Starting phenix.real_space_refine on Sun Apr 5 00:22:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w26_65567/04_2026/9w26_65567_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w26_65567/04_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_65567/04_2026/9w26_65567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w26_65567/04_2026/9w26_65567.map" model { file = "/net/cci-nas-00/data/ceres_data/9w26_65567/04_2026/9w26_65567_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w26_65567/04_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-2.1rc1-6017/lib/python3.9/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: 1.53, per 1000 atoms: 0.24 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: 0.89 Conformation dependent library (CDL) restraints added in 171.2 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: 0.77 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: 1.24 Time building geometry restraints manager: 1.03 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=" C ALA B 122 " pdb=" N GLN B 123 " ideal model delta sigma weight residual 1.334 1.301 0.033 1.27e-02 6.20e+03 6.77e+00 bond pdb=" P A C 37 " pdb=" OP1 A C 37 " ideal model delta sigma weight residual 1.480 1.515 -0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" P A C 37 " pdb=" OP2 A C 37 " ideal model delta sigma weight residual 1.480 1.515 -0.035 2.00e-02 2.50e+03 3.10e+00 bond pdb=" N GLN A 66 " pdb=" CA GLN A 66 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N GLN B 123 " pdb=" CA GLN B 123 " ideal model delta sigma weight residual 1.459 1.440 0.020 1.19e-02 7.06e+03 2.76e+00 ... (remaining 6738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 9379 2.14 - 4.28: 158 4.28 - 6.41: 8 6.41 - 8.55: 2 8.55 - 10.69: 1 Bond angle restraints: 9548 Sorted by residual: 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=" CA VAL B 29 " pdb=" CB VAL B 29 " pdb=" CG1 VAL B 29 " ideal model delta sigma weight residual 110.40 117.37 -6.97 1.70e+00 3.46e-01 1.68e+01 angle pdb=" CA VAL B 29 " pdb=" CB VAL B 29 " pdb=" CG2 VAL B 29 " ideal model delta sigma weight residual 110.40 116.63 -6.23 1.70e+00 3.46e-01 1.34e+01 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 1.50e+00 4.44e-01 9.17e+00 angle pdb=" C3' G C 36 " pdb=" C2' G C 36 " pdb=" C1' G C 36 " ideal model delta sigma weight residual 101.50 98.63 2.87 1.00e+00 1.00e+00 8.26e+00 ... (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 2.35 -2.87 -0.52 2.00e-01 2.50e+01 6.76e+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: 3.290 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.370 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:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 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 : 0.003 0.043 6743 Z= 0.157 Angle : 0.612 10.688 9548 Z= 0.355 Chirality : 0.062 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 covalent geometry : bond 0.00319 ( 6743) covalent geometry : angle 0.61228 ( 9548) hydrogen bonds : bond 0.11423 ( 359) hydrogen bonds : angle 4.41771 ( 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 : 0.140 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.5125 time to fit residues: 26.6122 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 : 0.145 ------------------------------------------------------------------------------- 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: 6.9990 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 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: 0.8980 chunk 25 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3563 r_free = 0.3563 target = 0.077167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.060546 restraints weight = 18135.601| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.08 r_work: 0.3045 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1145 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= 0.167 Angle : 0.573 5.277 9548 Z= 0.325 Chirality : 0.038 0.170 1075 Planarity : 0.003 0.026 873 Dihedral : 24.235 172.951 1824 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.97 % Allowed : 8.95 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.64 (0.36), residues: 540 helix: 3.06 (0.26), residues: 341 sheet: -1.34 (0.91), residues: 30 loop : 1.93 (0.53), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 286 TYR 0.019 0.002 TYR B 175 PHE 0.011 0.001 PHE B 269 TRP 0.005 0.001 TRP B 309 HIS 0.004 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6743) covalent geometry : angle 0.57348 ( 9548) hydrogen bonds : bond 0.04286 ( 359) hydrogen bonds : angle 3.47001 ( 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 53 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.208 Fit side-chains REVERT: B 238 ARG cc_start: 0.8784 (ptp-170) cc_final: 0.8405 (ptp-170) REVERT: B 239 ASN cc_start: 0.8302 (p0) cc_final: 0.7967 (p0) outliers start: 9 outliers final: 3 residues processed: 51 average time/residue: 0.4962 time to fit residues: 26.8143 Evaluate side-chains 46 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.078653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.061899 restraints weight = 17864.121| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.14 r_work: 0.3069 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1641 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= 0.146 Angle : 0.544 7.657 9548 Z= 0.307 Chirality : 0.036 0.164 1075 Planarity : 0.003 0.026 873 Dihedral : 24.220 174.112 1824 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 2.18 % Allowed : 9.83 % 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: 3.80 (0.36), residues: 540 helix: 3.17 (0.26), residues: 343 sheet: -1.53 (0.84), residues: 30 loop : 2.10 (0.52), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 286 TYR 0.030 0.002 TYR A 175 PHE 0.008 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 covalent geometry : bond 0.00323 ( 6743) covalent geometry : angle 0.54388 ( 9548) hydrogen bonds : bond 0.03973 ( 359) hydrogen bonds : angle 3.25758 ( 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 56 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.190 Fit side-chains REVERT: A 157 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9044 (mp) REVERT: B 238 ARG cc_start: 0.8783 (ptp-170) cc_final: 0.8423 (ptp-170) outliers start: 10 outliers final: 3 residues processed: 50 average time/residue: 0.5089 time to fit residues: 27.0206 Evaluate side-chains 46 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 48 optimal weight: 0.0170 chunk 18 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 overall best weight: 1.2624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.077578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.060766 restraints weight = 18017.638| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.11 r_work: 0.3033 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1750 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= 0.172 Angle : 0.548 5.815 9548 Z= 0.309 Chirality : 0.036 0.158 1075 Planarity : 0.003 0.033 873 Dihedral : 24.244 173.778 1824 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.40 % Allowed : 12.01 % Favored : 85.59 % 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: 3.70 (0.36), residues: 540 helix: 3.08 (0.26), residues: 343 sheet: -1.61 (0.81), residues: 30 loop : 2.08 (0.51), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 286 TYR 0.030 0.002 TYR A 175 PHE 0.006 0.001 PHE B 269 TRP 0.004 0.001 TRP A 274 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 6743) covalent geometry : angle 0.54810 ( 9548) hydrogen bonds : bond 0.04035 ( 359) hydrogen bonds : angle 3.28983 ( 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 55 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.194 Fit side-chains REVERT: A 157 LEU cc_start: 0.9293 (mp) cc_final: 0.9049 (mp) REVERT: B 225 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8783 (tttt) REVERT: B 238 ARG cc_start: 0.8760 (ptp-170) cc_final: 0.8447 (ptp-170) outliers start: 11 outliers final: 3 residues processed: 50 average time/residue: 0.5398 time to fit residues: 28.5077 Evaluate side-chains 46 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.078628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.061893 restraints weight = 18165.326| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.12 r_work: 0.3086 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1921 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= 0.150 Angle : 0.537 6.182 9548 Z= 0.301 Chirality : 0.035 0.163 1075 Planarity : 0.003 0.035 873 Dihedral : 24.187 173.901 1824 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 3.79 (0.35), residues: 540 helix: 3.16 (0.26), residues: 343 sheet: -1.67 (0.79), residues: 30 loop : 2.11 (0.51), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 286 TYR 0.018 0.001 TYR B 175 PHE 0.009 0.001 PHE A 269 TRP 0.003 0.001 TRP B 203 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6743) covalent geometry : angle 0.53741 ( 9548) hydrogen bonds : bond 0.03862 ( 359) hydrogen bonds : angle 3.20679 ( 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 55 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.191 Fit side-chains REVERT: B 225 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8786 (tttt) REVERT: B 238 ARG cc_start: 0.8709 (ptp-170) cc_final: 0.8384 (ptp-170) outliers start: 10 outliers final: 3 residues processed: 52 average time/residue: 0.5093 time to fit residues: 28.1378 Evaluate side-chains 46 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.077747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.061069 restraints weight = 18156.243| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.12 r_work: 0.3059 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2001 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= 0.173 Angle : 0.562 7.625 9548 Z= 0.309 Chirality : 0.036 0.158 1075 Planarity : 0.003 0.042 873 Dihedral : 24.129 173.500 1824 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.18 % Allowed : 11.14 % 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: 3.81 (0.35), residues: 540 helix: 3.22 (0.26), residues: 342 sheet: -1.62 (0.80), residues: 30 loop : 2.02 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 286 TYR 0.023 0.002 TYR A 175 PHE 0.007 0.002 PHE A 269 TRP 0.004 0.001 TRP A 274 HIS 0.003 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 6743) covalent geometry : angle 0.56228 ( 9548) hydrogen bonds : bond 0.04019 ( 359) hydrogen bonds : angle 3.24604 ( 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 53 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.211 Fit side-chains REVERT: A 175 TYR cc_start: 0.8384 (t80) cc_final: 0.8132 (t80) REVERT: B 225 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8831 (tttt) REVERT: B 238 ARG cc_start: 0.8727 (ptp-170) cc_final: 0.8394 (ptp-170) outliers start: 10 outliers final: 4 residues processed: 50 average time/residue: 0.5493 time to fit residues: 29.0954 Evaluate side-chains 46 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.076691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.059697 restraints weight = 18153.414| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.18 r_work: 0.3025 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6743 Z= 0.192 Angle : 0.592 8.732 9548 Z= 0.320 Chirality : 0.038 0.163 1075 Planarity : 0.004 0.048 873 Dihedral : 24.137 173.090 1824 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.75 % Allowed : 12.23 % 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: 3.67 (0.36), residues: 540 helix: 3.07 (0.26), residues: 343 sheet: -1.52 (0.83), residues: 30 loop : 2.01 (0.51), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 286 TYR 0.023 0.002 TYR A 175 PHE 0.007 0.001 PHE A 269 TRP 0.004 0.001 TRP A 274 HIS 0.003 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 6743) covalent geometry : angle 0.59208 ( 9548) hydrogen bonds : bond 0.04178 ( 359) hydrogen bonds : angle 3.35460 ( 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 52 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.191 Fit side-chains REVERT: B 225 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8849 (tttt) REVERT: B 238 ARG cc_start: 0.8704 (ptp-170) cc_final: 0.8362 (ptp-170) outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 0.4856 time to fit residues: 25.6998 Evaluate side-chains 46 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN B 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.079229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.062473 restraints weight = 18186.878| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.18 r_work: 0.3094 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2293 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= 0.140 Angle : 0.584 14.239 9548 Z= 0.311 Chirality : 0.036 0.170 1075 Planarity : 0.004 0.055 873 Dihedral : 24.128 174.356 1824 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.75 % Allowed : 12.88 % Favored : 85.37 % 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: 3.73 (0.35), residues: 540 helix: 3.10 (0.26), residues: 343 sheet: -1.59 (0.81), residues: 30 loop : 2.09 (0.51), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 286 TYR 0.018 0.001 TYR A 175 PHE 0.006 0.001 PHE A 269 TRP 0.005 0.001 TRP A 203 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6743) covalent geometry : angle 0.58402 ( 9548) hydrogen bonds : bond 0.03871 ( 359) hydrogen bonds : angle 3.21814 ( 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 55 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.150 Fit side-chains REVERT: B 225 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8839 (tttt) REVERT: B 238 ARG cc_start: 0.8678 (ptp-170) cc_final: 0.8378 (ptp-170) outliers start: 8 outliers final: 4 residues processed: 51 average time/residue: 0.4939 time to fit residues: 26.8408 Evaluate side-chains 47 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 245 ILE Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 2 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 9 optimal weight: 0.1980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.079391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.062642 restraints weight = 18355.305| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.22 r_work: 0.3102 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2421 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= 0.141 Angle : 0.596 12.378 9548 Z= 0.315 Chirality : 0.036 0.195 1075 Planarity : 0.004 0.057 873 Dihedral : 24.087 174.807 1824 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.53 % Allowed : 13.54 % Favored : 84.93 % 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: 3.63 (0.35), residues: 540 helix: 2.99 (0.26), residues: 343 sheet: -1.64 (0.80), residues: 30 loop : 2.15 (0.52), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 286 TYR 0.032 0.002 TYR B 95 PHE 0.007 0.001 PHE A 269 TRP 0.003 0.001 TRP B 203 HIS 0.002 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6743) covalent geometry : angle 0.59556 ( 9548) hydrogen bonds : bond 0.03850 ( 359) hydrogen bonds : angle 3.30304 ( 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 56 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.196 Fit side-chains REVERT: B 15 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8283 (pp) REVERT: B 225 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8823 (tttt) REVERT: B 238 ARG cc_start: 0.8657 (ptp-170) cc_final: 0.8346 (ptp-170) outliers start: 7 outliers final: 5 residues processed: 54 average time/residue: 0.4956 time to fit residues: 28.4089 Evaluate side-chains 52 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN 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 245 ILE 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: 0.0870 chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 37 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 0.0010 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.4766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.080760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.064251 restraints weight = 18093.778| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.19 r_work: 0.3159 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6743 Z= 0.133 Angle : 0.603 12.366 9548 Z= 0.320 Chirality : 0.036 0.215 1075 Planarity : 0.004 0.060 873 Dihedral : 24.050 175.462 1824 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.31 % Allowed : 14.85 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.58 (0.35), residues: 540 helix: 2.90 (0.26), residues: 344 sheet: -1.57 (0.81), residues: 30 loop : 2.23 (0.52), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 286 TYR 0.030 0.001 TYR B 95 PHE 0.008 0.001 PHE A 269 TRP 0.004 0.001 TRP B 203 HIS 0.002 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 6743) covalent geometry : angle 0.60306 ( 9548) hydrogen bonds : bond 0.03924 ( 359) hydrogen bonds : angle 3.25702 ( 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 59 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.198 Fit side-chains REVERT: B 15 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8234 (pp) REVERT: B 205 MET cc_start: 0.9010 (ttp) cc_final: 0.8398 (tmm) REVERT: B 225 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8784 (tttt) REVERT: B 238 ARG cc_start: 0.8657 (ptp-170) cc_final: 0.8355 (ptp-170) outliers start: 6 outliers final: 3 residues processed: 58 average time/residue: 0.4831 time to fit residues: 29.7190 Evaluate side-chains 51 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 18 optimal weight: 0.0770 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.080859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.064520 restraints weight = 18248.321| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.19 r_work: 0.3167 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6743 Z= 0.139 Angle : 0.613 13.665 9548 Z= 0.327 Chirality : 0.037 0.206 1075 Planarity : 0.004 0.061 873 Dihedral : 24.007 175.753 1824 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.87 % Allowed : 16.81 % Favored : 82.31 % 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: 3.61 (0.35), residues: 540 helix: 2.96 (0.26), residues: 344 sheet: -1.46 (0.82), residues: 30 loop : 2.14 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 286 TYR 0.033 0.002 TYR B 95 PHE 0.010 0.001 PHE B 269 TRP 0.006 0.001 TRP A 307 HIS 0.002 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6743) covalent geometry : angle 0.61324 ( 9548) hydrogen bonds : bond 0.03864 ( 359) hydrogen bonds : angle 3.24009 ( 952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2187.81 seconds wall clock time: 38 minutes 4.24 seconds (2284.24 seconds total)