Starting phenix.real_space_refine on Tue Aug 4 19:57:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w26_65567/08_2026/9w26_65567_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w26_65567/08_2026/9w26_65567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w26_65567/08_2026/9w26_65567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w26_65567/08_2026/9w26_65567.map" model { file = "/net/cci-nas-00/data/ceres_data/9w26_65567/08_2026/9w26_65567_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w26_65567/08_2026/9w26_65567_neut.cif" } resolution = 2.62 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 98 5.49 5 Mg 1 5.21 5 S 27 5.16 5 C 3679 2.51 5 N 1188 2.21 5 O 1419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s 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: 6412 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1897 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2468 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 12, 'TRANS': 296} Chain: "C" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 775 Classifications: {'DNA': 1, 'RNA': 36} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 12, 'rna3p_pyr': 10} Link IDs: {'rna2p': 14, 'rna3p': 22} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "E" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 242 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "F" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 640 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.48, per 1000 atoms: 0.23 Number of scatterers: 6412 At special positions: 0 Unit cell: (74.736, 77.504, 99.648, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 27 16.00 P 98 15.00 Mg 1 11.99 O 1419 8.00 N 1188 7.00 C 3679 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: 0.66 Conformation dependent library (CDL) restraints added in 265.1 milliseconds 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 3 sheets defined 69.4% alpha, 2.9% beta 33 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 66 through 97 Processing helix chain 'A' and resid 103 through 134 Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.823A pdb=" N LEU A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TRP A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'A' and resid 195 through 212 removed outlier: 3.780A pdb=" N LYS A 211 " --> pdb=" O ASN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 231 removed outlier: 4.157A pdb=" N VAL A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 253 through 282 removed outlier: 3.579A pdb=" N ARG A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 4.016A pdb=" N GLY A 306 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 34 through 38 Processing helix chain 'B' and resid 50 through 58 Processing helix chain 'B' and resid 65 through 97 Processing helix chain 'B' and resid 103 through 134 Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.510A pdb=" N GLN B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 168 through 177 removed outlier: 3.627A pdb=" N LEU B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TRP B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'B' and resid 195 through 210 Processing helix chain 'B' and resid 217 through 231 Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 253 through 282 Processing helix chain 'B' and resid 288 through 293 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.851A pdb=" N GLY B 306 " --> pdb=" O GLN B 303 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 238 Processing sheet with id=AA2, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AA3, first strand: chain 'B' and resid 234 through 235 277 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1673 1.34 - 1.45: 1660 1.45 - 1.57: 3168 1.57 - 1.69: 193 1.69 - 1.81: 49 Bond restraints: 6743 Sorted by residual: bond pdb=" C1' DT F 5 " pdb=" N1 DT F 5 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" C3' DT F 5 " pdb=" C2' DT F 5 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.01e+00 bond pdb=" C3' DT F 33 " pdb=" C2' DT F 33 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.57e+00 bond pdb=" C1' DC F 32 " pdb=" N1 DC F 32 " ideal model delta sigma weight residual 1.468 1.506 -0.038 1.40e-02 5.10e+03 7.27e+00 bond pdb=" C1' DT E 30 " pdb=" N1 DT E 30 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 7.03e+00 ... (remaining 6738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 9269 2.14 - 4.28: 268 4.28 - 6.41: 8 6.41 - 8.55: 2 8.55 - 10.69: 1 Bond angle restraints: 9548 Sorted by residual: angle pdb=" O4' C C 8 " pdb=" C1' C C 8 " pdb=" N1 C C 8 " ideal model delta sigma weight residual 108.20 112.74 -4.54 8.00e-01 1.56e+00 3.22e+01 angle pdb=" CG1 VAL B 29 " pdb=" CB VAL B 29 " pdb=" CG2 VAL B 29 " ideal model delta sigma weight residual 110.80 121.49 -10.69 2.20e+00 2.07e-01 2.36e+01 angle pdb=" N3 DT D 4 " pdb=" C4 DT D 4 " pdb=" O4 DT D 4 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT F 28 " pdb=" C4 DT F 28 " pdb=" O4 DT F 28 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT E 28 " pdb=" C4 DT E 28 " pdb=" O4 DT E 28 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 ... (remaining 9543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.29: 3579 33.29 - 66.58: 325 66.58 - 99.87: 26 99.87 - 133.16: 0 133.16 - 166.45: 8 Dihedral angle restraints: 3938 sinusoidal: 2358 harmonic: 1580 Sorted by residual: dihedral pdb=" C4' DG F 30 " pdb=" C3' DG F 30 " pdb=" O3' DG F 30 " pdb=" P DC F 31 " ideal model delta sinusoidal sigma weight residual 220.00 53.55 166.45 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DA F 8 " pdb=" C3' DA F 8 " pdb=" O3' DA F 8 " pdb=" P DA F 9 " ideal model delta sinusoidal sigma weight residual 220.00 54.92 165.08 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DC F 12 " pdb=" C3' DC F 12 " pdb=" O3' DC F 12 " pdb=" P DG F 13 " ideal model delta sinusoidal sigma weight residual 220.00 55.42 164.58 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 3935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.294: 1072 0.294 - 0.588: 2 0.588 - 0.882: 0 0.882 - 1.175: 0 1.175 - 1.469: 1 Chirality restraints: 1075 Sorted by residual: chirality pdb=" CB VAL B 29 " pdb=" CA VAL B 29 " pdb=" CG1 VAL B 29 " pdb=" CG2 VAL B 29 " both_signs ideal model delta sigma weight residual False -2.63 -1.16 -1.47 2.00e-01 2.50e+01 5.40e+01 chirality pdb=" P A C 37 " pdb=" OP1 A C 37 " pdb=" OP2 A C 37 " pdb=" O5' A C 37 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.53 2.00e-01 2.50e+01 7.03e+00 chirality pdb=" P G C 36 " pdb=" OP1 G C 36 " pdb=" OP2 G C 36 " pdb=" O5' G C 36 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.41e+00 ... (remaining 1072 not shown) Planarity restraints: 873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C C 8 " 0.039 2.00e-02 2.50e+03 2.06e-02 9.53e+00 pdb=" N1 C C 8 " -0.046 2.00e-02 2.50e+03 pdb=" C2 C C 8 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C C 8 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C C 8 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C C 8 " 0.005 2.00e-02 2.50e+03 pdb=" N4 C C 8 " 0.010 2.00e-02 2.50e+03 pdb=" C5 C C 8 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C C 8 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 7 " -0.023 2.00e-02 2.50e+03 1.24e-02 3.47e+00 pdb=" N1 U C 7 " 0.028 2.00e-02 2.50e+03 pdb=" C2 U C 7 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U C 7 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U C 7 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U C 7 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U C 7 " -0.007 2.00e-02 2.50e+03 pdb=" C5 U C 7 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U C 7 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 16 " 0.024 2.00e-02 2.50e+03 1.02e-02 3.09e+00 pdb=" N9 G C 16 " -0.024 2.00e-02 2.50e+03 pdb=" C8 G C 16 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G C 16 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G C 16 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G C 16 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G C 16 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G C 16 " 0.000 2.00e-02 2.50e+03 pdb=" C2 G C 16 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G C 16 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G C 16 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G C 16 " -0.001 2.00e-02 2.50e+03 ... (remaining 870 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 24 2.43 - 3.05: 4109 3.05 - 3.67: 10972 3.67 - 4.28: 16852 4.28 - 4.90: 25302 Nonbonded interactions: 57259 Sorted by model distance: nonbonded pdb=" OD1 ASP B 30 " pdb="MG MG B 401 " model vdw 1.816 2.170 nonbonded pdb=" OG SER A 170 " pdb=" OP2 C C 18 " model vdw 1.883 3.040 nonbonded pdb=" O3' DT D 22 " pdb="MG MG B 401 " model vdw 1.907 2.170 nonbonded pdb=" OP1 DC E 23 " pdb="MG MG B 401 " model vdw 1.935 2.170 nonbonded pdb=" NE2 HIS B 58 " pdb="MG MG B 401 " model vdw 2.066 2.250 ... (remaining 57254 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.940 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 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 0.045 6743 Z= 0.353 Angle : 0.717 10.688 9548 Z= 0.571 Chirality : 0.071 1.469 1075 Planarity : 0.004 0.066 873 Dihedral : 21.977 166.446 2918 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 0.22 % Allowed : 9.17 % Favored : 90.61 % 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: 3.20 (0.37), residues: 540 helix: 2.77 (0.27), residues: 335 sheet: -1.72 (0.87), residues: 30 loop : 1.73 (0.53), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 286 TYR 0.019 0.001 TYR A 175 PHE 0.007 0.001 PHE B 269 TRP 0.004 0.001 TRP A 67 HIS 0.004 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.35 ( 6743) covalent geometry : angle 0.71747 / 0.57 ( 9548) hydrogen bonds : bond 0.11423 / 7.46 ( 359) hydrogen bonds : angle 4.41771 / 3.32 ( 952) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.211 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.4626 time to fit residues: 24.1414 Evaluate side-chains 43 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN B 134 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.077021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.060190 restraints weight = 18022.748| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.06 r_work: 0.3026 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6743 Z= 0.167 Angle : 0.623 7.303 9548 Z= 0.363 Chirality : 0.045 0.314 1075 Planarity : 0.004 0.023 873 Dihedral : 24.217 171.980 1824 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.75 % Allowed : 9.61 % Favored : 88.65 % 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: 3.38 (0.36), residues: 540 helix: 2.88 (0.26), residues: 342 sheet: -1.33 (0.91), residues: 30 loop : 1.76 (0.53), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 286 TYR 0.020 0.002 TYR A 289 PHE 0.011 0.001 PHE B 269 TRP 0.006 0.001 TRP B 309 HIS 0.005 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.17 ( 6743) covalent geometry : angle 0.62298 / 0.36 ( 9548) hydrogen bonds : bond 0.05238 / 3.46 ( 359) hydrogen bonds : angle 3.70183 / 2.78 ( 952) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.211 Fit side-chains REVERT: B 225 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8856 (mtpt) REVERT: B 239 ASN cc_start: 0.8388 (p0) cc_final: 0.8048 (p0) outliers start: 8 outliers final: 3 residues processed: 51 average time/residue: 0.5133 time to fit residues: 27.6497 Evaluate side-chains 47 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 225 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 60 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.076702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.060019 restraints weight = 18035.389| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.06 r_work: 0.3029 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6743 Z= 0.180 Angle : 0.605 7.658 9548 Z= 0.351 Chirality : 0.045 0.327 1075 Planarity : 0.003 0.025 873 Dihedral : 24.246 174.818 1824 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.40 % Allowed : 9.61 % Favored : 87.99 % 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 are not related in a simple way. whole: 3.54 (0.36), residues: 540 helix: 3.00 (0.26), residues: 341 sheet: -1.40 (0.87), residues: 30 loop : 1.86 (0.53), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 286 TYR 0.024 0.002 TYR A 175 PHE 0.011 0.002 PHE B 269 TRP 0.004 0.001 TRP B 309 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.18 ( 6743) covalent geometry : angle 0.60453 / 0.35 ( 9548) hydrogen bonds : bond 0.04784 / 3.15 ( 359) hydrogen bonds : angle 3.52325 / 2.64 ( 952) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.170 Fit side-chains REVERT: B 239 ASN cc_start: 0.8375 (p0) cc_final: 0.7928 (p0) outliers start: 11 outliers final: 4 residues processed: 54 average time/residue: 0.4533 time to fit residues: 25.9841 Evaluate side-chains 44 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 15 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 45 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.077816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.061096 restraints weight = 18005.073| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.09 r_work: 0.3063 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6743 Z= 0.147 Angle : 0.596 8.015 9548 Z= 0.342 Chirality : 0.045 0.341 1075 Planarity : 0.004 0.042 873 Dihedral : 24.254 176.753 1824 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.40 % Allowed : 10.92 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.66 (0.36), residues: 540 helix: 3.08 (0.26), residues: 341 sheet: -1.49 (0.84), residues: 30 loop : 1.98 (0.52), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 286 TYR 0.026 0.002 TYR A 175 PHE 0.007 0.001 PHE B 269 TRP 0.003 0.001 TRP B 309 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 ( 6743) covalent geometry : angle 0.59575 / 0.34 ( 9548) hydrogen bonds : bond 0.04448 / 2.93 ( 359) hydrogen bonds : angle 3.43261 / 2.56 ( 952) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.140 Fit side-chains REVERT: A 157 LEU cc_start: 0.9272 (mp) cc_final: 0.9046 (mp) REVERT: B 239 ASN cc_start: 0.8311 (p0) cc_final: 0.7863 (p0) outliers start: 11 outliers final: 3 residues processed: 50 average time/residue: 0.4271 time to fit residues: 22.8253 Evaluate side-chains 45 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 15 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 0.0470 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.075859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.059031 restraints weight = 18210.501| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.08 r_work: 0.3011 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6743 Z= 0.219 Angle : 0.634 8.702 9548 Z= 0.357 Chirality : 0.046 0.348 1075 Planarity : 0.004 0.042 873 Dihedral : 24.297 177.159 1824 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.40 % Allowed : 10.26 % Favored : 87.34 % 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: 3.54 (0.36), residues: 540 helix: 2.98 (0.26), residues: 341 sheet: -1.57 (0.81), residues: 30 loop : 1.95 (0.53), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 286 TYR 0.024 0.002 TYR A 175 PHE 0.009 0.002 PHE B 269 TRP 0.005 0.001 TRP A 274 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.22 ( 6743) covalent geometry : angle 0.63391 / 0.36 ( 9548) hydrogen bonds : bond 0.04781 / 3.16 ( 359) hydrogen bonds : angle 3.51211 / 2.63 ( 952) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.206 Fit side-chains REVERT: A 88 MET cc_start: 0.9364 (OUTLIER) cc_final: 0.8765 (mmm) REVERT: B 225 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8873 (mtpt) outliers start: 11 outliers final: 5 residues processed: 50 average time/residue: 0.4318 time to fit residues: 23.0312 Evaluate side-chains 48 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.0370 chunk 29 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.076040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.059119 restraints weight = 18121.176| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.08 r_work: 0.2998 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6743 Z= 0.204 Angle : 0.619 8.799 9548 Z= 0.351 Chirality : 0.046 0.359 1075 Planarity : 0.004 0.046 873 Dihedral : 24.348 178.069 1824 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.18 % Allowed : 11.57 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.49 (0.36), residues: 540 helix: 2.97 (0.26), residues: 341 sheet: -1.59 (0.82), residues: 30 loop : 1.87 (0.52), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 286 TYR 0.023 0.002 TYR A 175 PHE 0.008 0.002 PHE B 269 TRP 0.005 0.001 TRP A 274 HIS 0.004 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.20 ( 6743) covalent geometry : angle 0.61863 / 0.35 ( 9548) hydrogen bonds : bond 0.04632 / 3.04 ( 359) hydrogen bonds : angle 3.49057 / 2.61 ( 952) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.209 Fit side-chains REVERT: A 88 MET cc_start: 0.9358 (OUTLIER) cc_final: 0.8751 (mmm) REVERT: B 225 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8733 (mtpt) outliers start: 10 outliers final: 5 residues processed: 47 average time/residue: 0.4744 time to fit residues: 23.6730 Evaluate side-chains 47 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.077779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.060935 restraints weight = 17971.027| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.15 r_work: 0.3062 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6743 Z= 0.145 Angle : 0.598 8.546 9548 Z= 0.340 Chirality : 0.044 0.365 1075 Planarity : 0.004 0.049 873 Dihedral : 24.375 179.517 1824 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.40 % Allowed : 10.92 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.48 (0.36), residues: 540 helix: 2.95 (0.26), residues: 341 sheet: -1.73 (0.78), residues: 30 loop : 1.91 (0.52), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 286 TYR 0.026 0.002 TYR A 175 PHE 0.008 0.001 PHE B 269 TRP 0.003 0.001 TRP A 274 HIS 0.004 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 ( 6743) covalent geometry : angle 0.59815 / 0.34 ( 9548) hydrogen bonds : bond 0.04386 / 2.89 ( 359) hydrogen bonds : angle 3.43063 / 2.56 ( 952) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.158 Fit side-chains REVERT: A 88 MET cc_start: 0.9342 (OUTLIER) cc_final: 0.8771 (mmm) REVERT: A 157 LEU cc_start: 0.9267 (mp) cc_final: 0.9061 (mp) REVERT: B 225 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8809 (mtpt) outliers start: 11 outliers final: 6 residues processed: 47 average time/residue: 0.4781 time to fit residues: 23.8551 Evaluate side-chains 48 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.077656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.060950 restraints weight = 18029.996| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.11 r_work: 0.3058 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6743 Z= 0.156 Angle : 0.601 8.487 9548 Z= 0.339 Chirality : 0.044 0.367 1075 Planarity : 0.004 0.055 873 Dihedral : 24.372 179.959 1824 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.97 % Allowed : 11.35 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.48 (0.36), residues: 540 helix: 2.92 (0.26), residues: 343 sheet: -1.70 (0.78), residues: 30 loop : 1.98 (0.52), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 286 TYR 0.025 0.002 TYR B 95 PHE 0.007 0.001 PHE B 36 TRP 0.004 0.001 TRP A 274 HIS 0.002 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 ( 6743) covalent geometry : angle 0.60124 / 0.34 ( 9548) hydrogen bonds : bond 0.04349 / 2.86 ( 359) hydrogen bonds : angle 3.41318 / 2.56 ( 952) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.211 Fit side-chains REVERT: A 88 MET cc_start: 0.9337 (OUTLIER) cc_final: 0.8735 (mmm) REVERT: A 157 LEU cc_start: 0.9278 (mp) cc_final: 0.9046 (mp) REVERT: B 225 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8810 (mtpt) outliers start: 9 outliers final: 6 residues processed: 49 average time/residue: 0.4789 time to fit residues: 25.0617 Evaluate side-chains 48 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 2 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 9 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.2980 chunk 33 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.078757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.062033 restraints weight = 18548.726| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.16 r_work: 0.3070 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 6743 Z= 0.135 Angle : 0.590 8.865 9548 Z= 0.334 Chirality : 0.043 0.369 1075 Planarity : 0.004 0.055 873 Dihedral : 24.362 178.714 1824 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.18 % Allowed : 11.79 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.47 (0.36), residues: 540 helix: 2.91 (0.26), residues: 343 sheet: -1.75 (0.78), residues: 30 loop : 1.99 (0.52), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 286 TYR 0.023 0.002 TYR B 95 PHE 0.006 0.001 PHE A 269 TRP 0.003 0.001 TRP B 309 HIS 0.004 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 ( 6743) covalent geometry : angle 0.59037 / 0.33 ( 9548) hydrogen bonds : bond 0.04190 / 2.78 ( 359) hydrogen bonds : angle 3.38505 / 2.53 ( 952) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.195 Fit side-chains REVERT: B 225 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8803 (mtpt) outliers start: 10 outliers final: 7 residues processed: 49 average time/residue: 0.4595 time to fit residues: 24.0578 Evaluate side-chains 47 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 14 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.078032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.061330 restraints weight = 18061.989| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.10 r_work: 0.3068 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6743 Z= 0.166 Angle : 0.609 8.242 9548 Z= 0.340 Chirality : 0.044 0.370 1075 Planarity : 0.004 0.063 873 Dihedral : 24.354 178.676 1824 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.75 % Allowed : 12.45 % Favored : 85.81 % 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 are not related in a simple way. whole: 3.46 (0.36), residues: 540 helix: 2.89 (0.26), residues: 343 sheet: -1.78 (0.77), residues: 30 loop : 2.00 (0.52), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 286 TYR 0.021 0.002 TYR B 175 PHE 0.006 0.001 PHE B 36 TRP 0.010 0.001 TRP A 67 HIS 0.002 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 ( 6743) covalent geometry : angle 0.60884 / 0.34 ( 9548) hydrogen bonds : bond 0.04280 / 2.81 ( 359) hydrogen bonds : angle 3.50095 / 2.59 ( 952) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.213 Fit side-chains REVERT: B 225 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8831 (mtpt) outliers start: 8 outliers final: 5 residues processed: 47 average time/residue: 0.4960 time to fit residues: 24.7894 Evaluate side-chains 45 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.078323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.061438 restraints weight = 18366.168| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.19 r_work: 0.3070 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6743 Z= 0.142 Angle : 0.599 8.501 9548 Z= 0.337 Chirality : 0.044 0.371 1075 Planarity : 0.004 0.063 873 Dihedral : 24.346 178.140 1824 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.97 % Allowed : 12.23 % Favored : 85.81 % 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 are not related in a simple way. whole: 3.45 (0.36), residues: 540 helix: 2.89 (0.26), residues: 344 sheet: -1.75 (0.77), residues: 30 loop : 1.98 (0.52), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 286 TYR 0.023 0.002 TYR B 175 PHE 0.006 0.001 PHE B 36 TRP 0.003 0.001 TRP A 274 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 ( 6743) covalent geometry : angle 0.59858 / 0.34 ( 9548) hydrogen bonds : bond 0.04225 / 2.78 ( 359) hydrogen bonds : angle 3.39029 / 2.53 ( 952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2053.95 seconds wall clock time: 35 minutes 46.52 seconds (2146.52 seconds total)