Starting phenix.real_space_refine on Fri Sep 11 16:15:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m4d_30076/09_2026/6m4d_30076.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m4d_30076/09_2026/6m4d_30076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m4d_30076/09_2026/6m4d_30076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m4d_30076/09_2026/6m4d_30076.map" model { file = "/net/cci-nas-00/data/ceres_data/6m4d_30076/09_2026/6m4d_30076.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m4d_30076/09_2026/6m4d_30076.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 250 5.49 5 S 14 5.16 5 C 5801 2.51 5 N 1962 2.21 5 O 2470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10497 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 693 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "D" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2548 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Chain: "J" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2577 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Restraints were copied for chains: E, F, G, H Time building chain proxies: 2.39, per 1000 atoms: 0.23 Number of scatterers: 10497 At special positions: 0 Unit cell: (131.04, 79.04, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 250 15.00 O 2470 8.00 N 1962 7.00 C 5801 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: 0.95 Conformation dependent library (CDL) restraints added in 136.4 milliseconds 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1272 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 3 sheets defined 75.1% alpha, 0.9% beta 123 base pairs and 185 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.724A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 50 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 18 through 24 Processing helix chain 'C' and resid 28 through 38 Processing helix chain 'C' and resid 47 through 75 Processing helix chain 'C' and resid 82 through 91 removed outlier: 3.571A pdb=" N LEU C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 63 through 77 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.723A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 18 through 24 Processing helix chain 'G' and resid 28 through 38 Processing helix chain 'G' and resid 47 through 75 Processing helix chain 'G' and resid 82 through 91 removed outlier: 3.571A pdb=" N LEU G 86 " --> pdb=" O THR G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 100 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.952A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.068A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 381 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 317 hydrogen bonds 622 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 185 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1934 1.33 - 1.45: 3674 1.45 - 1.57: 5056 1.57 - 1.68: 498 1.68 - 1.80: 24 Bond restraints: 11186 Sorted by residual: bond pdb=" C5' DG J 136 " pdb=" C4' DG J 136 " ideal model delta sigma weight residual 1.512 1.551 -0.039 7.00e-03 2.04e+04 3.05e+01 bond pdb=" P DG J 136 " pdb=" O5' DG J 136 " ideal model delta sigma weight residual 1.593 1.639 -0.046 1.00e-02 1.00e+04 2.16e+01 bond pdb=" C3' DG I 101 " pdb=" O3' DG I 101 " ideal model delta sigma weight residual 1.435 1.382 0.053 1.30e-02 5.92e+03 1.69e+01 bond pdb=" C3' DT J 13 " pdb=" O3' DT J 13 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.26e+01 bond pdb=" C3' DA J 80 " pdb=" O3' DA J 80 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.21e+01 ... (remaining 11181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 15887 2.78 - 5.56: 270 5.56 - 8.35: 10 8.35 - 11.13: 4 11.13 - 13.91: 2 Bond angle restraints: 16173 Sorted by residual: angle pdb=" C3' DC J 135 " pdb=" O3' DC J 135 " pdb=" P DG J 136 " ideal model delta sigma weight residual 119.70 131.11 -11.41 1.20e+00 6.94e-01 9.05e+01 angle pdb=" O3' DC J 135 " pdb=" P DG J 136 " pdb=" O5' DG J 136 " ideal model delta sigma weight residual 104.00 117.91 -13.91 1.90e+00 2.77e-01 5.36e+01 angle pdb=" O4' DG J 69 " pdb=" C4' DG J 69 " pdb=" C3' DG J 69 " ideal model delta sigma weight residual 106.00 101.78 4.22 6.00e-01 2.78e+00 4.95e+01 angle pdb=" O4' DG J 136 " pdb=" C1' DG J 136 " pdb=" N9 DG J 136 " ideal model delta sigma weight residual 108.00 112.88 -4.88 7.00e-01 2.04e+00 4.86e+01 angle pdb=" O4' DG I 50 " pdb=" C4' DG I 50 " pdb=" C3' DG I 50 " ideal model delta sigma weight residual 106.00 102.13 3.87 6.00e-01 2.78e+00 4.15e+01 ... (remaining 16168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 4628 34.98 - 69.96: 1358 69.96 - 104.94: 65 104.94 - 139.92: 7 139.92 - 174.90: 2 Dihedral angle restraints: 6060 sinusoidal: 4090 harmonic: 1970 Sorted by residual: dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 157.08 22.92 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA LYS D 34 " pdb=" C LYS D 34 " pdb=" N GLU D 35 " pdb=" CA GLU D 35 " ideal model delta harmonic sigma weight residual -180.00 -157.78 -22.22 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 6057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1465 0.061 - 0.123: 345 0.123 - 0.184: 34 0.184 - 0.246: 2 0.246 - 0.307: 4 Chirality restraints: 1850 Sorted by residual: chirality pdb=" C1' DT J 13 " pdb=" O4' DT J 13 " pdb=" C2' DT J 13 " pdb=" N1 DT J 13 " both_signs ideal model delta sigma weight residual False 2.43 2.12 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C3' DC J 135 " pdb=" C4' DC J 135 " pdb=" O3' DC J 135 " pdb=" C2' DC J 135 " both_signs ideal model delta sigma weight residual False -2.73 -2.44 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1' DG I 19 " pdb=" O4' DG I 19 " pdb=" C2' DG I 19 " pdb=" N9 DG I 19 " both_signs ideal model delta sigma weight residual False 2.43 2.17 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1847 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 13 " -0.036 2.00e-02 2.50e+03 2.52e-02 1.91e+01 pdb=" N9 DG I 13 " 0.069 2.00e-02 2.50e+03 pdb=" C8 DG I 13 " -0.030 2.00e-02 2.50e+03 pdb=" N7 DG I 13 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 13 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 13 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 13 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DG I 13 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 13 " 0.016 2.00e-02 2.50e+03 pdb=" N2 DG I 13 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DG I 13 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DG I 13 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 14 " 0.026 2.00e-02 2.50e+03 2.54e-02 1.78e+01 pdb=" N9 DA J 14 " -0.068 2.00e-02 2.50e+03 pdb=" C8 DA J 14 " 0.040 2.00e-02 2.50e+03 pdb=" N7 DA J 14 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA J 14 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DA J 14 " -0.000 2.00e-02 2.50e+03 pdb=" N6 DA J 14 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DA J 14 " 0.015 2.00e-02 2.50e+03 pdb=" C2 DA J 14 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA J 14 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DA J 14 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 72 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ALA C 72 " 0.059 2.00e-02 2.50e+03 pdb=" O ALA C 72 " -0.022 2.00e-02 2.50e+03 pdb=" N SER C 73 " -0.020 2.00e-02 2.50e+03 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 352 2.64 - 3.20: 10613 3.20 - 3.77: 22149 3.77 - 4.33: 26096 4.33 - 4.90: 35636 Nonbonded interactions: 94846 Sorted by model distance: nonbonded pdb=" NH2 ARG B 35 " pdb=" OP2 DC I 82 " model vdw 2.074 3.120 nonbonded pdb=" OG SER C 73 " pdb=" O VAL C 78 " model vdw 2.085 3.040 nonbonded pdb=" OG SER G 73 " pdb=" O VAL G 78 " model vdw 2.087 3.040 nonbonded pdb=" N2 DG I 132 " pdb=" O2 DC J 16 " model vdw 2.099 2.496 nonbonded pdb=" O HIS F 75 " pdb=" NH1 ARG H 92 " model vdw 2.154 3.120 ... (remaining 94841 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.770 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 : 0.008 0.053 11186 Z= 0.672 Angle : 0.960 13.910 16173 Z= 0.842 Chirality : 0.052 0.307 1850 Planarity : 0.005 0.068 1178 Dihedral : 31.368 174.897 4788 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 25.84 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.61 % Favored : 92.79 % Rotamer: Outliers : 0.71 % Allowed : 12.06 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.26), residues: 666 helix: -1.35 (0.20), residues: 490 sheet: None (None), residues: 0 loop : -2.95 (0.34), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 31 TYR 0.015 0.002 TYR D 40 PHE 0.015 0.003 PHE F 100 HIS 0.006 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00757 / 0.67 (11186) covalent geometry : angle 0.96020 / 0.84 (16173) hydrogen bonds : bond 0.13718 / 9.48 ( 698) hydrogen bonds : angle 5.54592 / 3.86 ( 1753) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 214 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7993 (mmp-170) cc_final: 0.7250 (mmp80) REVERT: A 84 PHE cc_start: 0.8620 (m-80) cc_final: 0.8364 (m-80) REVERT: A 90 MET cc_start: 0.8269 (mtp) cc_final: 0.7950 (mtp) REVERT: A 93 GLN cc_start: 0.9116 (tt0) cc_final: 0.8565 (tt0) REVERT: A 97 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8699 (mt-10) REVERT: A 123 ASP cc_start: 0.8910 (m-30) cc_final: 0.8613 (m-30) REVERT: B 27 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8814 (tm-30) REVERT: B 63 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7691 (mt-10) REVERT: B 88 TYR cc_start: 0.8335 (m-10) cc_final: 0.8044 (m-80) REVERT: D 46 LYS cc_start: 0.8548 (mmtt) cc_final: 0.8174 (pttt) REVERT: D 59 MET cc_start: 0.8768 (tpp) cc_final: 0.8410 (tpt) REVERT: D 83 TYR cc_start: 0.7935 (m-10) cc_final: 0.7480 (m-10) REVERT: D 105 GLU cc_start: 0.8752 (pp20) cc_final: 0.7934 (pm20) REVERT: D 106 LEU cc_start: 0.8870 (mt) cc_final: 0.8604 (mt) REVERT: E 60 LEU cc_start: 0.8171 (mt) cc_final: 0.7944 (mt) REVERT: E 97 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8687 (mt-10) REVERT: E 100 LEU cc_start: 0.9430 (tp) cc_final: 0.9152 (tt) REVERT: F 88 TYR cc_start: 0.8285 (m-10) cc_final: 0.7238 (m-80) REVERT: G 36 LEU cc_start: 0.9529 (tt) cc_final: 0.9306 (mm) REVERT: G 46 VAL cc_start: 0.8463 (t) cc_final: 0.8256 (t) REVERT: H 59 MET cc_start: 0.8789 (tpp) cc_final: 0.8308 (tpp) REVERT: H 105 GLU cc_start: 0.8773 (pp20) cc_final: 0.8549 (pp20) outliers start: 4 outliers final: 3 residues processed: 218 average time/residue: 0.1414 time to fit residues: 39.4226 Evaluate side-chains 147 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 HIS C 71 ASN G 43 HIS H 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.046773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.034937 restraints weight = 87165.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.036029 restraints weight = 50531.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.036741 restraints weight = 35333.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.037237 restraints weight = 28111.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.037507 restraints weight = 24203.630| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11186 Z= 0.216 Angle : 0.886 11.648 16173 Z= 0.496 Chirality : 0.059 0.336 1850 Planarity : 0.007 0.062 1178 Dihedral : 35.010 177.991 3476 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.25 % Favored : 97.15 % Rotamer: Outliers : 0.18 % Allowed : 5.50 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.30), residues: 666 helix: 0.37 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -3.14 (0.35), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 72 TYR 0.021 0.003 TYR F 72 PHE 0.015 0.002 PHE B 100 HIS 0.005 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.22 (11186) covalent geometry : angle 0.88640 / 0.50 (16173) hydrogen bonds : bond 0.08193 / 5.63 ( 698) hydrogen bonds : angle 4.49232 / 3.21 ( 1753) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.9252 (mm) cc_final: 0.8703 (mm) REVERT: A 63 ARG cc_start: 0.8490 (mmp-170) cc_final: 0.7669 (mmp80) REVERT: A 70 LEU cc_start: 0.9553 (tt) cc_final: 0.9344 (pp) REVERT: A 84 PHE cc_start: 0.8823 (m-80) cc_final: 0.8579 (m-80) REVERT: A 93 GLN cc_start: 0.9135 (tt0) cc_final: 0.8596 (tt0) REVERT: A 120 MET cc_start: 0.9137 (tpp) cc_final: 0.8910 (tpp) REVERT: A 126 LEU cc_start: 0.9502 (tp) cc_final: 0.9254 (tp) REVERT: B 27 GLN cc_start: 0.9313 (mm-40) cc_final: 0.8960 (tp-100) REVERT: C 31 ARG cc_start: 0.8854 (ttm170) cc_final: 0.8198 (ttp80) REVERT: D 42 TYR cc_start: 0.9082 (m-80) cc_final: 0.8811 (m-80) REVERT: D 46 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8324 (pttt) REVERT: D 83 TYR cc_start: 0.8041 (m-10) cc_final: 0.7392 (m-10) REVERT: D 102 LEU cc_start: 0.8444 (tp) cc_final: 0.8132 (tp) REVERT: E 100 LEU cc_start: 0.9327 (tp) cc_final: 0.9010 (tp) REVERT: F 88 TYR cc_start: 0.8609 (m-10) cc_final: 0.8387 (m-80) REVERT: G 31 ARG cc_start: 0.8820 (ttm170) cc_final: 0.7753 (ttp80) REVERT: G 36 LEU cc_start: 0.9661 (tt) cc_final: 0.9389 (mm) REVERT: H 79 ARG cc_start: 0.8604 (mtp180) cc_final: 0.8161 (mtp180) REVERT: H 80 LEU cc_start: 0.9688 (mt) cc_final: 0.9475 (mt) REVERT: H 83 TYR cc_start: 0.7729 (m-10) cc_final: 0.7138 (m-80) REVERT: H 102 LEU cc_start: 0.8751 (tp) cc_final: 0.8491 (tp) REVERT: H 109 HIS cc_start: 0.9130 (m170) cc_final: 0.8755 (m170) outliers start: 1 outliers final: 1 residues processed: 199 average time/residue: 0.1205 time to fit residues: 32.2917 Evaluate side-chains 148 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 24 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 87 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 78 optimal weight: 40.0000 chunk 69 optimal weight: 20.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.046317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.035050 restraints weight = 85086.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.036120 restraints weight = 47893.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.036836 restraints weight = 33025.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.037316 restraints weight = 25952.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.037555 restraints weight = 22219.985| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11186 Z= 0.223 Angle : 0.811 8.391 16173 Z= 0.469 Chirality : 0.055 0.327 1850 Planarity : 0.006 0.056 1178 Dihedral : 34.839 178.147 3476 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.15 % Favored : 96.25 % Rotamer: Outliers : 0.18 % Allowed : 5.50 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.31), residues: 666 helix: 0.92 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -2.94 (0.37), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 131 TYR 0.032 0.002 TYR B 88 PHE 0.014 0.002 PHE E 67 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.22 (11186) covalent geometry : angle 0.81122 / 0.47 (16173) hydrogen bonds : bond 0.08154 / 5.63 ( 698) hydrogen bonds : angle 4.27733 / 3.04 ( 1753) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.9249 (mm) cc_final: 0.8960 (mm) REVERT: A 63 ARG cc_start: 0.8576 (mmp-170) cc_final: 0.7848 (mmp80) REVERT: A 70 LEU cc_start: 0.9524 (tt) cc_final: 0.9323 (pp) REVERT: A 74 ILE cc_start: 0.9523 (tt) cc_final: 0.9317 (tt) REVERT: A 93 GLN cc_start: 0.9044 (tt0) cc_final: 0.8682 (tp40) REVERT: A 126 LEU cc_start: 0.9560 (tp) cc_final: 0.9286 (tp) REVERT: C 34 ARG cc_start: 0.9114 (mtp180) cc_final: 0.8836 (mtp180) REVERT: C 35 HIS cc_start: 0.8998 (m90) cc_final: 0.8745 (m-70) REVERT: D 42 TYR cc_start: 0.9166 (m-80) cc_final: 0.8690 (m-80) REVERT: D 59 MET cc_start: 0.8763 (tpp) cc_final: 0.8519 (mmm) REVERT: D 83 TYR cc_start: 0.7877 (m-10) cc_final: 0.7179 (m-10) REVERT: D 102 LEU cc_start: 0.8390 (tp) cc_final: 0.8086 (tp) REVERT: D 106 LEU cc_start: 0.9331 (mt) cc_final: 0.8758 (mt) REVERT: E 100 LEU cc_start: 0.9440 (tp) cc_final: 0.9119 (tp) REVERT: F 58 LEU cc_start: 0.9424 (tp) cc_final: 0.8926 (pp) REVERT: H 79 ARG cc_start: 0.8607 (mtp180) cc_final: 0.8248 (mtp180) REVERT: H 83 TYR cc_start: 0.7559 (m-10) cc_final: 0.6815 (m-10) REVERT: H 109 HIS cc_start: 0.8961 (m170) cc_final: 0.8685 (m170) outliers start: 1 outliers final: 1 residues processed: 184 average time/residue: 0.1105 time to fit residues: 28.0776 Evaluate side-chains 138 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 84 optimal weight: 30.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN C 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.047925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.036230 restraints weight = 85202.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.037318 restraints weight = 48643.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.038040 restraints weight = 33771.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.038541 restraints weight = 26634.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.038855 restraints weight = 22891.880| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11186 Z= 0.167 Angle : 0.769 8.781 16173 Z= 0.439 Chirality : 0.053 0.332 1850 Planarity : 0.006 0.059 1178 Dihedral : 34.717 179.679 3476 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.55 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.31), residues: 666 helix: 1.19 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -2.93 (0.38), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 31 TYR 0.025 0.003 TYR B 88 PHE 0.012 0.002 PHE E 67 HIS 0.005 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.17 (11186) covalent geometry : angle 0.76909 / 0.44 (16173) hydrogen bonds : bond 0.06723 / 4.68 ( 698) hydrogen bonds : angle 3.92632 / 2.82 ( 1753) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.9208 (mm) cc_final: 0.8817 (mm) REVERT: A 63 ARG cc_start: 0.8557 (mmp-170) cc_final: 0.7865 (mmp80) REVERT: A 93 GLN cc_start: 0.9017 (tt0) cc_final: 0.8569 (tt0) REVERT: A 123 ASP cc_start: 0.9101 (m-30) cc_final: 0.8892 (m-30) REVERT: A 126 LEU cc_start: 0.9521 (tp) cc_final: 0.9303 (tp) REVERT: B 27 GLN cc_start: 0.8504 (tp-100) cc_final: 0.8042 (tp-100) REVERT: C 34 ARG cc_start: 0.9102 (mtp180) cc_final: 0.8775 (mtp180) REVERT: D 83 TYR cc_start: 0.7793 (m-10) cc_final: 0.7548 (m-80) REVERT: D 102 LEU cc_start: 0.8406 (tp) cc_final: 0.8045 (tp) REVERT: E 100 LEU cc_start: 0.9399 (tp) cc_final: 0.9123 (tp) REVERT: F 27 GLN cc_start: 0.9318 (mm-40) cc_final: 0.9019 (mp10) REVERT: F 58 LEU cc_start: 0.9352 (tp) cc_final: 0.8856 (pp) REVERT: G 25 LEU cc_start: 0.9341 (mm) cc_final: 0.8913 (tt) REVERT: G 31 ARG cc_start: 0.8649 (ttm170) cc_final: 0.8208 (ttp80) REVERT: G 59 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8572 (mm-30) REVERT: H 79 ARG cc_start: 0.8491 (mtp180) cc_final: 0.8109 (mtp85) REVERT: H 80 LEU cc_start: 0.9670 (mt) cc_final: 0.9421 (mt) REVERT: H 83 TYR cc_start: 0.7514 (m-10) cc_final: 0.7078 (m-80) REVERT: H 102 LEU cc_start: 0.8644 (tp) cc_final: 0.8403 (tp) REVERT: H 109 HIS cc_start: 0.8950 (m170) cc_final: 0.8719 (m170) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1121 time to fit residues: 29.5068 Evaluate side-chains 145 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 23 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 87 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 30.0000 chunk 89 optimal weight: 30.0000 chunk 58 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.046363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.034755 restraints weight = 88197.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.035819 restraints weight = 51001.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.036544 restraints weight = 35709.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.036979 restraints weight = 28257.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.037314 restraints weight = 24532.580| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11186 Z= 0.231 Angle : 0.800 8.936 16173 Z= 0.454 Chirality : 0.053 0.315 1850 Planarity : 0.006 0.057 1178 Dihedral : 34.661 177.438 3476 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.60 % Allowed : 3.00 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.31), residues: 666 helix: 0.96 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -2.90 (0.38), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 39 TYR 0.037 0.003 TYR H 40 PHE 0.031 0.003 PHE A 67 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.23 (11186) covalent geometry : angle 0.80002 / 0.45 (16173) hydrogen bonds : bond 0.08285 / 5.73 ( 698) hydrogen bonds : angle 4.18904 / 2.97 ( 1753) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8623 (mmp-170) cc_final: 0.8023 (mmp80) REVERT: A 70 LEU cc_start: 0.9657 (pp) cc_final: 0.9450 (tt) REVERT: A 123 ASP cc_start: 0.9197 (m-30) cc_final: 0.8995 (m-30) REVERT: A 126 LEU cc_start: 0.9571 (tp) cc_final: 0.9343 (tp) REVERT: B 27 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8242 (tp-100) REVERT: C 34 ARG cc_start: 0.9134 (mtp180) cc_final: 0.8761 (mtp180) REVERT: D 80 LEU cc_start: 0.9734 (mt) cc_final: 0.9474 (mt) REVERT: D 102 LEU cc_start: 0.8318 (tp) cc_final: 0.8045 (tp) REVERT: D 109 HIS cc_start: 0.9057 (m170) cc_final: 0.8495 (m170) REVERT: E 76 GLN cc_start: 0.9046 (tp40) cc_final: 0.8844 (tp-100) REVERT: E 100 LEU cc_start: 0.9475 (tp) cc_final: 0.9202 (tp) REVERT: E 128 ARG cc_start: 0.9531 (mmm-85) cc_final: 0.8932 (mmm-85) REVERT: F 27 GLN cc_start: 0.9331 (mm-40) cc_final: 0.8970 (mp10) REVERT: F 58 LEU cc_start: 0.9434 (tp) cc_final: 0.8895 (pp) REVERT: G 31 ARG cc_start: 0.8422 (ttm170) cc_final: 0.8221 (ttp-170) REVERT: G 59 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8904 (mm-30) REVERT: H 79 ARG cc_start: 0.8557 (mtp180) cc_final: 0.8196 (mtp180) REVERT: H 80 LEU cc_start: 0.9664 (mt) cc_final: 0.9431 (mp) REVERT: H 102 LEU cc_start: 0.8778 (tp) cc_final: 0.8492 (tp) REVERT: H 105 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8450 (tm-30) REVERT: H 109 HIS cc_start: 0.8922 (m170) cc_final: 0.8649 (m170) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1160 time to fit residues: 28.5589 Evaluate side-chains 126 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 19 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 30.0000 chunk 72 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 83 optimal weight: 30.0000 chunk 4 optimal weight: 0.8980 chunk 82 optimal weight: 30.0000 chunk 51 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.046895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.035295 restraints weight = 88313.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.036391 restraints weight = 49604.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.037128 restraints weight = 34242.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.037567 restraints weight = 27054.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.037909 restraints weight = 23455.831| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11186 Z= 0.197 Angle : 0.780 9.602 16173 Z= 0.444 Chirality : 0.053 0.322 1850 Planarity : 0.006 0.071 1178 Dihedral : 34.645 178.382 3476 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.55 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.31), residues: 666 helix: 0.92 (0.22), residues: 502 sheet: None (None), residues: 0 loop : -2.91 (0.38), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 31 TYR 0.037 0.002 TYR H 40 PHE 0.012 0.002 PHE F 100 HIS 0.006 0.002 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.20 (11186) covalent geometry : angle 0.77980 / 0.44 (16173) hydrogen bonds : bond 0.07093 / 4.90 ( 698) hydrogen bonds : angle 4.09967 / 2.93 ( 1753) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8650 (mmp-170) cc_final: 0.8009 (mmp80) REVERT: A 100 LEU cc_start: 0.9144 (tp) cc_final: 0.8908 (tp) REVERT: A 126 LEU cc_start: 0.9565 (tp) cc_final: 0.9355 (tp) REVERT: B 27 GLN cc_start: 0.8710 (tp-100) cc_final: 0.8244 (tp-100) REVERT: C 35 HIS cc_start: 0.9073 (m90) cc_final: 0.8691 (m-70) REVERT: D 79 ARG cc_start: 0.8561 (mtp180) cc_final: 0.8232 (mtp85) REVERT: D 102 LEU cc_start: 0.8420 (tp) cc_final: 0.8109 (tp) REVERT: D 109 HIS cc_start: 0.9048 (m170) cc_final: 0.8486 (m170) REVERT: E 76 GLN cc_start: 0.9041 (tp40) cc_final: 0.8825 (tp40) REVERT: E 83 ARG cc_start: 0.9238 (mpp80) cc_final: 0.8880 (mtt180) REVERT: E 100 LEU cc_start: 0.9453 (tp) cc_final: 0.9193 (tp) REVERT: E 128 ARG cc_start: 0.9521 (mmm-85) cc_final: 0.8888 (mmm-85) REVERT: F 27 GLN cc_start: 0.9290 (mm-40) cc_final: 0.8942 (mp10) REVERT: F 58 LEU cc_start: 0.9387 (tp) cc_final: 0.8893 (pp) REVERT: G 25 LEU cc_start: 0.9397 (mm) cc_final: 0.8904 (tt) REVERT: G 59 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8864 (mm-30) REVERT: G 100 ILE cc_start: 0.8878 (mp) cc_final: 0.8673 (mp) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1104 time to fit residues: 26.6292 Evaluate side-chains 134 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 80 optimal weight: 30.0000 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 40.0000 chunk 42 optimal weight: 6.9990 chunk 79 optimal weight: 30.0000 chunk 77 optimal weight: 30.0000 chunk 53 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.046314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.035054 restraints weight = 84893.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.036177 restraints weight = 47214.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.036906 restraints weight = 32209.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.037380 restraints weight = 25158.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.037703 restraints weight = 21534.457| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11186 Z= 0.204 Angle : 0.783 8.276 16173 Z= 0.445 Chirality : 0.052 0.318 1850 Planarity : 0.007 0.094 1178 Dihedral : 34.605 178.495 3476 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.85 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.32), residues: 666 helix: 1.00 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -2.86 (0.37), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 79 TYR 0.049 0.003 TYR D 83 PHE 0.044 0.002 PHE A 67 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.20 (11186) covalent geometry : angle 0.78304 / 0.44 (16173) hydrogen bonds : bond 0.07307 / 5.06 ( 698) hydrogen bonds : angle 4.09624 / 2.90 ( 1753) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8635 (mmp-170) cc_final: 0.8042 (mmp80) REVERT: A 100 LEU cc_start: 0.9168 (tp) cc_final: 0.8890 (tp) REVERT: B 27 GLN cc_start: 0.8764 (tp-100) cc_final: 0.8287 (tp-100) REVERT: C 35 HIS cc_start: 0.9121 (m90) cc_final: 0.8719 (m-70) REVERT: C 59 GLU cc_start: 0.9087 (tt0) cc_final: 0.8846 (tt0) REVERT: D 37 TYR cc_start: 0.8968 (m-80) cc_final: 0.8766 (m-80) REVERT: D 93 GLU cc_start: 0.8759 (pm20) cc_final: 0.8553 (pm20) REVERT: D 102 LEU cc_start: 0.8420 (tp) cc_final: 0.8124 (tp) REVERT: D 109 HIS cc_start: 0.9053 (m170) cc_final: 0.8425 (m170) REVERT: E 83 ARG cc_start: 0.9199 (mpp80) cc_final: 0.8786 (mtt180) REVERT: E 100 LEU cc_start: 0.9443 (tp) cc_final: 0.9202 (tp) REVERT: E 128 ARG cc_start: 0.9511 (mmm-85) cc_final: 0.9245 (mmm-85) REVERT: F 27 GLN cc_start: 0.9303 (mm-40) cc_final: 0.8936 (mp10) REVERT: F 58 LEU cc_start: 0.9387 (tp) cc_final: 0.8890 (pp) REVERT: G 59 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8786 (mm-30) REVERT: G 100 ILE cc_start: 0.8885 (mp) cc_final: 0.8678 (mp) REVERT: H 42 TYR cc_start: 0.9052 (m-80) cc_final: 0.8804 (m-80) REVERT: H 105 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8579 (tm-30) REVERT: H 106 LEU cc_start: 0.9150 (mt) cc_final: 0.8928 (mt) REVERT: H 109 HIS cc_start: 0.8842 (m90) cc_final: 0.8481 (m90) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1057 time to fit residues: 25.0680 Evaluate side-chains 135 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 59 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 31 optimal weight: 0.0970 chunk 80 optimal weight: 30.0000 chunk 66 optimal weight: 40.0000 chunk 58 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.048014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.036188 restraints weight = 85759.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.037288 restraints weight = 48373.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.038018 restraints weight = 33752.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.038493 restraints weight = 26947.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.038770 restraints weight = 23441.096| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11186 Z= 0.172 Angle : 0.760 7.866 16173 Z= 0.430 Chirality : 0.051 0.321 1850 Planarity : 0.006 0.076 1178 Dihedral : 34.548 179.753 3476 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.40 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.31), residues: 666 helix: 0.94 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -2.69 (0.38), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 31 TYR 0.038 0.003 TYR D 40 PHE 0.018 0.003 PHE D 70 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.17 (11186) covalent geometry : angle 0.75964 / 0.43 (16173) hydrogen bonds : bond 0.06368 / 4.46 ( 698) hydrogen bonds : angle 4.00193 / 2.86 ( 1753) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8602 (mmp-170) cc_final: 0.8142 (mmp80) REVERT: A 100 LEU cc_start: 0.9024 (tp) cc_final: 0.8762 (tp) REVERT: A 123 ASP cc_start: 0.9149 (m-30) cc_final: 0.8940 (m-30) REVERT: A 126 LEU cc_start: 0.9591 (tp) cc_final: 0.9345 (tp) REVERT: B 27 GLN cc_start: 0.8723 (tp-100) cc_final: 0.8224 (tp-100) REVERT: C 35 HIS cc_start: 0.9121 (m90) cc_final: 0.8788 (m-70) REVERT: C 45 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.8114 (ttm-80) REVERT: C 57 ILE cc_start: 0.9162 (mm) cc_final: 0.8959 (mm) REVERT: D 102 LEU cc_start: 0.8353 (tp) cc_final: 0.7993 (tp) REVERT: D 109 HIS cc_start: 0.9081 (m170) cc_final: 0.8455 (m170) REVERT: E 76 GLN cc_start: 0.9014 (tp40) cc_final: 0.8772 (tp40) REVERT: E 83 ARG cc_start: 0.9246 (mpp80) cc_final: 0.8827 (mtt180) REVERT: E 97 GLU cc_start: 0.8908 (pp20) cc_final: 0.8693 (pp20) REVERT: E 100 LEU cc_start: 0.9259 (tp) cc_final: 0.9045 (tp) REVERT: E 128 ARG cc_start: 0.9489 (mmm-85) cc_final: 0.9262 (mmm-85) REVERT: F 27 GLN cc_start: 0.9303 (mm-40) cc_final: 0.8927 (mp10) REVERT: F 58 LEU cc_start: 0.9338 (tp) cc_final: 0.8893 (pp) REVERT: F 63 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8093 (mt-10) REVERT: G 25 LEU cc_start: 0.9392 (mm) cc_final: 0.8809 (tt) REVERT: G 59 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8626 (mm-30) REVERT: G 66 LEU cc_start: 0.9121 (mt) cc_final: 0.8785 (pp) REVERT: G 100 ILE cc_start: 0.8798 (mp) cc_final: 0.8569 (mp) REVERT: H 109 HIS cc_start: 0.8882 (m90) cc_final: 0.8412 (m170) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0992 time to fit residues: 24.9368 Evaluate side-chains 134 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 38 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 0.0030 chunk 27 optimal weight: 0.9980 chunk 82 optimal weight: 30.0000 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 80 optimal weight: 30.0000 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 109 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.048218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.036311 restraints weight = 84681.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.037438 restraints weight = 47656.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.038196 restraints weight = 33094.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.038658 restraints weight = 26214.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.038883 restraints weight = 22832.105| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11186 Z= 0.168 Angle : 0.758 8.652 16173 Z= 0.427 Chirality : 0.051 0.317 1850 Planarity : 0.006 0.058 1178 Dihedral : 34.449 179.630 3476 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.55 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.31), residues: 666 helix: 0.87 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -2.57 (0.39), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 83 TYR 0.049 0.003 TYR D 83 PHE 0.012 0.002 PHE E 104 HIS 0.021 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.17 (11186) covalent geometry : angle 0.75791 / 0.43 (16173) hydrogen bonds : bond 0.06352 / 4.45 ( 698) hydrogen bonds : angle 3.87029 / 2.76 ( 1753) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8530 (mmp-170) cc_final: 0.8041 (mmp80) REVERT: A 83 ARG cc_start: 0.8620 (mtt-85) cc_final: 0.8309 (mtt90) REVERT: A 100 LEU cc_start: 0.9000 (tp) cc_final: 0.8731 (tp) REVERT: A 126 LEU cc_start: 0.9597 (tp) cc_final: 0.9358 (tp) REVERT: B 27 GLN cc_start: 0.8599 (tp-100) cc_final: 0.8121 (tp-100) REVERT: B 85 ASP cc_start: 0.9009 (m-30) cc_final: 0.8425 (m-30) REVERT: C 35 HIS cc_start: 0.9102 (m90) cc_final: 0.8689 (m-70) REVERT: C 59 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8670 (mm-30) REVERT: D 102 LEU cc_start: 0.8300 (tp) cc_final: 0.7993 (tp) REVERT: E 83 ARG cc_start: 0.9102 (mpp80) cc_final: 0.8663 (mtt180) REVERT: E 100 LEU cc_start: 0.9236 (tp) cc_final: 0.9008 (tp) REVERT: E 128 ARG cc_start: 0.9492 (mmm-85) cc_final: 0.9291 (mmm-85) REVERT: F 27 GLN cc_start: 0.9265 (mm-40) cc_final: 0.8919 (mp10) REVERT: F 58 LEU cc_start: 0.9347 (tp) cc_final: 0.8929 (pp) REVERT: F 63 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8053 (mt-10) REVERT: G 59 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8737 (mm-30) REVERT: G 66 LEU cc_start: 0.9083 (mt) cc_final: 0.8766 (pp) REVERT: G 100 ILE cc_start: 0.8775 (mp) cc_final: 0.8547 (mp) REVERT: H 109 HIS cc_start: 0.8795 (m90) cc_final: 0.8496 (m170) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.0927 time to fit residues: 22.2038 Evaluate side-chains 135 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 87 optimal weight: 30.0000 chunk 14 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 chunk 42 optimal weight: 0.6980 chunk 80 optimal weight: 40.0000 chunk 25 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN D 109 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.048282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.037398 restraints weight = 80733.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.038515 restraints weight = 43423.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.039303 restraints weight = 29459.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.039787 restraints weight = 22564.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.040082 restraints weight = 19120.165| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11186 Z= 0.161 Angle : 0.755 8.636 16173 Z= 0.423 Chirality : 0.050 0.319 1850 Planarity : 0.006 0.054 1178 Dihedral : 34.389 179.774 3476 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.85 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.32), residues: 666 helix: 0.86 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -2.44 (0.41), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 31 TYR 0.038 0.002 TYR F 72 PHE 0.014 0.002 PHE E 104 HIS 0.008 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.16 (11186) covalent geometry : angle 0.75455 / 0.42 (16173) hydrogen bonds : bond 0.06028 / 4.25 ( 698) hydrogen bonds : angle 3.80721 / 2.70 ( 1753) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8531 (mmp-170) cc_final: 0.8032 (mmp80) REVERT: A 100 LEU cc_start: 0.8981 (tp) cc_final: 0.8737 (tp) REVERT: A 126 LEU cc_start: 0.9563 (tp) cc_final: 0.9350 (tp) REVERT: B 27 GLN cc_start: 0.8534 (tp-100) cc_final: 0.8080 (tp-100) REVERT: C 35 HIS cc_start: 0.9147 (m90) cc_final: 0.8716 (m-70) REVERT: C 45 ARG cc_start: 0.8221 (mtm-85) cc_final: 0.7994 (ttm-80) REVERT: C 59 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8742 (mm-30) REVERT: C 100 ILE cc_start: 0.8906 (mp) cc_final: 0.8670 (mp) REVERT: D 102 LEU cc_start: 0.8192 (tp) cc_final: 0.7851 (tp) REVERT: E 72 ARG cc_start: 0.9168 (tpp80) cc_final: 0.8923 (mmt-90) REVERT: E 83 ARG cc_start: 0.9067 (mpp80) cc_final: 0.8685 (mtt180) REVERT: E 123 ASP cc_start: 0.8367 (m-30) cc_final: 0.8150 (m-30) REVERT: E 128 ARG cc_start: 0.9456 (mmm-85) cc_final: 0.9076 (mmm-85) REVERT: F 27 GLN cc_start: 0.9223 (mm-40) cc_final: 0.8910 (mp10) REVERT: F 58 LEU cc_start: 0.9314 (tp) cc_final: 0.8918 (pp) REVERT: F 63 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8078 (mt-10) REVERT: G 35 HIS cc_start: 0.8917 (m90) cc_final: 0.8700 (m170) REVERT: G 59 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8737 (mm-30) REVERT: G 66 LEU cc_start: 0.9032 (mt) cc_final: 0.8730 (pp) REVERT: G 100 ILE cc_start: 0.8736 (mp) cc_final: 0.8526 (mp) REVERT: H 109 HIS cc_start: 0.8796 (m90) cc_final: 0.8445 (m170) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1051 time to fit residues: 26.3870 Evaluate side-chains 139 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 53 optimal weight: 9.9990 chunk 70 optimal weight: 30.0000 chunk 4 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 85 optimal weight: 20.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 109 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.048344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.037211 restraints weight = 83591.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.038394 restraints weight = 45415.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.039101 restraints weight = 30545.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.039674 restraints weight = 24197.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.040023 restraints weight = 20208.918| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11186 Z= 0.158 Angle : 0.750 8.585 16173 Z= 0.422 Chirality : 0.050 0.317 1850 Planarity : 0.006 0.055 1178 Dihedral : 34.328 179.078 3476 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.85 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 0.07 (0.32), residues: 666 helix: 0.86 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -2.39 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 83 TYR 0.027 0.002 TYR D 83 PHE 0.012 0.002 PHE E 104 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.16 (11186) covalent geometry : angle 0.75026 / 0.42 (16173) hydrogen bonds : bond 0.06073 / 4.29 ( 698) hydrogen bonds : angle 3.86155 / 2.72 ( 1753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1505.34 seconds wall clock time: 26 minutes 49.78 seconds (1609.78 seconds total)