Starting phenix.real_space_refine on Thu Oct 22 22:08:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u9k_63967/10_2026/9u9k_63967.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u9k_63967/10_2026/9u9k_63967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u9k_63967/10_2026/9u9k_63967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u9k_63967/10_2026/9u9k_63967.map" model { file = "/net/cci-nas-00/data/ceres_data/9u9k_63967/10_2026/9u9k_63967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u9k_63967/10_2026/9u9k_63967.cif" } resolution = 2.96 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= 0.111 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 38 5.49 5 S 24 5.16 5 C 3830 2.51 5 N 1057 2.21 5 O 1256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 6205 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1924 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "B" Number of atoms: 2157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2157 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "C" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 282 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "D" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1035 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain: "E" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 396 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "F" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 384 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Time building chain proxies: 1.46, per 1000 atoms: 0.24 Number of scatterers: 6205 At special positions: 0 Unit cell: (79.7202, 84.0294, 117.426, 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 24 16.00 P 38 15.00 O 1256 8.00 N 1057 7.00 C 3830 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 305.1 milliseconds 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1250 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 2 sheets defined 37.0% alpha, 10.9% beta 17 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 135 through 167 Processing helix chain 'A' and resid 187 through 200 removed outlier: 3.895A pdb=" N LEU A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 238 removed outlier: 3.924A pdb=" N MET A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 257 through 268 Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'B' and resid 54 through 58 removed outlier: 3.736A pdb=" N SER B 57 " --> pdb=" O LYS B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'B' and resid 201 through 208 removed outlier: 3.728A pdb=" N CYS B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 Processing helix chain 'C' and resid 162 through 185 Processing helix chain 'D' and resid 13 through 26 removed outlier: 3.641A pdb=" N TYR D 17 " --> pdb=" O ASP D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 65 removed outlier: 3.906A pdb=" N GLU D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 76 Processing helix chain 'D' and resid 83 through 96 removed outlier: 3.872A pdb=" N MET D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 removed outlier: 3.770A pdb=" N TYR D 104 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 128 Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 180 removed outlier: 6.426A pdb=" N TYR A 351 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE A 368 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU A 353 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE A 206 " --> pdb=" O PHE A 250 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N TRP A 252 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N MET A 208 " --> pdb=" O TRP A 252 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 305 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 301 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 306 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU A 272 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ILE A 324 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR A 277 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N SER A 326 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL A 279 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 71 through 73 removed outlier: 5.984A pdb=" N LYS B 72 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ALA B 93 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU B 305 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE B 95 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TRP B 132 " --> pdb=" O ILE B 96 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU B 236 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASN B 155 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N MET B 238 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N PHE B 259 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N MET B 157 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ASP B 261 " --> pdb=" O MET B 157 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASN B 159 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE B 263 " --> pdb=" O ASN B 159 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU B 161 " --> pdb=" O PHE B 263 " (cutoff:3.500A) 186 hydrogen bonds defined for protein. 546 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 0.61 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: 1613 1.33 - 1.45: 1400 1.45 - 1.58: 3271 1.58 - 1.70: 75 1.70 - 1.82: 42 Bond restraints: 6401 Sorted by residual: bond pdb=" P 6MA F 13 " pdb=" O5' 6MA F 13 " ideal model delta sigma weight residual 1.724 1.613 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C1' DT F 14 " pdb=" N1 DT F 14 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.46e+01 bond pdb=" C GLN B 312 " pdb=" N PRO B 313 " ideal model delta sigma weight residual 1.332 1.371 -0.039 1.12e-02 7.97e+03 1.23e+01 bond pdb=" C3' DA F 11 " pdb=" C2' DA F 11 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DT F 14 " pdb=" C2' DT F 14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 ... (remaining 6396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.48: 8722 4.48 - 8.96: 39 8.96 - 13.45: 6 13.45 - 17.93: 1 17.93 - 22.41: 2 Bond angle restraints: 8770 Sorted by residual: angle pdb=" O3' DC F 12 " pdb=" P 6MA F 13 " pdb=" OP2 6MA F 13 " ideal model delta sigma weight residual 108.00 85.59 22.41 3.00e+00 1.11e-01 5.58e+01 angle pdb=" O3' DC F 12 " pdb=" P 6MA F 13 " pdb=" OP1 6MA F 13 " ideal model delta sigma weight residual 108.00 85.86 22.14 3.00e+00 1.11e-01 5.45e+01 angle pdb=" CA GLU B 85 " pdb=" CB GLU B 85 " pdb=" CG GLU B 85 " ideal model delta sigma weight residual 114.10 126.93 -12.83 2.00e+00 2.50e-01 4.11e+01 angle pdb=" CA LEU C 170 " pdb=" CB LEU C 170 " pdb=" CG LEU C 170 " ideal model delta sigma weight residual 116.30 133.63 -17.33 3.50e+00 8.16e-02 2.45e+01 angle pdb=" N TYR B 292 " pdb=" CA TYR B 292 " pdb=" C TYR B 292 " ideal model delta sigma weight residual 107.99 116.54 -8.55 1.76e+00 3.23e-01 2.36e+01 ... (remaining 8765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 3499 35.64 - 71.28: 332 71.28 - 106.93: 14 106.93 - 142.57: 0 142.57 - 178.21: 2 Dihedral angle restraints: 3847 sinusoidal: 1918 harmonic: 1929 Sorted by residual: dihedral pdb=" C4' DA E 5 " pdb=" C3' DA E 5 " pdb=" O3' DA E 5 " pdb=" P DA E 6 " ideal model delta sinusoidal sigma weight residual -140.00 38.21 -178.21 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT E 3 " pdb=" C3' DT E 3 " pdb=" O3' DT E 3 " pdb=" P DT E 4 " ideal model delta sinusoidal sigma weight residual 220.00 73.98 146.02 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" CA LEU A 361 " pdb=" C LEU A 361 " pdb=" N HIS A 362 " pdb=" CA HIS A 362 " ideal model delta harmonic sigma weight residual -180.00 -162.98 -17.02 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 3844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 831 0.081 - 0.162: 101 0.162 - 0.243: 6 0.243 - 0.324: 0 0.324 - 0.405: 2 Chirality restraints: 940 Sorted by residual: chirality pdb=" CG LEU C 170 " pdb=" CB LEU C 170 " pdb=" CD1 LEU C 170 " pdb=" CD2 LEU C 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CB ILE B 74 " pdb=" CA ILE B 74 " pdb=" CG1 ILE B 74 " pdb=" CG2 ILE B 74 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" C3' 6MA F 13 " pdb=" C4' 6MA F 13 " pdb=" O3' 6MA F 13 " pdb=" C2' 6MA F 13 " both_signs ideal model delta sigma weight residual False -2.54 -2.77 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 937 not shown) Planarity restraints: 994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 328 " 0.172 9.50e-02 1.11e+02 7.69e-02 3.64e+00 pdb=" NE ARG A 328 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 328 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 328 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 328 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 13 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" CG ASP D 13 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASP D 13 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP D 13 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 241 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.01e+00 pdb=" C LYS B 241 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS B 241 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE B 242 " 0.010 2.00e-02 2.50e+03 ... (remaining 991 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 893 2.76 - 3.29: 5604 3.29 - 3.83: 10797 3.83 - 4.36: 12816 4.36 - 4.90: 20857 Nonbonded interactions: 50967 Sorted by model distance: nonbonded pdb=" OG SER A 176 " pdb=" O HIS A 362 " model vdw 2.221 3.040 nonbonded pdb=" OG SER D 109 " pdb=" OE1 GLU D 111 " model vdw 2.222 3.040 nonbonded pdb=" OD1 ASN A 350 " pdb=" OH TYR D 17 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR B 152 " pdb=" OD1 ASN B 155 " model vdw 2.234 3.040 nonbonded pdb=" NE2 HIS A 198 " pdb=" OD2 ASP D 24 " model vdw 2.243 3.120 ... (remaining 50962 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.620 Find NCS groups from input model: 0.030 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:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 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 : 0.006 0.111 6403 Z= 0.371 Angle : 0.988 22.409 8770 Z= 0.586 Chirality : 0.055 0.405 940 Planarity : 0.005 0.077 994 Dihedral : 23.259 178.211 2597 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.24 % Favored : 90.60 % Rotamer: Outliers : 4.03 % Allowed : 38.82 % Favored : 57.14 % 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: -2.27 (0.30), residues: 649 helix: -0.24 (0.34), residues: 226 sheet: -2.07 (0.49), residues: 103 loop : -2.26 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 221 TYR 0.014 0.002 TYR D 41 PHE 0.018 0.002 PHE B 242 TRP 0.010 0.002 TRP A 212 HIS 0.008 0.002 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.37 ( 6401) covalent geometry : angle 0.98784 / 0.59 ( 8770) hydrogen bonds : bond 0.13664 / 9.54 ( 224) hydrogen bonds : angle 6.10208 / 4.31 ( 622) Misc. bond : bond 0.00233 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.232 Fit side-chains REVERT: D 17 TYR cc_start: 0.7430 (t80) cc_final: 0.5001 (t80) REVERT: D 25 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6729 (pp) REVERT: D 125 LYS cc_start: 0.7091 (ptpt) cc_final: 0.6479 (tmmt) REVERT: D 126 LYS cc_start: 0.7481 (mttt) cc_final: 0.7142 (tppp) outliers start: 24 outliers final: 16 residues processed: 89 average time/residue: 0.5088 time to fit residues: 47.7063 Evaluate side-chains 85 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 51 THR 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: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.0970 chunk 27 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 ASN ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN D 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.216268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.178479 restraints weight = 6355.866| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 1.74 r_work: 0.4064 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3923 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6403 Z= 0.230 Angle : 0.739 9.355 8770 Z= 0.396 Chirality : 0.051 0.315 940 Planarity : 0.004 0.040 994 Dihedral : 21.976 176.705 1206 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 9.58 % Allowed : 32.94 % Favored : 57.48 % 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: -2.10 (0.31), residues: 649 helix: 0.09 (0.34), residues: 226 sheet: -2.33 (0.47), residues: 104 loop : -2.18 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 22 TYR 0.015 0.002 TYR B 306 PHE 0.016 0.002 PHE B 242 TRP 0.012 0.002 TRP A 212 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 ( 6401) covalent geometry : angle 0.73855 / 0.40 ( 8770) hydrogen bonds : bond 0.05200 / 3.53 ( 224) hydrogen bonds : angle 5.04392 / 3.57 ( 622) Misc. bond : bond 0.00117 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 71 time to evaluate : 0.222 Fit side-chains REVERT: A 171 MET cc_start: 0.5583 (OUTLIER) cc_final: 0.4774 (mpm) REVERT: A 197 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7030 (ptm160) REVERT: B 238 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.5649 (mtp) REVERT: B 253 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7569 (tt0) REVERT: B 258 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7629 (tp) REVERT: C 174 LYS cc_start: 0.7236 (ttmt) cc_final: 0.6935 (tttm) REVERT: D 25 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6338 (pp) REVERT: D 117 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7468 (tppt) REVERT: D 125 LYS cc_start: 0.6957 (ptpt) cc_final: 0.6379 (tmmt) REVERT: D 126 LYS cc_start: 0.7446 (mttt) cc_final: 0.7124 (tppp) outliers start: 57 outliers final: 19 residues processed: 114 average time/residue: 0.4730 time to fit residues: 56.9590 Evaluate side-chains 92 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 117 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [61, 30, 54, 31, 27, 12, 42, 22, 37, 13, 57] chunk 61 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 57 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN D 113 GLN D 133 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.219592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.185214 restraints weight = 6303.848| |-----------------------------------------------------------------------------| r_work (start): 0.4306 rms_B_bonded: 1.50 r_work: 0.4121 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3987 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6403 Z= 0.154 Angle : 0.667 12.385 8770 Z= 0.359 Chirality : 0.047 0.382 940 Planarity : 0.004 0.042 994 Dihedral : 21.925 178.233 1189 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 8.74 % Allowed : 33.61 % Favored : 57.65 % 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: -1.91 (0.31), residues: 649 helix: 0.33 (0.35), residues: 227 sheet: -2.37 (0.46), residues: 104 loop : -2.09 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.013 0.002 TYR A 258 PHE 0.021 0.002 PHE B 228 TRP 0.007 0.001 TRP A 212 HIS 0.004 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 6401) covalent geometry : angle 0.66732 / 0.36 ( 8770) hydrogen bonds : bond 0.04164 / 2.84 ( 224) hydrogen bonds : angle 4.72086 / 3.30 ( 622) Misc. bond : bond 0.00057 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 72 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 MET cc_start: 0.5558 (OUTLIER) cc_final: 0.4734 (mpm) REVERT: A 204 ASP cc_start: 0.6823 (OUTLIER) cc_final: 0.6175 (p0) REVERT: B 235 ILE cc_start: 0.6650 (OUTLIER) cc_final: 0.6318 (tp) REVERT: B 258 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7570 (tp) REVERT: C 157 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7899 (tp30) REVERT: D 17 TYR cc_start: 0.7342 (t80) cc_final: 0.5087 (t80) REVERT: D 117 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7402 (tppt) REVERT: D 125 LYS cc_start: 0.6866 (ptpt) cc_final: 0.6351 (tmmt) REVERT: D 126 LYS cc_start: 0.7441 (mttt) cc_final: 0.7209 (tppp) outliers start: 52 outliers final: 19 residues processed: 110 average time/residue: 0.4427 time to fit residues: 51.6767 Evaluate side-chains 89 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 117 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [9, 35, 14, 38, 59, 49, 24, 48, 31, 13, 52] chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 38 optimal weight: 0.0970 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.0050 chunk 13 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 214 ASN ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.220685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.185656 restraints weight = 6333.979| |-----------------------------------------------------------------------------| r_work (start): 0.4307 rms_B_bonded: 1.55 r_work: 0.4142 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4008 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6403 Z= 0.139 Angle : 0.643 12.711 8770 Z= 0.346 Chirality : 0.046 0.314 940 Planarity : 0.004 0.050 994 Dihedral : 21.870 178.502 1187 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 9.08 % Allowed : 33.11 % Favored : 57.82 % 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: -1.83 (0.32), residues: 649 helix: 0.42 (0.35), residues: 227 sheet: -2.46 (0.49), residues: 95 loop : -2.04 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.013 0.001 TYR B 292 PHE 0.017 0.001 PHE B 228 TRP 0.005 0.001 TRP A 212 HIS 0.004 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 6401) covalent geometry : angle 0.64251 / 0.35 ( 8770) hydrogen bonds : bond 0.03823 / 2.60 ( 224) hydrogen bonds : angle 4.60173 / 3.21 ( 622) Misc. bond : bond 0.00063 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 80 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 MET cc_start: 0.5554 (OUTLIER) cc_final: 0.4681 (mpm) REVERT: A 197 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6961 (ptm160) REVERT: A 204 ASP cc_start: 0.6716 (OUTLIER) cc_final: 0.6085 (p0) REVERT: B 235 ILE cc_start: 0.6700 (OUTLIER) cc_final: 0.6383 (tp) REVERT: B 238 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.5489 (mtp) REVERT: B 258 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7426 (tp) REVERT: D 25 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6464 (pp) REVERT: D 117 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7350 (tppt) REVERT: D 125 LYS cc_start: 0.6821 (ptpt) cc_final: 0.6345 (tmmt) outliers start: 54 outliers final: 21 residues processed: 119 average time/residue: 0.4766 time to fit residues: 59.8709 Evaluate side-chains 102 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 117 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [24, 43, 28, 41, 65, 34, 9, 11, 18, 21, 44] chunk 24 optimal weight: 0.2980 chunk 43 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 GLN ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 214 ASN ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.220525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.183867 restraints weight = 6446.073| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 1.73 r_work: 0.4114 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3975 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6403 Z= 0.140 Angle : 0.677 13.749 8770 Z= 0.360 Chirality : 0.046 0.305 940 Planarity : 0.004 0.039 994 Dihedral : 21.839 178.682 1187 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 7.73 % Allowed : 35.46 % Favored : 56.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.32), residues: 649 helix: 0.52 (0.35), residues: 227 sheet: -2.43 (0.50), residues: 95 loop : -2.05 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 314 TYR 0.012 0.001 TYR D 17 PHE 0.014 0.001 PHE B 228 TRP 0.005 0.001 TRP A 212 HIS 0.004 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 6401) covalent geometry : angle 0.67666 / 0.36 ( 8770) hydrogen bonds : bond 0.03781 / 2.57 ( 224) hydrogen bonds : angle 4.57337 / 3.21 ( 622) Misc. bond : bond 0.00060 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 74 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 MET cc_start: 0.5536 (OUTLIER) cc_final: 0.4698 (mpm) REVERT: A 197 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6958 (ptm160) REVERT: B 235 ILE cc_start: 0.6663 (OUTLIER) cc_final: 0.6335 (tp) REVERT: B 238 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.5601 (mtp) REVERT: D 25 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6355 (pp) REVERT: D 125 LYS cc_start: 0.6956 (ptpt) cc_final: 0.6384 (tppt) REVERT: D 126 LYS cc_start: 0.7017 (OUTLIER) cc_final: 0.6776 (tppt) outliers start: 46 outliers final: 22 residues processed: 106 average time/residue: 0.4620 time to fit residues: 51.8075 Evaluate side-chains 99 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 126 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [37, 61, 54, 7, 22, 63, 29, 3, 15, 12, 6] chunk 37 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 214 ASN ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 ASN D 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.216693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.178303 restraints weight = 6374.513| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 1.82 r_work: 0.4066 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3925 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6403 Z= 0.194 Angle : 0.711 13.786 8770 Z= 0.380 Chirality : 0.049 0.266 940 Planarity : 0.004 0.038 994 Dihedral : 21.897 178.145 1185 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 9.24 % Allowed : 33.45 % Favored : 57.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.31), residues: 649 helix: 0.39 (0.34), residues: 226 sheet: -2.74 (0.47), residues: 101 loop : -2.18 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 314 TYR 0.017 0.002 TYR D 17 PHE 0.014 0.002 PHE B 242 TRP 0.010 0.002 TRP A 212 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 ( 6401) covalent geometry : angle 0.71135 / 0.38 ( 8770) hydrogen bonds : bond 0.04308 / 2.90 ( 224) hydrogen bonds : angle 4.64728 / 3.26 ( 622) Misc. bond : bond 0.00099 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 77 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 MET cc_start: 0.5585 (OUTLIER) cc_final: 0.4801 (mpm) REVERT: A 197 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7041 (ptm160) REVERT: B 227 SER cc_start: 0.7250 (p) cc_final: 0.6946 (t) REVERT: B 235 ILE cc_start: 0.6475 (OUTLIER) cc_final: 0.6206 (tp) REVERT: B 238 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.5637 (mtp) REVERT: C 167 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6698 (tt) REVERT: D 25 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6181 (pp) REVERT: D 110 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7501 (mp0) REVERT: D 117 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7398 (tppt) REVERT: D 125 LYS cc_start: 0.6953 (ptpt) cc_final: 0.6372 (tppt) REVERT: D 126 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6764 (tppt) outliers start: 55 outliers final: 20 residues processed: 116 average time/residue: 0.4798 time to fit residues: 58.6131 Evaluate side-chains 95 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 126 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [15, 25, 20, 47, 16, 49, 36, 39, 35, 14, 34] chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 214 ASN ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.223001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.182015 restraints weight = 6283.805| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 1.95 r_work: 0.4063 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3921 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6403 Z= 0.175 Angle : 0.708 13.490 8770 Z= 0.379 Chirality : 0.047 0.255 940 Planarity : 0.004 0.039 994 Dihedral : 21.933 178.129 1185 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 7.73 % Allowed : 35.29 % Favored : 56.97 % 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: -1.95 (0.32), residues: 649 helix: 0.47 (0.35), residues: 226 sheet: -2.70 (0.48), residues: 100 loop : -2.15 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 314 TYR 0.017 0.002 TYR B 292 PHE 0.026 0.002 PHE B 228 TRP 0.008 0.001 TRP A 212 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 6401) covalent geometry : angle 0.70761 / 0.38 ( 8770) hydrogen bonds : bond 0.03932 / 2.65 ( 224) hydrogen bonds : angle 4.59915 / 3.23 ( 622) Misc. bond : bond 0.00074 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 75 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 MET cc_start: 0.5618 (OUTLIER) cc_final: 0.4789 (mpm) REVERT: A 197 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.6976 (ptm160) REVERT: B 235 ILE cc_start: 0.6451 (OUTLIER) cc_final: 0.6189 (tp) REVERT: B 238 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.5600 (mtp) REVERT: D 25 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.6331 (pp) REVERT: D 86 GLU cc_start: 0.6414 (tp30) cc_final: 0.5889 (tp30) REVERT: D 110 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7511 (mp0) REVERT: D 117 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7340 (tppt) REVERT: D 125 LYS cc_start: 0.7003 (ptpt) cc_final: 0.6382 (tppt) REVERT: D 129 LYS cc_start: 0.5867 (pttt) cc_final: 0.5415 (pttp) outliers start: 46 outliers final: 21 residues processed: 110 average time/residue: 0.5147 time to fit residues: 59.4948 Evaluate side-chains 97 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 117 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [16, 38, 4, 48, 14, 12, 49, 58, 33, 32, 55] chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 214 ASN ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.217810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.178812 restraints weight = 6412.743| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 1.76 r_work: 0.4070 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3928 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 6403 Z= 0.172 Angle : 0.723 15.347 8770 Z= 0.379 Chirality : 0.049 0.425 940 Planarity : 0.004 0.040 994 Dihedral : 21.930 178.442 1185 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 6.22 % Allowed : 36.64 % Favored : 57.14 % 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 (0.32), residues: 649 helix: 0.43 (0.34), residues: 226 sheet: -2.72 (0.48), residues: 100 loop : -2.13 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 22 TYR 0.012 0.002 TYR A 258 PHE 0.022 0.002 PHE B 228 TRP 0.007 0.001 TRP A 212 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 6401) covalent geometry : angle 0.72326 / 0.38 ( 8770) hydrogen bonds : bond 0.03888 / 2.59 ( 224) hydrogen bonds : angle 4.54462 / 3.18 ( 622) Misc. bond : bond 0.00072 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 71 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 MET cc_start: 0.5556 (OUTLIER) cc_final: 0.4676 (mpm) REVERT: A 197 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7033 (ptm160) REVERT: B 235 ILE cc_start: 0.6426 (OUTLIER) cc_final: 0.6169 (tp) REVERT: B 238 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.5551 (mtp) REVERT: D 25 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6207 (pp) REVERT: D 110 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7528 (mp0) REVERT: D 117 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7413 (tppt) REVERT: D 125 LYS cc_start: 0.6989 (ptpt) cc_final: 0.6338 (tmmt) outliers start: 37 outliers final: 22 residues processed: 98 average time/residue: 0.4902 time to fit residues: 50.4675 Evaluate side-chains 93 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 117 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [42, 65, 53, 62, 20, 0, 59, 33, 57, 47, 64] chunk 42 optimal weight: 0.0870 chunk 65 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 214 ASN ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.218627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.181274 restraints weight = 6405.062| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 1.70 r_work: 0.4117 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3981 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6403 Z= 0.159 Angle : 0.709 15.638 8770 Z= 0.376 Chirality : 0.047 0.317 940 Planarity : 0.004 0.040 994 Dihedral : 21.920 178.652 1185 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 6.05 % Allowed : 37.14 % Favored : 56.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.32), residues: 649 helix: 0.45 (0.34), residues: 226 sheet: -2.71 (0.48), residues: 100 loop : -2.13 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 22 TYR 0.015 0.002 TYR D 17 PHE 0.021 0.001 PHE B 228 TRP 0.006 0.001 TRP B 55 HIS 0.003 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 6401) covalent geometry : angle 0.70940 / 0.38 ( 8770) hydrogen bonds : bond 0.03740 / 2.51 ( 224) hydrogen bonds : angle 4.52098 / 3.17 ( 622) Misc. bond : bond 0.00070 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 69 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 MET cc_start: 0.5591 (OUTLIER) cc_final: 0.4726 (mpm) REVERT: A 197 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6988 (ptm160) REVERT: B 235 ILE cc_start: 0.6568 (OUTLIER) cc_final: 0.6296 (tp) REVERT: B 238 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.5497 (mtp) REVERT: D 25 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6289 (pp) REVERT: D 110 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7602 (mp0) REVERT: D 117 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7441 (tppt) REVERT: D 125 LYS cc_start: 0.6963 (ptpt) cc_final: 0.6357 (tmmt) outliers start: 36 outliers final: 20 residues processed: 95 average time/residue: 0.5364 time to fit residues: 53.5429 Evaluate side-chains 93 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 117 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [6, 7, 25, 37, 0, 60, 14, 24, 54, 12, 19] chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.0870 chunk 25 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.220107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.182434 restraints weight = 6309.245| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 1.69 r_work: 0.4104 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3964 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6403 Z= 0.144 Angle : 0.696 15.818 8770 Z= 0.369 Chirality : 0.046 0.289 940 Planarity : 0.004 0.039 994 Dihedral : 21.869 179.231 1185 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 5.38 % Allowed : 37.65 % Favored : 56.97 % 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: -1.82 (0.32), residues: 649 helix: 0.58 (0.35), residues: 226 sheet: -2.56 (0.50), residues: 101 loop : -2.10 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 22 TYR 0.012 0.001 TYR D 17 PHE 0.022 0.001 PHE B 228 TRP 0.005 0.001 TRP B 55 HIS 0.003 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 6401) covalent geometry : angle 0.69570 / 0.37 ( 8770) hydrogen bonds : bond 0.03519 / 2.37 ( 224) hydrogen bonds : angle 4.41768 / 3.09 ( 622) Misc. bond : bond 0.00067 / 0.03 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 MET cc_start: 0.5572 (OUTLIER) cc_final: 0.4665 (mpm) REVERT: A 197 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7025 (ptm160) REVERT: B 235 ILE cc_start: 0.6606 (OUTLIER) cc_final: 0.6346 (tp) REVERT: B 238 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.5535 (mtp) REVERT: D 25 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6112 (pp) REVERT: D 110 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7569 (mp0) REVERT: D 117 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7396 (tppt) REVERT: D 125 LYS cc_start: 0.7026 (ptpt) cc_final: 0.6349 (tmmt) REVERT: D 127 GLU cc_start: 0.4632 (pt0) cc_final: 0.4411 (pt0) REVERT: D 129 LYS cc_start: 0.6005 (pttt) cc_final: 0.5391 (pttp) outliers start: 32 outliers final: 19 residues processed: 95 average time/residue: 0.4934 time to fit residues: 49.3559 Evaluate side-chains 91 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 117 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: [8, 61, 52, 32, 53, 39, 62, 1, 64, 11, 23] chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.223859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.183552 restraints weight = 6306.338| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 1.87 r_work: 0.4083 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3939 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6403 Z= 0.169 Angle : 0.725 15.833 8770 Z= 0.380 Chirality : 0.048 0.391 940 Planarity : 0.004 0.038 994 Dihedral : 21.856 179.123 1184 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 5.04 % Allowed : 38.32 % Favored : 56.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.32), residues: 649 helix: 0.53 (0.35), residues: 226 sheet: -2.70 (0.49), residues: 100 loop : -2.11 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 22 TYR 0.015 0.002 TYR D 17 PHE 0.022 0.002 PHE B 228 TRP 0.007 0.001 TRP A 212 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 6401) covalent geometry : angle 0.72460 / 0.38 ( 8770) hydrogen bonds : bond 0.03842 / 2.56 ( 224) hydrogen bonds : angle 4.53860 / 3.15 ( 622) Misc. bond : bond 0.00072 / 0.04 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2510.83 seconds wall clock time: 43 minutes 34.07 seconds (2614.07 seconds total)