Starting phenix.real_space_refine on Tue Aug 4 17:37:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w2s_43757/08_2026/8w2s_43757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w2s_43757/08_2026/8w2s_43757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w2s_43757/08_2026/8w2s_43757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w2s_43757/08_2026/8w2s_43757.map" model { file = "/net/cci-nas-00/data/ceres_data/8w2s_43757/08_2026/8w2s_43757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w2s_43757/08_2026/8w2s_43757.cif" } resolution = 3.4 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= 0.047 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 137 5.49 5 S 11 5.16 5 C 3025 2.51 5 N 1051 2.21 5 O 1464 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5688 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2761 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 332} Chain breaks: 3 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'PHE:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2927 Classifications: {'RNA': 137} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 69, 'rna3p_pyr': 55} Link IDs: {'rna2p': 13, 'rna3p': 123} Time building chain proxies: 1.01, per 1000 atoms: 0.18 Number of scatterers: 5688 At special positions: 0 Unit cell: (86.6528, 86.6528, 115.815, 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 11 16.00 P 137 15.00 O 1464 8.00 N 1051 7.00 C 3025 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: 0.41 Conformation dependent library (CDL) restraints added in 112.6 milliseconds 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 652 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 2 sheets defined 56.0% alpha, 5.3% beta 50 base pairs and 94 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 44 through 75 removed outlier: 3.690A pdb=" N GLY A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 91 removed outlier: 3.836A pdb=" N GLU A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 91 " --> pdb=" O TYR A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 105 through 110 Processing helix chain 'A' and resid 113 through 132 removed outlier: 3.665A pdb=" N ARG A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 151 Processing helix chain 'A' and resid 154 through 167 Processing helix chain 'A' and resid 197 through 207 Processing helix chain 'A' and resid 212 through 225 removed outlier: 3.521A pdb=" N ASP A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 239 Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.518A pdb=" N ARG A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.617A pdb=" N ILE A 268 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 583 removed outlier: 4.166A pdb=" N GLU A 580 " --> pdb=" O CYS A 577 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASP A 581 " --> pdb=" O GLY A 578 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 583 " --> pdb=" O GLU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 599 Processing helix chain 'A' and resid 608 through 614 Processing sheet with id=AA1, first strand: chain 'A' and resid 560 through 562 Processing sheet with id=AA2, first strand: chain 'A' and resid 640 through 643 removed outlier: 3.569A pdb=" N ILE A 641 " --> pdb=" O PHE A 648 " (cutoff:3.500A) 134 hydrogen bonds defined for protein. 378 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 120 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 94 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 0.59 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: 1109 1.33 - 1.45: 2107 1.45 - 1.57: 2567 1.57 - 1.69: 273 1.69 - 1.81: 16 Bond restraints: 6072 Sorted by residual: bond pdb=" C2' G B 142 " pdb=" C1' G B 142 " ideal model delta sigma weight residual 1.526 1.506 0.020 8.00e-03 1.56e+04 6.05e+00 bond pdb=" C3' U B 92 " pdb=" O3' U B 92 " ideal model delta sigma weight residual 1.427 1.451 -0.024 1.20e-02 6.94e+03 3.93e+00 bond pdb=" N9 A B 118 " pdb=" C4 A B 118 " ideal model delta sigma weight residual 1.374 1.385 -0.011 6.00e-03 2.78e+04 3.13e+00 bond pdb=" O3' G B 142 " pdb=" P G B 143 " ideal model delta sigma weight residual 1.607 1.627 -0.020 1.20e-02 6.94e+03 2.85e+00 bond pdb=" N1 C B 126 " pdb=" C2 C B 126 " ideal model delta sigma weight residual 1.397 1.413 -0.016 1.00e-02 1.00e+04 2.68e+00 ... (remaining 6067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 8586 2.69 - 5.37: 214 5.37 - 8.06: 27 8.06 - 10.74: 6 10.74 - 13.43: 4 Bond angle restraints: 8837 Sorted by residual: angle pdb=" O4' G B 142 " pdb=" C1' G B 142 " pdb=" N9 G B 142 " ideal model delta sigma weight residual 108.20 117.21 -9.01 8.00e-01 1.56e+00 1.27e+02 angle pdb=" N LYS A 172 " pdb=" CA LYS A 172 " pdb=" C LYS A 172 " ideal model delta sigma weight residual 108.67 95.45 13.22 1.55e+00 4.16e-01 7.27e+01 angle pdb=" C2' G B 142 " pdb=" C1' G B 142 " pdb=" N9 G B 142 " ideal model delta sigma weight residual 114.00 124.83 -10.83 1.30e+00 5.92e-01 6.93e+01 angle pdb=" N ARG A 198 " pdb=" CA ARG A 198 " pdb=" C ARG A 198 " ideal model delta sigma weight residual 111.33 120.20 -8.87 1.21e+00 6.83e-01 5.38e+01 angle pdb=" C3' U B 92 " pdb=" O3' U B 92 " pdb=" P U B 93 " ideal model delta sigma weight residual 119.70 127.22 -7.52 1.20e+00 6.94e-01 3.93e+01 ... (remaining 8832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 3552 35.33 - 70.66: 282 70.66 - 105.99: 33 105.99 - 141.32: 1 141.32 - 176.65: 2 Dihedral angle restraints: 3870 sinusoidal: 2874 harmonic: 996 Sorted by residual: dihedral pdb=" O4' U B 92 " pdb=" C1' U B 92 " pdb=" N1 U B 92 " pdb=" C2 U B 92 " ideal model delta sinusoidal sigma weight residual -128.00 48.65 -176.65 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA LYS A 181 " pdb=" C LYS A 181 " pdb=" N CYS A 182 " pdb=" CA CYS A 182 " ideal model delta harmonic sigma weight residual 180.00 153.49 26.51 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" O4' G B 142 " pdb=" C1' G B 142 " pdb=" N9 G B 142 " pdb=" C4 G B 142 " ideal model delta sinusoidal sigma weight residual 254.00 176.43 77.57 1 1.70e+01 3.46e-03 2.61e+01 ... (remaining 3867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.174: 1084 0.174 - 0.349: 4 0.349 - 0.523: 0 0.523 - 0.698: 0 0.698 - 0.872: 1 Chirality restraints: 1089 Sorted by residual: chirality pdb=" C1' G B 142 " pdb=" O4' G B 142 " pdb=" C2' G B 142 " pdb=" N9 G B 142 " both_signs ideal model delta sigma weight residual False 2.44 1.56 0.87 2.00e-01 2.50e+01 1.90e+01 chirality pdb=" C3' U B 92 " pdb=" C4' U B 92 " pdb=" O3' U B 92 " pdb=" C2' U B 92 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C3' G B 122 " pdb=" C4' G B 122 " pdb=" O3' G B 122 " pdb=" C2' G B 122 " both_signs ideal model delta sigma weight residual False -2.48 -2.20 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 1086 not shown) Planarity restraints: 621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 142 " 0.066 2.00e-02 2.50e+03 3.07e-02 2.82e+01 pdb=" N9 G B 142 " -0.081 2.00e-02 2.50e+03 pdb=" C8 G B 142 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G B 142 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 142 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G B 142 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G B 142 " 0.020 2.00e-02 2.50e+03 pdb=" N1 G B 142 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G B 142 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G B 142 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 142 " -0.008 2.00e-02 2.50e+03 pdb=" C4 G B 142 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 137 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" C ARG A 137 " 0.035 2.00e-02 2.50e+03 pdb=" O ARG A 137 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 138 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 173 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C ARG A 173 " 0.034 2.00e-02 2.50e+03 pdb=" O ARG A 173 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE A 174 " -0.011 2.00e-02 2.50e+03 ... (remaining 618 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1441 2.81 - 3.33: 5025 3.33 - 3.86: 11190 3.86 - 4.38: 12754 4.38 - 4.90: 17411 Nonbonded interactions: 47821 Sorted by model distance: nonbonded pdb=" O2' G B 11 " pdb=" O4' A B 12 " model vdw 2.289 3.040 nonbonded pdb=" OP2 U B 91 " pdb=" O2' U B 92 " model vdw 2.296 3.040 nonbonded pdb=" O PRO A 558 " pdb=" O2' U B 22 " model vdw 2.311 3.040 nonbonded pdb=" OE1 GLU A 212 " pdb=" OG SER A 214 " model vdw 2.322 3.040 nonbonded pdb=" N2 G B 117 " pdb=" OP2 A B 120 " model vdw 2.340 3.120 ... (remaining 47816 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: 3.090 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.750 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6072 Z= 0.278 Angle : 1.026 13.428 8837 Z= 0.777 Chirality : 0.067 0.872 1089 Planarity : 0.005 0.048 621 Dihedral : 20.847 176.648 3218 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 14.33 % Favored : 85.67 % 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: -1.36 (0.44), residues: 331 helix: -0.51 (0.37), residues: 170 sheet: 1.34 (1.12), residues: 10 loop : -1.46 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 173 TYR 0.021 0.003 TYR A 97 PHE 0.016 0.002 PHE A 236 TRP 0.013 0.002 TRP A 127 HIS 0.008 0.002 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.28 ( 6072) covalent geometry : angle 1.02581 / 0.78 ( 8837) hydrogen bonds : bond 0.12798 / 9.62 ( 254) hydrogen bonds : angle 5.40498 / 3.95 ( 578) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.153 Fit side-chains REVERT: A 124 LYS cc_start: 0.8091 (tppt) cc_final: 0.7772 (mtpt) REVERT: A 248 GLN cc_start: 0.9077 (mt0) cc_final: 0.8659 (mp10) REVERT: A 579 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7959 (mtpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1134 time to fit residues: 7.2874 Evaluate side-chains 49 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.151200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.107447 restraints weight = 11879.290| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.09 r_work: 0.3439 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6072 Z= 0.143 Angle : 0.587 9.722 8837 Z= 0.342 Chirality : 0.041 0.447 1089 Planarity : 0.004 0.037 621 Dihedral : 21.730 166.002 2488 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.39 % Allowed : 11.95 % Favored : 85.67 % 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: -0.27 (0.47), residues: 331 helix: 0.64 (0.40), residues: 171 sheet: 0.94 (1.10), residues: 10 loop : -1.20 (0.53), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 173 TYR 0.019 0.002 TYR A 97 PHE 0.007 0.001 PHE A 570 TRP 0.009 0.002 TRP A 120 HIS 0.004 0.001 HIS A 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 ( 6072) covalent geometry : angle 0.58667 / 0.34 ( 8837) hydrogen bonds : bond 0.05855 / 3.91 ( 254) hydrogen bonds : angle 3.91205 / 2.85 ( 578) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8163 (tppt) cc_final: 0.7786 (mtpt) REVERT: A 248 GLN cc_start: 0.9026 (mt0) cc_final: 0.8570 (mp10) REVERT: A 579 LYS cc_start: 0.8504 (mtpt) cc_final: 0.8174 (mtpp) outliers start: 7 outliers final: 4 residues processed: 49 average time/residue: 0.1153 time to fit residues: 7.0008 Evaluate side-chains 45 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 619 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 30 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 20.0000 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.147073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.102671 restraints weight = 11602.119| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.04 r_work: 0.3354 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6072 Z= 0.129 Angle : 0.538 8.925 8837 Z= 0.315 Chirality : 0.039 0.440 1089 Planarity : 0.004 0.033 621 Dihedral : 21.625 170.840 2488 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.39 % Allowed : 12.97 % Favored : 84.64 % 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: 0.17 (0.48), residues: 331 helix: 1.10 (0.41), residues: 174 sheet: 0.85 (1.10), residues: 10 loop : -1.16 (0.56), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 173 TYR 0.013 0.002 TYR A 97 PHE 0.012 0.001 PHE A 570 TRP 0.007 0.001 TRP A 120 HIS 0.002 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 ( 6072) covalent geometry : angle 0.53823 / 0.31 ( 8837) hydrogen bonds : bond 0.05317 / 3.53 ( 254) hydrogen bonds : angle 3.70153 / 2.71 ( 578) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.9085 (mt0) cc_final: 0.8586 (mp10) REVERT: A 579 LYS cc_start: 0.8505 (mtpt) cc_final: 0.8183 (mtpp) REVERT: A 679 LYS cc_start: 0.7457 (ttpt) cc_final: 0.7113 (ttpp) outliers start: 7 outliers final: 5 residues processed: 53 average time/residue: 0.1219 time to fit residues: 7.9334 Evaluate side-chains 50 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 619 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 41 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 36 optimal weight: 20.0000 chunk 30 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.143977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.099309 restraints weight = 11660.000| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.08 r_work: 0.3295 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6072 Z= 0.168 Angle : 0.571 8.830 8837 Z= 0.327 Chirality : 0.042 0.444 1089 Planarity : 0.004 0.040 621 Dihedral : 21.564 168.206 2488 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.44 % Allowed : 10.24 % Favored : 85.32 % 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: 0.35 (0.49), residues: 331 helix: 1.38 (0.41), residues: 174 sheet: 0.99 (1.09), residues: 10 loop : -1.26 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 152 TYR 0.016 0.002 TYR A 169 PHE 0.011 0.002 PHE A 570 TRP 0.008 0.001 TRP A 120 HIS 0.006 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 ( 6072) covalent geometry : angle 0.57136 / 0.33 ( 8837) hydrogen bonds : bond 0.05662 / 3.71 ( 254) hydrogen bonds : angle 3.62018 / 2.64 ( 578) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 248 GLN cc_start: 0.9081 (mt0) cc_final: 0.8517 (mp10) REVERT: A 579 LYS cc_start: 0.8527 (mtpt) cc_final: 0.8215 (mtpp) REVERT: A 607 LEU cc_start: 0.5682 (OUTLIER) cc_final: 0.5373 (tt) REVERT: A 679 LYS cc_start: 0.7510 (ttpt) cc_final: 0.7201 (ttpp) outliers start: 13 outliers final: 7 residues processed: 59 average time/residue: 0.1082 time to fit residues: 7.9218 Evaluate side-chains 54 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 649 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 35 optimal weight: 20.0000 chunk 22 optimal weight: 0.1980 chunk 34 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 ASN A 645 ASN A 646 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.147761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.103818 restraints weight = 11918.858| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.12 r_work: 0.3383 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6072 Z= 0.132 Angle : 0.530 8.601 8837 Z= 0.308 Chirality : 0.039 0.425 1089 Planarity : 0.004 0.033 621 Dihedral : 21.546 170.284 2488 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.41 % Allowed : 11.60 % Favored : 84.98 % 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: 0.42 (0.49), residues: 331 helix: 1.45 (0.41), residues: 176 sheet: 1.17 (1.17), residues: 10 loop : -1.31 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 228 TYR 0.013 0.002 TYR A 76 PHE 0.020 0.002 PHE A 236 TRP 0.007 0.001 TRP A 120 HIS 0.002 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 ( 6072) covalent geometry : angle 0.53010 / 0.31 ( 8837) hydrogen bonds : bond 0.05212 / 3.44 ( 254) hydrogen bonds : angle 3.55910 / 2.59 ( 578) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8743 (mmm160) cc_final: 0.8473 (mmm160) REVERT: A 248 GLN cc_start: 0.9044 (mt0) cc_final: 0.8498 (mp10) REVERT: A 579 LYS cc_start: 0.8520 (mtpt) cc_final: 0.8212 (mtpp) REVERT: A 607 LEU cc_start: 0.5705 (OUTLIER) cc_final: 0.5431 (tt) REVERT: A 679 LYS cc_start: 0.7487 (ttpt) cc_final: 0.7229 (ttpp) outliers start: 10 outliers final: 5 residues processed: 54 average time/residue: 0.1168 time to fit residues: 7.7495 Evaluate side-chains 52 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 635 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 39 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.146188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.102271 restraints weight = 11784.299| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.09 r_work: 0.3357 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6072 Z= 0.160 Angle : 0.552 8.601 8837 Z= 0.316 Chirality : 0.041 0.432 1089 Planarity : 0.004 0.035 621 Dihedral : 21.468 168.878 2488 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.39 % Allowed : 12.63 % Favored : 84.98 % 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: 0.39 (0.48), residues: 331 helix: 1.47 (0.40), residues: 176 sheet: 1.19 (1.11), residues: 10 loop : -1.39 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 152 TYR 0.014 0.002 TYR A 76 PHE 0.010 0.002 PHE A 236 TRP 0.007 0.001 TRP A 120 HIS 0.003 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 ( 6072) covalent geometry : angle 0.55238 / 0.32 ( 8837) hydrogen bonds : bond 0.05471 / 3.57 ( 254) hydrogen bonds : angle 3.58186 / 2.62 ( 578) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8821 (mmm160) cc_final: 0.8403 (mmm160) REVERT: A 248 GLN cc_start: 0.9060 (mt0) cc_final: 0.8550 (mp10) REVERT: A 579 LYS cc_start: 0.8533 (mtpt) cc_final: 0.8233 (mtpp) REVERT: A 607 LEU cc_start: 0.5793 (OUTLIER) cc_final: 0.5484 (tt) REVERT: A 649 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7911 (tmmt) REVERT: A 679 LYS cc_start: 0.7560 (ttpt) cc_final: 0.7294 (ttpp) outliers start: 7 outliers final: 4 residues processed: 51 average time/residue: 0.0909 time to fit residues: 5.6388 Evaluate side-chains 51 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 649 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 38 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.141393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.096717 restraints weight = 11879.120| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.11 r_work: 0.3268 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6072 Z= 0.187 Angle : 0.603 8.979 8837 Z= 0.340 Chirality : 0.043 0.438 1089 Planarity : 0.004 0.034 621 Dihedral : 21.453 169.744 2488 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.41 % Allowed : 11.26 % Favored : 85.32 % 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: 0.32 (0.49), residues: 331 helix: 1.43 (0.41), residues: 174 sheet: 1.11 (1.11), residues: 10 loop : -1.42 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 152 TYR 0.018 0.002 TYR A 76 PHE 0.014 0.002 PHE A 83 TRP 0.009 0.001 TRP A 120 HIS 0.006 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.19 ( 6072) covalent geometry : angle 0.60273 / 0.34 ( 8837) hydrogen bonds : bond 0.06091 / 3.92 ( 254) hydrogen bonds : angle 3.65619 / 2.68 ( 578) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8893 (mmm160) cc_final: 0.8482 (mmm160) REVERT: A 248 GLN cc_start: 0.9059 (mt0) cc_final: 0.8522 (mp10) REVERT: A 579 LYS cc_start: 0.8582 (mtpt) cc_final: 0.8270 (mtpp) REVERT: A 607 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5626 (tt) REVERT: A 649 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7904 (tmmt) outliers start: 10 outliers final: 5 residues processed: 51 average time/residue: 0.1160 time to fit residues: 7.2798 Evaluate side-chains 51 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 649 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.144686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.100923 restraints weight = 11775.448| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.06 r_work: 0.3341 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6072 Z= 0.125 Angle : 0.530 8.688 8837 Z= 0.308 Chirality : 0.039 0.420 1089 Planarity : 0.004 0.035 621 Dihedral : 21.447 169.118 2488 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.05 % Allowed : 13.31 % Favored : 84.64 % 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: 0.42 (0.49), residues: 331 helix: 1.56 (0.41), residues: 174 sheet: 1.13 (1.09), residues: 10 loop : -1.43 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 152 TYR 0.012 0.002 TYR A 97 PHE 0.009 0.001 PHE A 236 TRP 0.007 0.001 TRP A 120 HIS 0.002 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 ( 6072) covalent geometry : angle 0.52955 / 0.31 ( 8837) hydrogen bonds : bond 0.05320 / 3.46 ( 254) hydrogen bonds : angle 3.57930 / 2.62 ( 578) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8912 (mmm160) cc_final: 0.8524 (mmm160) REVERT: A 248 GLN cc_start: 0.9052 (mt0) cc_final: 0.8480 (mp10) REVERT: A 579 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8244 (mtpp) REVERT: A 607 LEU cc_start: 0.5979 (OUTLIER) cc_final: 0.5606 (tt) REVERT: A 649 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7867 (tmmt) outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 0.1159 time to fit residues: 7.1498 Evaluate side-chains 49 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 649 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 34 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 0.0030 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.142908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.099107 restraints weight = 11794.634| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.10 r_work: 0.3317 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6072 Z= 0.164 Angle : 0.563 8.722 8837 Z= 0.320 Chirality : 0.041 0.427 1089 Planarity : 0.004 0.036 621 Dihedral : 21.368 167.649 2488 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.05 % Allowed : 12.97 % Favored : 84.98 % 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: 0.41 (0.49), residues: 331 helix: 1.62 (0.41), residues: 174 sheet: 0.80 (1.08), residues: 10 loop : -1.49 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 556 TYR 0.014 0.002 TYR A 169 PHE 0.012 0.002 PHE A 83 TRP 0.009 0.002 TRP A 120 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 ( 6072) covalent geometry : angle 0.56317 / 0.32 ( 8837) hydrogen bonds : bond 0.05749 / 3.69 ( 254) hydrogen bonds : angle 3.61937 / 2.65 ( 578) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 248 GLN cc_start: 0.9043 (mt0) cc_final: 0.8470 (mp10) REVERT: A 579 LYS cc_start: 0.8581 (mtpt) cc_final: 0.8265 (mtpp) REVERT: A 607 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5819 (tt) REVERT: A 649 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7944 (tmmt) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 0.1175 time to fit residues: 7.3675 Evaluate side-chains 52 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 649 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.144083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.100520 restraints weight = 11871.419| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.13 r_work: 0.3343 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6072 Z= 0.129 Angle : 0.522 8.371 8837 Z= 0.302 Chirality : 0.038 0.413 1089 Planarity : 0.004 0.037 621 Dihedral : 21.371 168.408 2488 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.05 % Allowed : 13.65 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.53 (0.49), residues: 331 helix: 1.69 (0.41), residues: 174 sheet: 0.77 (1.01), residues: 10 loop : -1.39 (0.56), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 152 TYR 0.012 0.002 TYR A 76 PHE 0.009 0.001 PHE A 236 TRP 0.008 0.001 TRP A 120 HIS 0.002 0.000 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 ( 6072) covalent geometry : angle 0.52181 / 0.30 ( 8837) hydrogen bonds : bond 0.05096 / 3.32 ( 254) hydrogen bonds : angle 3.55160 / 2.60 ( 578) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8949 (mmm160) cc_final: 0.8590 (mmm160) REVERT: A 248 GLN cc_start: 0.9040 (mt0) cc_final: 0.8467 (mp10) REVERT: A 579 LYS cc_start: 0.8562 (mtpt) cc_final: 0.8239 (mtpp) REVERT: A 607 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.5826 (tt) REVERT: A 649 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7865 (tmmt) outliers start: 6 outliers final: 4 residues processed: 48 average time/residue: 0.1130 time to fit residues: 6.6630 Evaluate side-chains 46 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 649 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 0.0970 chunk 12 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.144855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.101622 restraints weight = 11693.461| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.10 r_work: 0.3368 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6072 Z= 0.113 Angle : 0.501 8.043 8837 Z= 0.290 Chirality : 0.037 0.401 1089 Planarity : 0.003 0.037 621 Dihedral : 21.319 167.184 2488 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.05 % Allowed : 13.99 % Favored : 83.96 % 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: 0.70 (0.50), residues: 331 helix: 1.81 (0.41), residues: 174 sheet: 0.68 (1.03), residues: 10 loop : -1.28 (0.57), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 152 TYR 0.012 0.002 TYR A 70 PHE 0.008 0.001 PHE A 236 TRP 0.006 0.001 TRP A 120 HIS 0.002 0.000 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 ( 6072) covalent geometry : angle 0.50102 / 0.29 ( 8837) hydrogen bonds : bond 0.04783 / 3.13 ( 254) hydrogen bonds : angle 3.47871 / 2.55 ( 578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1587.98 seconds wall clock time: 27 minutes 59.77 seconds (1679.77 seconds total)