Starting phenix.real_space_refine on Thu Oct 22 23:48:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25qk_80301/10_2026/25qk_80301_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/25qk_80301/10_2026/25qk_80301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25qk_80301/10_2026/25qk_80301_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25qk_80301/10_2026/25qk_80301_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25qk_80301/10_2026/25qk_80301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25qk_80301/10_2026/25qk_80301.map" } resolution = 3.04 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= 0.021 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 97 5.49 5 Mg 2 5.21 5 S 30 5.16 5 C 3917 2.51 5 N 1265 2.21 5 O 1492 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-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6803 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2412 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 12, 'TRANS': 289} Chain breaks: 1 Chain: "B" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2366 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 12, 'TRANS': 283} Chain breaks: 1 Chain: "C" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 773 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 12, 'rna3p_pyr': 10} Link IDs: {'rna2p': 13, 'rna3p': 22} Chain: "D" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 390 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "E" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 221 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "F" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 374 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "G" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 265 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.48, per 1000 atoms: 0.22 Number of scatterers: 6803 At special positions: 0 Unit cell: (88.576, 72.66, 98.956, 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 30 16.00 P 97 15.00 Mg 2 11.99 O 1492 8.00 N 1265 7.00 C 3917 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: 0.57 Conformation dependent library (CDL) restraints added in 292.4 milliseconds 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1118 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 4 sheets defined 63.0% alpha, 4.7% beta 29 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 50 through 58 Processing helix chain 'A' and resid 65 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 176 removed outlier: 3.987A pdb=" N LEU A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 4.082A 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 210 Processing helix chain 'A' and resid 216 through 231 removed outlier: 4.019A pdb=" N VAL A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 227 " --> pdb=" O GLN A 223 " (cutoff:3.500A) removed outlier: 3.741A 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: 3.610A pdb=" N ARG A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 9 Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' 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 removed outlier: 3.544A pdb=" N HIS B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.519A pdb=" N GLN B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) removed outlier: 3.584A 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 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 230 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 281 removed outlier: 3.753A pdb=" N ARG B 257 " --> pdb=" O LYS B 253 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 234 through 238 Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AA4, first strand: chain 'B' and resid 234 through 238 282 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 0.72 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: 1723 1.33 - 1.45: 1773 1.45 - 1.57: 3396 1.57 - 1.70: 189 1.70 - 1.82: 54 Bond restraints: 7135 Sorted by residual: bond pdb=" C3' DC F 12 " pdb=" O3' DC F 12 " ideal model delta sigma weight residual 1.435 1.471 -0.036 1.30e-02 5.92e+03 7.87e+00 bond pdb=" C1' DT D 13 " pdb=" N1 DT D 13 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 6.84e+00 bond pdb=" C3' DA D 5 " pdb=" C2' DA D 5 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.77e+00 bond pdb=" C3' DT G 29 " pdb=" C2' DT G 29 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.54e+00 bond pdb=" C1' DT D 4 " pdb=" N1 DT D 4 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.45e+00 ... (remaining 7130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 9641 1.91 - 3.82: 391 3.82 - 5.73: 27 5.73 - 7.63: 6 7.63 - 9.54: 2 Bond angle restraints: 10067 Sorted by residual: angle pdb=" O4' DC G 32 " pdb=" C4' DC G 32 " pdb=" C3' DC G 32 " ideal model delta sigma weight residual 106.00 103.19 2.81 6.00e-01 2.78e+00 2.19e+01 angle pdb=" O5' C C 8 " pdb=" C5' C C 8 " pdb=" C4' C C 8 " ideal model delta sigma weight residual 109.40 113.00 -3.60 8.00e-01 1.56e+00 2.02e+01 angle pdb=" N3 DT G 29 " pdb=" C4 DT G 29 " pdb=" O4 DT G 29 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.97e+01 angle pdb=" C3' DT G 34 " pdb=" C2' DT G 34 " pdb=" C1' DT G 34 " ideal model delta sigma weight residual 102.50 97.20 5.30 1.20e+00 6.94e-01 1.95e+01 angle pdb=" O4' DT G 34 " pdb=" C1' DT G 34 " pdb=" N1 DT G 34 " ideal model delta sigma weight residual 108.00 111.09 -3.09 7.00e-01 2.04e+00 1.95e+01 ... (remaining 10062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.72: 3846 33.72 - 67.44: 305 67.44 - 101.16: 22 101.16 - 134.88: 0 134.88 - 168.60: 7 Dihedral angle restraints: 4180 sinusoidal: 2451 harmonic: 1729 Sorted by residual: dihedral pdb=" CA GLN A 37 " pdb=" C GLN A 37 " pdb=" N GLY A 38 " pdb=" CA GLY A 38 " ideal model delta harmonic sigma weight residual 180.00 155.97 24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA PHE A 36 " pdb=" C PHE A 36 " pdb=" N GLN A 37 " pdb=" CA GLN A 37 " ideal model delta harmonic sigma weight residual -180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+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 51.40 168.60 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 4177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 859 0.046 - 0.093: 168 0.093 - 0.139: 66 0.139 - 0.185: 35 0.185 - 0.232: 5 Chirality restraints: 1133 Sorted by residual: chirality pdb=" C1' U C 7 " pdb=" O4' U C 7 " pdb=" C2' U C 7 " pdb=" N1 U C 7 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C3' DT G 28 " pdb=" C4' DT G 28 " pdb=" O3' DT G 28 " pdb=" C2' DT G 28 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C3' DG G 30 " pdb=" C4' DG G 30 " pdb=" O3' DG G 30 " pdb=" C2' DG G 30 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.20 2.00e-01 2.50e+01 9.53e-01 ... (remaining 1130 not shown) Planarity restraints: 950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C C 8 " -0.027 2.00e-02 2.50e+03 1.44e-02 4.65e+00 pdb=" N1 C C 8 " 0.032 2.00e-02 2.50e+03 pdb=" C2 C C 8 " 0.003 2.00e-02 2.50e+03 pdb=" O2 C C 8 " 0.002 2.00e-02 2.50e+03 pdb=" N3 C C 8 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C C 8 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C C 8 " -0.006 2.00e-02 2.50e+03 pdb=" C5 C C 8 " -0.002 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 " 0.026 2.00e-02 2.50e+03 1.41e-02 4.50e+00 pdb=" N1 U C 7 " -0.032 2.00e-02 2.50e+03 pdb=" C2 U C 7 " -0.000 2.00e-02 2.50e+03 pdb=" O2 U C 7 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U C 7 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U C 7 " 0.004 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 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 2 " 0.026 2.00e-02 2.50e+03 1.18e-02 4.19e+00 pdb=" N9 G C 2 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G C 2 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G C 2 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G C 2 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G C 2 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G C 2 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G C 2 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G C 2 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G C 2 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G C 2 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G C 2 " 0.001 2.00e-02 2.50e+03 ... (remaining 947 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 32 2.46 - 3.07: 4718 3.07 - 3.68: 11862 3.68 - 4.29: 17349 4.29 - 4.90: 26236 Nonbonded interactions: 60197 Sorted by model distance: nonbonded pdb=" O3' DT D 22 " pdb="MG MG B 401 " model vdw 1.853 2.170 nonbonded pdb=" OD1 ASP B 30 " pdb="MG MG B 401 " model vdw 1.905 2.170 nonbonded pdb=" OP1 DC E 23 " pdb="MG MG B 401 " model vdw 1.912 2.170 nonbonded pdb=" OD1 ASP A 30 " pdb="MG MG A 401 " model vdw 1.984 2.170 nonbonded pdb=" O3' DA F 22 " pdb="MG MG A 401 " model vdw 2.029 2.170 ... (remaining 60192 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' and (resid 1 through 287 or resid 301 through 401)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.830 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7135 Z= 0.366 Angle : 0.796 9.542 10067 Z= 0.622 Chirality : 0.053 0.232 1133 Planarity : 0.005 0.068 950 Dihedral : 20.977 168.595 3062 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % 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: 1.42 (0.33), residues: 590 helix: 1.58 (0.25), residues: 350 sheet: -1.46 (0.70), residues: 44 loop : 0.56 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 31 TYR 0.011 0.001 TYR B 41 PHE 0.009 0.002 PHE A 36 TRP 0.011 0.001 TRP B 307 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.37 ( 7135) covalent geometry : angle 0.79628 / 0.62 (10067) hydrogen bonds : bond 0.12604 / 8.08 ( 355) hydrogen bonds : angle 5.05131 / 3.50 ( 962) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 170 SER cc_start: 0.8938 (p) cc_final: 0.8523 (m) REVERT: A 173 TRP cc_start: 0.8835 (m-10) cc_final: 0.8346 (m-90) REVERT: A 205 MET cc_start: 0.8969 (tmm) cc_final: 0.8515 (tmm) REVERT: A 243 GLN cc_start: 0.8822 (mt0) cc_final: 0.8595 (pt0) REVERT: A 273 TYR cc_start: 0.9247 (t80) cc_final: 0.9046 (t80) REVERT: B 1 MET cc_start: 0.8051 (tmm) cc_final: 0.7658 (tmm) REVERT: B 88 MET cc_start: 0.9053 (mpp) cc_final: 0.8405 (mpp) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0610 time to fit residues: 5.3829 Evaluate side-chains 46 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 27] chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.064211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.051300 restraints weight = 31199.601| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.56 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7135 Z= 0.179 Angle : 0.718 10.086 10067 Z= 0.405 Chirality : 0.048 0.397 1133 Planarity : 0.004 0.032 950 Dihedral : 23.482 175.430 1858 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.99 % Allowed : 6.56 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.33), residues: 590 helix: 2.06 (0.25), residues: 351 sheet: -1.38 (0.91), residues: 20 loop : 0.46 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 103 TYR 0.027 0.003 TYR B 95 PHE 0.019 0.003 PHE A 269 TRP 0.028 0.002 TRP A 307 HIS 0.006 0.001 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.18 ( 7135) covalent geometry : angle 0.71751 / 0.41 (10067) hydrogen bonds : bond 0.05825 / 3.75 ( 355) hydrogen bonds : angle 4.09484 / 2.84 ( 962) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 12 HIS cc_start: 0.8794 (m170) cc_final: 0.8564 (m-70) REVERT: A 170 SER cc_start: 0.8818 (p) cc_final: 0.8099 (m) REVERT: A 173 TRP cc_start: 0.8686 (m-10) cc_final: 0.8132 (m-90) REVERT: A 205 MET cc_start: 0.9246 (tmm) cc_final: 0.9036 (tmm) REVERT: A 243 GLN cc_start: 0.9007 (mt0) cc_final: 0.8771 (pt0) REVERT: B 1 MET cc_start: 0.7820 (tmm) cc_final: 0.7614 (tmm) REVERT: B 88 MET cc_start: 0.8943 (mpp) cc_final: 0.8425 (mpp) REVERT: B 195 ASN cc_start: 0.7836 (m110) cc_final: 0.7461 (m-40) outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 0.0593 time to fit residues: 4.9695 Evaluate side-chains 51 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain B residue 176 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [37, 59, 46, 61, 8, 39, 26, 53, 45, 56, 18] chunk 37 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.063896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.050858 restraints weight = 31141.628| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.71 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7135 Z= 0.187 Angle : 0.666 6.786 10067 Z= 0.380 Chirality : 0.045 0.270 1133 Planarity : 0.004 0.030 950 Dihedral : 23.514 176.626 1858 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.59 % Allowed : 7.16 % Favored : 91.25 % 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: 2.19 (0.34), residues: 590 helix: 2.20 (0.26), residues: 357 sheet: -1.46 (0.85), residues: 20 loop : 0.57 (0.45), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 57 TYR 0.031 0.003 TYR A 175 PHE 0.019 0.002 PHE B 269 TRP 0.032 0.002 TRP A 307 HIS 0.006 0.001 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.19 ( 7135) covalent geometry : angle 0.66587 / 0.38 (10067) hydrogen bonds : bond 0.05326 / 3.47 ( 355) hydrogen bonds : angle 3.96922 / 2.75 ( 962) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 12 HIS cc_start: 0.8719 (m170) cc_final: 0.8485 (m-70) REVERT: A 243 GLN cc_start: 0.9049 (mt0) cc_final: 0.8809 (pt0) REVERT: B 1 MET cc_start: 0.7795 (tmm) cc_final: 0.7544 (tmm) REVERT: B 88 MET cc_start: 0.9024 (mpp) cc_final: 0.8498 (mpp) REVERT: B 125 ASP cc_start: 0.8900 (m-30) cc_final: 0.8585 (m-30) REVERT: B 195 ASN cc_start: 0.8006 (m110) cc_final: 0.7761 (m-40) outliers start: 8 outliers final: 4 residues processed: 56 average time/residue: 0.0628 time to fit residues: 5.4044 Evaluate side-chains 49 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [14, 39, 58, 45, 18, 23, 21, 32, 33, 37, 38] chunk 14 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN A 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.063409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.050505 restraints weight = 31350.064| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.64 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7135 Z= 0.194 Angle : 0.658 6.840 10067 Z= 0.374 Chirality : 0.045 0.267 1133 Planarity : 0.004 0.030 950 Dihedral : 23.552 176.931 1858 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.19 % Allowed : 9.15 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.34), residues: 590 helix: 2.16 (0.25), residues: 359 sheet: -1.53 (0.81), residues: 20 loop : 0.68 (0.46), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 31 TYR 0.032 0.003 TYR A 95 PHE 0.014 0.002 PHE B 269 TRP 0.022 0.002 TRP A 307 HIS 0.005 0.001 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.19 ( 7135) covalent geometry : angle 0.65817 / 0.37 (10067) hydrogen bonds : bond 0.05019 / 3.26 ( 355) hydrogen bonds : angle 3.91022 / 2.71 ( 962) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 12 HIS cc_start: 0.8724 (m170) cc_final: 0.8482 (m-70) REVERT: A 95 TYR cc_start: 0.9130 (m-80) cc_final: 0.8920 (m-80) REVERT: B 1 MET cc_start: 0.7847 (tmm) cc_final: 0.7617 (tmm) REVERT: B 88 MET cc_start: 0.9055 (mpp) cc_final: 0.8451 (mpp) REVERT: B 125 ASP cc_start: 0.8909 (m-30) cc_final: 0.8660 (m-30) outliers start: 11 outliers final: 8 residues processed: 55 average time/residue: 0.0586 time to fit residues: 5.0691 Evaluate side-chains 52 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 240 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [8, 15, 39, 17, 25, 37, 20, 5, 32, 16, 57] chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.0070 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN A 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.064922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.051787 restraints weight = 30986.723| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.82 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7135 Z= 0.138 Angle : 0.624 11.530 10067 Z= 0.352 Chirality : 0.043 0.272 1133 Planarity : 0.004 0.031 950 Dihedral : 23.550 178.333 1858 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.99 % Allowed : 9.15 % Favored : 88.87 % 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: 2.38 (0.34), residues: 590 helix: 2.29 (0.25), residues: 359 sheet: -1.91 (0.65), residues: 32 loop : 1.03 (0.49), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 31 TYR 0.034 0.003 TYR A 175 PHE 0.019 0.002 PHE A 269 TRP 0.021 0.002 TRP B 307 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 ( 7135) covalent geometry : angle 0.62363 / 0.35 (10067) hydrogen bonds : bond 0.04364 / 2.86 ( 355) hydrogen bonds : angle 3.70434 / 2.55 ( 962) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 12 HIS cc_start: 0.8739 (m170) cc_final: 0.8504 (m-70) REVERT: A 243 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8350 (mp10) REVERT: B 1 MET cc_start: 0.7770 (tmm) cc_final: 0.7467 (tmm) REVERT: B 88 MET cc_start: 0.8953 (mpp) cc_final: 0.8441 (mpp) REVERT: B 125 ASP cc_start: 0.8813 (m-30) cc_final: 0.8506 (m-30) outliers start: 10 outliers final: 6 residues processed: 55 average time/residue: 0.0535 time to fit residues: 4.5903 Evaluate side-chains 51 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 240 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [48, 60, 22, 33, 12, 10, 20, 8, 9, 7, 1] chunk 48 optimal weight: 0.4980 chunk 60 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN A 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.064761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.051804 restraints weight = 31343.942| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.67 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7135 Z= 0.152 Angle : 0.633 9.543 10067 Z= 0.354 Chirality : 0.043 0.266 1133 Planarity : 0.004 0.027 950 Dihedral : 23.540 179.183 1858 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.99 % Allowed : 9.74 % Favored : 88.27 % 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: 2.53 (0.34), residues: 590 helix: 2.42 (0.26), residues: 357 sheet: -1.76 (0.62), residues: 32 loop : 1.07 (0.48), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 31 TYR 0.031 0.002 TYR A 175 PHE 0.017 0.002 PHE A 269 TRP 0.021 0.001 TRP B 307 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 ( 7135) covalent geometry : angle 0.63315 / 0.35 (10067) hydrogen bonds : bond 0.04424 / 2.89 ( 355) hydrogen bonds : angle 3.72480 / 2.58 ( 962) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 HIS cc_start: 0.8734 (m170) cc_final: 0.8493 (m-70) REVERT: A 243 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8490 (mp10) REVERT: A 247 CYS cc_start: 0.8906 (m) cc_final: 0.8344 (t) REVERT: B 1 MET cc_start: 0.7878 (tmm) cc_final: 0.7522 (tmm) REVERT: B 88 MET cc_start: 0.8983 (mpp) cc_final: 0.8453 (mpp) REVERT: B 125 ASP cc_start: 0.8829 (m-30) cc_final: 0.8580 (m-30) outliers start: 10 outliers final: 8 residues processed: 53 average time/residue: 0.0569 time to fit residues: 4.7756 Evaluate side-chains 54 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 240 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [50, 47, 32, 17, 9, 42, 62, 36, 51, 30, 6] chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 62 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 6 optimal weight: 0.0000 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN A 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.065793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.052988 restraints weight = 30530.392| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.74 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7135 Z= 0.130 Angle : 0.616 9.991 10067 Z= 0.344 Chirality : 0.042 0.271 1133 Planarity : 0.003 0.026 950 Dihedral : 23.537 179.431 1858 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.79 % Allowed : 9.94 % Favored : 88.27 % 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: 2.61 (0.34), residues: 590 helix: 2.47 (0.26), residues: 357 sheet: -1.23 (0.65), residues: 30 loop : 1.00 (0.48), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 57 TYR 0.027 0.002 TYR A 175 PHE 0.018 0.002 PHE A 269 TRP 0.023 0.001 TRP B 307 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.13 ( 7135) covalent geometry : angle 0.61564 / 0.34 (10067) hydrogen bonds : bond 0.04122 / 2.71 ( 355) hydrogen bonds : angle 3.63118 / 2.51 ( 962) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 HIS cc_start: 0.8746 (m170) cc_final: 0.8505 (m-70) REVERT: A 243 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8608 (mp10) REVERT: A 247 CYS cc_start: 0.8848 (m) cc_final: 0.8231 (t) REVERT: B 1 MET cc_start: 0.7804 (tmm) cc_final: 0.7460 (tmm) REVERT: B 88 MET cc_start: 0.8901 (mpp) cc_final: 0.8482 (mpp) REVERT: B 125 ASP cc_start: 0.8780 (m-30) cc_final: 0.8532 (m-30) REVERT: B 209 MET cc_start: 0.8941 (mtp) cc_final: 0.8643 (mtp) outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 0.0524 time to fit residues: 4.4084 Evaluate side-chains 56 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 240 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [30, 25, 28, 62, 61, 50, 63, 41, 38, 54, 45] chunk 30 optimal weight: 30.0000 chunk 25 optimal weight: 0.0270 chunk 28 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN A 243 GLN B 89 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.065945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.053289 restraints weight = 30878.163| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.64 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7135 Z= 0.135 Angle : 0.612 11.011 10067 Z= 0.344 Chirality : 0.042 0.268 1133 Planarity : 0.003 0.025 950 Dihedral : 23.545 179.740 1858 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.99 % Allowed : 10.34 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.34), residues: 590 helix: 2.42 (0.26), residues: 359 sheet: -1.10 (0.68), residues: 30 loop : 1.02 (0.48), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 31 TYR 0.025 0.002 TYR A 175 PHE 0.021 0.002 PHE A 269 TRP 0.016 0.001 TRP B 307 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 ( 7135) covalent geometry : angle 0.61226 / 0.34 (10067) hydrogen bonds : bond 0.04123 / 2.71 ( 355) hydrogen bonds : angle 3.64857 / 2.51 ( 962) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 HIS cc_start: 0.8733 (m170) cc_final: 0.8489 (m-70) REVERT: A 243 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8639 (mp10) REVERT: A 247 CYS cc_start: 0.8830 (m) cc_final: 0.8203 (t) REVERT: B 1 MET cc_start: 0.7837 (tmm) cc_final: 0.7476 (tmm) REVERT: B 88 MET cc_start: 0.8932 (mpp) cc_final: 0.8460 (mpp) REVERT: B 95 TYR cc_start: 0.9186 (m-80) cc_final: 0.8939 (m-80) REVERT: B 125 ASP cc_start: 0.8801 (m-30) cc_final: 0.8532 (m-30) REVERT: B 209 MET cc_start: 0.8968 (mtp) cc_final: 0.8662 (mtp) outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 0.0550 time to fit residues: 4.6818 Evaluate side-chains 55 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 240 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [23, 60, 5, 27, 40, 26, 19, 49, 25, 24, 43] chunk 23 optimal weight: 0.5980 chunk 60 optimal weight: 20.0000 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.065107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.052180 restraints weight = 30702.803| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.80 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7135 Z= 0.158 Angle : 0.622 11.605 10067 Z= 0.348 Chirality : 0.042 0.265 1133 Planarity : 0.003 0.025 950 Dihedral : 23.587 179.580 1858 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.99 % Allowed : 10.74 % Favored : 87.28 % 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: 2.66 (0.34), residues: 590 helix: 2.58 (0.26), residues: 352 sheet: -1.18 (0.68), residues: 30 loop : 0.92 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 57 TYR 0.023 0.001 TYR A 175 PHE 0.050 0.003 PHE A 269 TRP 0.017 0.001 TRP B 307 HIS 0.003 0.001 HIS B 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 ( 7135) covalent geometry : angle 0.62180 / 0.35 (10067) hydrogen bonds : bond 0.04232 / 2.78 ( 355) hydrogen bonds : angle 3.70910 / 2.56 ( 962) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 HIS cc_start: 0.8720 (m170) cc_final: 0.8485 (m-70) REVERT: A 247 CYS cc_start: 0.8862 (m) cc_final: 0.8213 (t) REVERT: B 1 MET cc_start: 0.7721 (tmm) cc_final: 0.7435 (tmm) REVERT: B 88 MET cc_start: 0.8958 (mpp) cc_final: 0.8436 (mpp) REVERT: B 95 TYR cc_start: 0.9232 (m-80) cc_final: 0.9000 (m-80) REVERT: B 208 SER cc_start: 0.9347 (OUTLIER) cc_final: 0.9074 (p) REVERT: B 209 MET cc_start: 0.8948 (mtp) cc_final: 0.8586 (mtp) outliers start: 10 outliers final: 9 residues processed: 54 average time/residue: 0.0542 time to fit residues: 4.5817 Evaluate side-chains 57 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 240 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [33, 11, 39, 64, 5, 50, 10, 26, 41, 23, 42] chunk 33 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 64 optimal weight: 30.0000 chunk 5 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.066434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.053793 restraints weight = 30661.627| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.63 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7135 Z= 0.134 Angle : 0.612 12.282 10067 Z= 0.342 Chirality : 0.041 0.269 1133 Planarity : 0.003 0.025 950 Dihedral : 23.632 179.831 1858 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.59 % Allowed : 11.33 % Favored : 87.08 % 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: 2.64 (0.34), residues: 590 helix: 2.52 (0.26), residues: 352 sheet: -0.92 (0.71), residues: 30 loop : 0.94 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 57 TYR 0.023 0.001 TYR A 175 PHE 0.009 0.002 PHE B 269 TRP 0.015 0.001 TRP B 307 HIS 0.003 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.13 ( 7135) covalent geometry : angle 0.61177 / 0.34 (10067) hydrogen bonds : bond 0.04082 / 2.71 ( 355) hydrogen bonds : angle 3.66915 / 2.53 ( 962) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 HIS cc_start: 0.8767 (m170) cc_final: 0.8525 (m-70) REVERT: A 247 CYS cc_start: 0.8759 (m) cc_final: 0.8142 (t) REVERT: B 1 MET cc_start: 0.7886 (tmm) cc_final: 0.7548 (tmm) REVERT: B 88 MET cc_start: 0.8903 (mpp) cc_final: 0.8438 (mpp) REVERT: B 95 TYR cc_start: 0.9211 (m-80) cc_final: 0.8994 (m-80) REVERT: B 208 SER cc_start: 0.9321 (OUTLIER) cc_final: 0.9054 (p) REVERT: B 209 MET cc_start: 0.8967 (mtp) cc_final: 0.8626 (mtp) outliers start: 8 outliers final: 7 residues processed: 53 average time/residue: 0.0537 time to fit residues: 4.4495 Evaluate side-chains 54 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 240 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [53, 13, 65, 59, 22, 64, 21, 18, 34, 32, 49] chunk 53 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 30.0000 chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN B 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.065301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.052629 restraints weight = 30554.733| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.55 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7135 Z= 0.157 Angle : 0.624 12.327 10067 Z= 0.346 Chirality : 0.042 0.263 1133 Planarity : 0.003 0.026 950 Dihedral : 23.664 179.627 1858 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.39 % Allowed : 11.33 % Favored : 87.28 % 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: 2.63 (0.34), residues: 590 helix: 2.54 (0.26), residues: 352 sheet: -1.04 (0.72), residues: 30 loop : 0.92 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 57 TYR 0.021 0.002 TYR A 289 PHE 0.011 0.002 PHE A 269 TRP 0.034 0.002 TRP B 307 HIS 0.003 0.001 HIS B 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 ( 7135) covalent geometry : angle 0.62432 / 0.35 (10067) hydrogen bonds : bond 0.04292 / 2.83 ( 355) hydrogen bonds : angle 3.69150 / 2.55 ( 962) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1388.21 seconds wall clock time: 24 minutes 38.48 seconds (1478.48 seconds total)