N ASP A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N THR A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 143 Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 155 through 168 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.659A pdb=" N LYS A 174 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 204 Processing helix chain 'A' and resid 210 through 242 removed outlier: 3.563A pdb=" N HIS A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Proline residue: A 231 - end of helix Processing helix chain 'A' and resid 249 through 262 Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 269 through 297 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.772A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.772A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) 230 hydrogen bonds defined for protein. 639 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.37 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 743 1.33 - 1.45: 730 1.45 - 1.57: 1842 1.57 - 1.69: 8 1.69 - 1.81: 27 Bond restraints: 3350 Sorted by residual: bond pdb=" CA7 CDL A 401 " pdb=" OA8 CDL A 401 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.21e+02 bond pdb=" CB7 CDL A 401 " pdb=" OB8 CDL A 401 " ideal model delta sigma weight residual 1.334 1.443 -0.109 1.10e-02 8.26e+03 9.87e+01 bond pdb=" CA5 CDL A 401 " pdb=" OA6 CDL A 401 " ideal model delta sigma weight residual 1.342 1.453 -0.111 1.50e-02 4.44e+03 5.50e+01 bond pdb=" CB5 CDL A 401 " pdb=" OB6 CDL A 401 " ideal model delta sigma weight residual 1.342 1.446 -0.104 1.50e-02 4.44e+03 4.82e+01 bond pdb=" C21 PC1 A 402 " pdb=" O21 PC1 A 402 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.85e+01 ... (remaining 3345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 4374 2.16 - 4.33: 113 4.33 - 6.49: 44 6.49 - 8.66: 5 8.66 - 10.82: 5 Bond angle restraints: 4541 Sorted by residual: angle pdb=" C51 CDL A 401 " pdb=" CB5 CDL A 401 " pdb=" OB6 CDL A 401 " ideal model delta sigma weight residual 111.33 120.29 -8.96 1.32e+00 5.72e-01 4.60e+01 angle pdb=" C11 CDL A 401 " pdb=" CA5 CDL A 401 " pdb=" OA6 CDL A 401 " ideal model delta sigma weight residual 111.33 120.24 -8.91 1.32e+00 5.72e-01 4.54e+01 angle pdb=" C71 CDL A 401 " pdb=" CB7 CDL A 401 " pdb=" OB8 CDL A 401 " ideal model delta sigma weight residual 111.64 122.46 -10.82 1.65e+00 3.69e-01 4.32e+01 angle pdb=" C31 CDL A 401 " pdb=" CA7 CDL A 401 " pdb=" OA8 CDL A 401 " ideal model delta sigma weight residual 111.64 121.14 -9.50 1.65e+00 3.69e-01 3.33e+01 angle pdb=" OB8 CDL A 401 " pdb=" CB7 CDL A 401 " pdb=" OB9 CDL A 401 " ideal model delta sigma weight residual 123.94 117.51 6.43 1.21e+00 6.80e-01 2.81e+01 ... (remaining 4536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.33: 1803 19.33 - 38.67: 147 38.67 - 58.00: 41 58.00 - 77.33: 4 77.33 - 96.66: 4 Dihedral angle restraints: 1999 sinusoidal: 816 harmonic: 1183 Sorted by residual: dihedral pdb=" CA ALA A 208 " pdb=" C ALA A 208 " pdb=" N ASP A 209 " pdb=" CA ASP A 209 " ideal model delta harmonic sigma weight residual -180.00 -161.91 -18.09 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA5 CDL A 401 " pdb=" CA4 CDL A 401 " pdb=" OA6 CDL A 401 " pdb=" CA6 CDL A 401 " ideal model delta sinusoidal sigma weight residual 168.24 71.58 96.66 1 3.00e+01 1.11e-03 1.19e+01 dihedral pdb=" CA TRP B 111 " pdb=" C TRP B 111 " pdb=" N GLY B 112 " pdb=" CA GLY B 112 " ideal model delta harmonic sigma weight residual 180.00 163.81 16.19 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 1996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 237 0.030 - 0.059: 166 0.059 - 0.089: 64 0.089 - 0.118: 30 0.118 - 0.148: 9 Chirality restraints: 506 Sorted by residual: chirality pdb=" CA THR A 177 " pdb=" N THR A 177 " pdb=" C THR A 177 " pdb=" CB THR A 177 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA GLU A 167 " pdb=" N GLU A 167 " pdb=" C GLU A 167 " pdb=" CB GLU A 167 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ARG A 276 " pdb=" N ARG A 276 " pdb=" C ARG A 276 " pdb=" CB ARG A 276 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 503 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 101 " 0.022 2.00e-02 2.50e+03 3.04e-02 1.61e+01 pdb=" CG PHE B 101 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE B 101 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE B 101 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE B 101 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 101 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 101 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 211 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A 212 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 9 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO A 10 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 10 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 10 " -0.020 5.00e-02 4.00e+02 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 451 2.75 - 3.29: 3118 3.29 - 3.82: 5823 3.82 - 4.36: 6936 4.36 - 4.90: 11855 Nonbonded interactions: 28183 Sorted by model distance: nonbonded pdb=" OE2 GLU A 68 " pdb=" OG SER A 144 " model vdw 2.209 3.040 nonbonded pdb=" O VAL A 14 " pdb=" OG SER A 18 " model vdw 2.272 3.040 nonbonded pdb=" O TRP A 173 " pdb=" OG1 THR A 176 " model vdw 2.283 3.040 nonbonded pdb=" NH1 ARG A 238 " pdb=" OE2 GLU A 261 " model vdw 2.290 3.120 nonbonded pdb=" OD2 ASP B 100 " pdb=" NH1 ARG B 104 " model vdw 2.308 3.120 ... (remaining 28178 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.430 Find NCS groups from input model: 0.010 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:7.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 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 : 0.009 0.124 3351 Z= 0.506 Angle : 0.964 10.821 4543 Z= 0.501 Chirality : 0.048 0.148 506 Planarity : 0.005 0.052 566 Dihedral : 15.839 96.659 1242 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: 1.54 (0.38), residues: 410 helix: 1.88 (0.31), residues: 219 sheet: -0.75 (0.62), residues: 52 loop : 0.50 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 293 TYR 0.016 0.002 TYR A 157 PHE 0.069 0.004 PHE B 101 TRP 0.007 0.002 TRP A 173 HIS 0.002 0.001 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00941 ( 3350) covalent geometry : angle 0.96139 ( 4541) SS BOND : bond 0.00613 ( 1) SS BOND : angle 3.42459 ( 2) hydrogen bonds : bond 0.09123 ( 226) hydrogen bonds : angle 7.27625 ( 639) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.129 Fit side-chains REVERT: A 70 ARG cc_start: 0.7215 (mtt180) cc_final: 0.6688 (ptt90) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.8642 time to fit residues: 59.0089 Evaluate side-chains 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.133557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113124 restraints weight = 3994.165| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.28 r_work: 0.3266 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3351 Z= 0.147 Angle : 0.525 5.474 4543 Z= 0.273 Chirality : 0.041 0.145 506 Planarity : 0.006 0.056 566 Dihedral : 12.698 72.221 535 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.07 % Allowed : 9.47 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.39), residues: 410 helix: 2.57 (0.31), residues: 220 sheet: -0.41 (0.65), residues: 52 loop : 0.60 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 72 TYR 0.011 0.001 TYR A 157 PHE 0.023 0.002 PHE B 101 TRP 0.007 0.001 TRP B 57 HIS 0.002 0.000 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 3350) covalent geometry : angle 0.52393 ( 4541) SS BOND : bond 0.00324 ( 1) SS BOND : angle 1.83716 ( 2) hydrogen bonds : bond 0.03717 ( 226) hydrogen bonds : angle 5.65692 ( 639) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.141 Fit side-chains REVERT: A 70 ARG cc_start: 0.7914 (mtt180) cc_final: 0.6749 (ptt90) REVERT: A 91 ARG cc_start: 0.6923 (tmm-80) cc_final: 0.6629 (ptp-170) REVERT: A 117 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6775 (mm) REVERT: A 228 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8845 (mtp) REVERT: A 276 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8155 (tmt-80) REVERT: B 106 GLU cc_start: 0.8039 (mp0) cc_final: 0.7832 (pm20) outliers start: 7 outliers final: 2 residues processed: 75 average time/residue: 0.8127 time to fit residues: 62.2232 Evaluate side-chains 69 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 89 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.0870 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115185 restraints weight = 4035.546| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.28 r_work: 0.3286 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3351 Z= 0.117 Angle : 0.479 5.385 4543 Z= 0.249 Chirality : 0.040 0.138 506 Planarity : 0.005 0.049 566 Dihedral : 11.434 58.840 535 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.25 % Allowed : 13.91 % Favored : 82.84 % 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: 2.61 (0.40), residues: 410 helix: 2.93 (0.31), residues: 221 sheet: -0.44 (0.65), residues: 54 loop : 0.72 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 72 TYR 0.011 0.001 TYR A 157 PHE 0.012 0.001 PHE B 101 TRP 0.008 0.001 TRP B 57 HIS 0.001 0.000 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 3350) covalent geometry : angle 0.47793 ( 4541) SS BOND : bond 0.00324 ( 1) SS BOND : angle 1.26935 ( 2) hydrogen bonds : bond 0.03334 ( 226) hydrogen bonds : angle 5.29360 ( 639) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.133 Fit side-chains REVERT: A 70 ARG cc_start: 0.7892 (mtt180) cc_final: 0.6744 (ptt90) REVERT: A 167 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8308 (pm20) REVERT: A 276 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8080 (tmt-80) REVERT: B 106 GLU cc_start: 0.8086 (mp0) cc_final: 0.7794 (pm20) outliers start: 11 outliers final: 2 residues processed: 79 average time/residue: 0.7543 time to fit residues: 60.8895 Evaluate side-chains 71 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 53 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.134146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.113867 restraints weight = 4055.859| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.30 r_work: 0.3257 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3351 Z= 0.134 Angle : 0.493 5.386 4543 Z= 0.253 Chirality : 0.040 0.137 506 Planarity : 0.005 0.047 566 Dihedral : 11.204 56.515 535 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.96 % Allowed : 17.16 % Favored : 79.88 % 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: 2.70 (0.40), residues: 410 helix: 2.96 (0.31), residues: 221 sheet: -0.34 (0.66), residues: 54 loop : 0.81 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.013 0.001 TYR A 157 PHE 0.017 0.001 PHE A 17 TRP 0.007 0.001 TRP B 57 HIS 0.001 0.000 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 3350) covalent geometry : angle 0.49234 ( 4541) SS BOND : bond 0.00275 ( 1) SS BOND : angle 1.26138 ( 2) hydrogen bonds : bond 0.03403 ( 226) hydrogen bonds : angle 5.31482 ( 639) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.089 Fit side-chains REVERT: A 70 ARG cc_start: 0.7883 (mtt180) cc_final: 0.6770 (ptt90) REVERT: A 167 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8284 (pm20) REVERT: B 106 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7874 (pm20) outliers start: 10 outliers final: 4 residues processed: 71 average time/residue: 0.7676 time to fit residues: 55.6297 Evaluate side-chains 71 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 106 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.0060 chunk 39 optimal weight: 3.9990 chunk 33 optimal weight: 0.0050 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.0570 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 overall best weight: 0.3528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.135885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.115818 restraints weight = 4014.194| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.27 r_work: 0.3304 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 3351 Z= 0.105 Angle : 0.456 5.324 4543 Z= 0.235 Chirality : 0.038 0.131 506 Planarity : 0.005 0.044 566 Dihedral : 10.777 57.455 535 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.55 % Allowed : 17.46 % Favored : 78.99 % 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: 2.86 (0.40), residues: 410 helix: 3.13 (0.32), residues: 221 sheet: -0.26 (0.64), residues: 54 loop : 0.80 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 293 TYR 0.010 0.001 TYR A 157 PHE 0.006 0.001 PHE B 27 TRP 0.007 0.001 TRP B 57 HIS 0.001 0.000 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 3350) covalent geometry : angle 0.45582 ( 4541) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.88308 ( 2) hydrogen bonds : bond 0.03123 ( 226) hydrogen bonds : angle 5.09401 ( 639) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.130 Fit side-chains REVERT: A 70 ARG cc_start: 0.7855 (mtt180) cc_final: 0.6812 (ptt90) REVERT: A 115 LYS cc_start: 0.7033 (mttp) cc_final: 0.6629 (mtmt) REVERT: A 276 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8056 (tmt-80) REVERT: B 106 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7822 (pm20) outliers start: 12 outliers final: 5 residues processed: 76 average time/residue: 0.7125 time to fit residues: 55.3034 Evaluate side-chains 75 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 106 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS B 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.131016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110449 restraints weight = 3861.937| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.29 r_work: 0.3178 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3351 Z= 0.148 Angle : 0.500 5.361 4543 Z= 0.257 Chirality : 0.040 0.133 506 Planarity : 0.005 0.045 566 Dihedral : 11.035 59.430 535 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.55 % Allowed : 18.05 % Favored : 78.40 % 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: 2.75 (0.39), residues: 410 helix: 3.00 (0.31), residues: 221 sheet: -0.31 (0.64), residues: 54 loop : 0.82 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 293 TYR 0.013 0.001 TYR A 157 PHE 0.013 0.002 PHE A 17 TRP 0.009 0.001 TRP B 57 HIS 0.001 0.000 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 3350) covalent geometry : angle 0.49916 ( 4541) SS BOND : bond 0.00227 ( 1) SS BOND : angle 1.33258 ( 2) hydrogen bonds : bond 0.03441 ( 226) hydrogen bonds : angle 5.29175 ( 639) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.135 Fit side-chains REVERT: A 70 ARG cc_start: 0.7897 (mtt180) cc_final: 0.6736 (ptt90) REVERT: A 115 LYS cc_start: 0.6913 (mttp) cc_final: 0.6523 (mtmt) REVERT: A 291 LEU cc_start: 0.7778 (tp) cc_final: 0.7308 (mt) REVERT: B 106 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7761 (pm20) outliers start: 12 outliers final: 5 residues processed: 74 average time/residue: 0.7473 time to fit residues: 56.5000 Evaluate side-chains 72 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 106 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.0030 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS B 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.132142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.111564 restraints weight = 3932.702| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.31 r_work: 0.3194 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3351 Z= 0.123 Angle : 0.477 5.345 4543 Z= 0.247 Chirality : 0.039 0.129 506 Planarity : 0.005 0.044 566 Dihedral : 10.709 59.164 535 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.96 % Allowed : 18.34 % Favored : 78.70 % 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: 2.84 (0.39), residues: 410 helix: 3.07 (0.31), residues: 221 sheet: -0.22 (0.65), residues: 54 loop : 0.87 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 293 TYR 0.013 0.001 TYR A 157 PHE 0.007 0.001 PHE A 128 TRP 0.008 0.001 TRP B 57 HIS 0.001 0.000 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3350) covalent geometry : angle 0.47685 ( 4541) SS BOND : bond 0.00177 ( 1) SS BOND : angle 1.08604 ( 2) hydrogen bonds : bond 0.03247 ( 226) hydrogen bonds : angle 5.14025 ( 639) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.119 Fit side-chains REVERT: A 70 ARG cc_start: 0.7903 (mtt180) cc_final: 0.6729 (ptt90) REVERT: A 115 LYS cc_start: 0.6934 (mttp) cc_final: 0.6531 (mtmt) REVERT: A 276 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8007 (tmt-80) REVERT: A 291 LEU cc_start: 0.7787 (tp) cc_final: 0.7394 (mt) outliers start: 10 outliers final: 4 residues processed: 73 average time/residue: 0.7176 time to fit residues: 53.5047 Evaluate side-chains 73 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 53 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.131877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.111264 restraints weight = 3955.033| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.31 r_work: 0.3189 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3351 Z= 0.129 Angle : 0.484 5.356 4543 Z= 0.249 Chirality : 0.039 0.129 506 Planarity : 0.005 0.044 566 Dihedral : 10.602 59.943 535 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.78 % Allowed : 20.41 % Favored : 77.81 % 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: 2.88 (0.39), residues: 410 helix: 3.05 (0.31), residues: 221 sheet: -0.04 (0.65), residues: 54 loop : 0.89 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 293 TYR 0.013 0.001 TYR A 157 PHE 0.008 0.001 PHE A 128 TRP 0.008 0.001 TRP B 57 HIS 0.001 0.000 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3350) covalent geometry : angle 0.48366 ( 4541) SS BOND : bond 0.00203 ( 1) SS BOND : angle 1.11548 ( 2) hydrogen bonds : bond 0.03280 ( 226) hydrogen bonds : angle 5.15637 ( 639) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.117 Fit side-chains REVERT: A 70 ARG cc_start: 0.7914 (mtt180) cc_final: 0.6750 (ptt90) REVERT: A 115 LYS cc_start: 0.6943 (mttp) cc_final: 0.6563 (mtmt) REVERT: A 291 LEU cc_start: 0.7758 (tp) cc_final: 0.7364 (mt) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.6472 time to fit residues: 46.9215 Evaluate side-chains 68 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 53 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS B 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.130874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110214 restraints weight = 3904.383| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.30 r_work: 0.3176 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3351 Z= 0.151 Angle : 0.506 5.360 4543 Z= 0.260 Chirality : 0.040 0.170 506 Planarity : 0.005 0.044 566 Dihedral : 10.697 59.517 535 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.07 % Allowed : 19.82 % Favored : 78.11 % 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 aren not related in a simple way. whole: 2.81 (0.39), residues: 410 helix: 2.96 (0.31), residues: 221 sheet: 0.04 (0.68), residues: 54 loop : 0.87 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 293 TYR 0.015 0.001 TYR A 157 PHE 0.009 0.001 PHE A 128 TRP 0.008 0.001 TRP B 57 HIS 0.002 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 3350) covalent geometry : angle 0.50567 ( 4541) SS BOND : bond 0.00248 ( 1) SS BOND : angle 1.34870 ( 2) hydrogen bonds : bond 0.03435 ( 226) hydrogen bonds : angle 5.26088 ( 639) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.135 Fit side-chains REVERT: A 70 ARG cc_start: 0.7888 (mtt180) cc_final: 0.6727 (ptt90) REVERT: A 115 LYS cc_start: 0.6921 (mttp) cc_final: 0.6547 (mtmt) REVERT: A 291 LEU cc_start: 0.7797 (tp) cc_final: 0.7343 (mt) outliers start: 7 outliers final: 4 residues processed: 70 average time/residue: 0.6411 time to fit residues: 45.9046 Evaluate side-chains 69 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 53 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS B 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.130415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109853 restraints weight = 3853.951| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.28 r_work: 0.3172 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3351 Z= 0.160 Angle : 0.515 5.380 4543 Z= 0.265 Chirality : 0.041 0.157 506 Planarity : 0.005 0.044 566 Dihedral : 10.802 58.804 535 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.96 % Allowed : 18.64 % Favored : 78.40 % 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: 2.74 (0.39), residues: 410 helix: 2.89 (0.31), residues: 221 sheet: 0.01 (0.68), residues: 54 loop : 0.87 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 293 TYR 0.017 0.001 TYR A 157 PHE 0.010 0.002 PHE A 128 TRP 0.007 0.001 TRP B 57 HIS 0.001 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 3350) covalent geometry : angle 0.51420 ( 4541) SS BOND : bond 0.00243 ( 1) SS BOND : angle 1.38369 ( 2) hydrogen bonds : bond 0.03508 ( 226) hydrogen bonds : angle 5.31593 ( 639) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.085 Fit side-chains REVERT: A 70 ARG cc_start: 0.7864 (mtt180) cc_final: 0.6721 (ptt90) REVERT: A 115 LYS cc_start: 0.6929 (mttp) cc_final: 0.6548 (mtmt) outliers start: 10 outliers final: 5 residues processed: 70 average time/residue: 0.6710 time to fit residues: 47.9232 Evaluate side-chains 71 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 89 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS B 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.132031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111438 restraints weight = 3922.162| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.30 r_work: 0.3193 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3351 Z= 0.127 Angle : 0.483 5.351 4543 Z= 0.249 Chirality : 0.039 0.149 506 Planarity : 0.005 0.044 566 Dihedral : 10.540 58.215 535 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.07 % Allowed : 19.53 % Favored : 78.40 % 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: 2.87 (0.39), residues: 410 helix: 3.00 (0.31), residues: 221 sheet: 0.16 (0.68), residues: 54 loop : 0.87 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 293 TYR 0.014 0.001 TYR A 157 PHE 0.007 0.001 PHE A 128 TRP 0.005 0.001 TRP B 57 HIS 0.001 0.000 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 3350) covalent geometry : angle 0.48229 ( 4541) SS BOND : bond 0.00154 ( 1) SS BOND : angle 1.07248 ( 2) hydrogen bonds : bond 0.03266 ( 226) hydrogen bonds : angle 5.14271 ( 639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1713.02 seconds wall clock time: 29 minutes 51.09 seconds (1791.09 seconds total)