Starting phenix.real_space_refine on Wed Aug 5 05:55:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mn8_48416/08_2026/9mn8_48416.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mn8_48416/08_2026/9mn8_48416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mn8_48416/08_2026/9mn8_48416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mn8_48416/08_2026/9mn8_48416.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mn8_48416/08_2026/9mn8_48416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mn8_48416/08_2026/9mn8_48416.map" } resolution = 2.69 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= 0.019 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 38 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 5281 2.51 5 N 1532 2.21 5 O 1600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8500 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 7742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7742 Classifications: {'peptide': 971} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 64, 'TRANS': 906} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "N" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 343 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "R" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 178 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 7} Link IDs: {'rna3p': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.75, per 1000 atoms: 0.21 Number of scatterers: 8500 At special positions: 0 Unit cell: (94.17, 117.53, 97.82, 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 48 16.00 P 38 15.00 Mg 1 11.99 O 1600 8.00 N 1532 7.00 C 5281 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: 0.82 Conformation dependent library (CDL) restraints added in 281.2 milliseconds 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1850 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 7 sheets defined 63.0% alpha, 4.0% beta 13 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'E' and resid 220 through 236 Processing helix chain 'E' and resid 238 through 252 removed outlier: 3.754A pdb=" N ALA E 242 " --> pdb=" O GLN E 238 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN E 252 " --> pdb=" O VAL E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 260 through 275 removed outlier: 4.279A pdb=" N TYR E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 289 removed outlier: 3.761A pdb=" N LYS E 288 " --> pdb=" O LEU E 284 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP E 289 " --> pdb=" O PHE E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 311 through 316 Processing helix chain 'E' and resid 318 through 327 removed outlier: 3.813A pdb=" N GLY E 327 " --> pdb=" O MET E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 336 Processing helix chain 'E' and resid 340 through 354 removed outlier: 3.960A pdb=" N VAL E 354 " --> pdb=" O ALA E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 409 Processing helix chain 'E' and resid 424 through 462 removed outlier: 3.584A pdb=" N THR E 436 " --> pdb=" O LYS E 432 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG E 450 " --> pdb=" O CYS E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 472 Processing helix chain 'E' and resid 475 through 490 Processing helix chain 'E' and resid 496 through 520 removed outlier: 3.618A pdb=" N GLN E 517 " --> pdb=" O VAL E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 538 removed outlier: 4.448A pdb=" N CYS E 535 " --> pdb=" O ARG E 531 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LEU E 536 " --> pdb=" O LYS E 532 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU E 537 " --> pdb=" O TYR E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 556 Processing helix chain 'E' and resid 568 through 585 removed outlier: 3.663A pdb=" N GLN E 585 " --> pdb=" O GLU E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 624 through 633 removed outlier: 3.779A pdb=" N VAL E 628 " --> pdb=" O HIS E 624 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 685 Processing helix chain 'E' and resid 692 through 704 Processing helix chain 'E' and resid 710 through 723 removed outlier: 3.520A pdb=" N ALA E 723 " --> pdb=" O GLN E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 758 through 789 Processing helix chain 'E' and resid 818 through 824 Processing helix chain 'E' and resid 836 through 850 removed outlier: 3.575A pdb=" N TRP E 840 " --> pdb=" O HIS E 836 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY E 850 " --> pdb=" O VAL E 846 " (cutoff:3.500A) Processing helix chain 'E' and resid 856 through 867 Processing helix chain 'E' and resid 867 through 877 Processing helix chain 'E' and resid 883 through 888 Processing helix chain 'E' and resid 890 through 906 Processing helix chain 'E' and resid 925 through 936 Processing helix chain 'E' and resid 937 through 944 Processing helix chain 'E' and resid 954 through 972 removed outlier: 4.277A pdb=" N PHE E 966 " --> pdb=" O GLN E 962 " (cutoff:3.500A) Processing helix chain 'E' and resid 975 through 980 Processing helix chain 'E' and resid 986 through 997 removed outlier: 3.807A pdb=" N VAL E 990 " --> pdb=" O THR E 986 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLN E 992 " --> pdb=" O LYS E 988 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N THR E 993 " --> pdb=" O VAL E 989 " (cutoff:3.500A) Processing helix chain 'E' and resid 1002 through 1016 removed outlier: 3.863A pdb=" N ARG E1013 " --> pdb=" O GLN E1009 " (cutoff:3.500A) Processing helix chain 'E' and resid 1024 through 1034 Processing helix chain 'E' and resid 1036 through 1040 removed outlier: 4.137A pdb=" N SER E1039 " --> pdb=" O VAL E1036 " (cutoff:3.500A) Processing helix chain 'E' and resid 1044 through 1065 Processing helix chain 'E' and resid 1111 through 1141 Proline residue: E1120 - end of helix Processing helix chain 'E' and resid 1159 through 1177 removed outlier: 3.505A pdb=" N PHE E1171 " --> pdb=" O CYS E1167 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL E1172 " --> pdb=" O ARG E1168 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU E1177 " --> pdb=" O ARG E1173 " (cutoff:3.500A) Processing helix chain 'E' and resid 1178 through 1191 Processing helix chain 'E' and resid 1197 through 1210 Processing helix chain 'E' and resid 1218 through 1225 Processing sheet with id=AA1, first strand: chain 'E' and resid 411 through 415 Processing sheet with id=AA2, first strand: chain 'E' and resid 588 through 590 Processing sheet with id=AA3, first strand: chain 'E' and resid 794 through 795 Processing sheet with id=AA4, first strand: chain 'E' and resid 798 through 800 Processing sheet with id=AA5, first strand: chain 'E' and resid 831 through 832 Processing sheet with id=AA6, first strand: chain 'E' and resid 1146 through 1149 Processing sheet with id=AA7, first strand: chain 'E' and resid 1069 through 1071 439 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 1.06 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: 2311 1.33 - 1.45: 1717 1.45 - 1.57: 4599 1.57 - 1.69: 71 1.69 - 1.81: 72 Bond restraints: 8770 Sorted by residual: bond pdb=" C1' DC T 12 " pdb=" N1 DC T 12 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.45e+01 bond pdb=" N9 DA N 46 " pdb=" C4 DA N 46 " ideal model delta sigma weight residual 1.374 1.393 -0.019 6.00e-03 2.78e+04 1.04e+01 bond pdb=" C3' DG N 44 " pdb=" C2' DG N 44 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C5 DT T 13 " pdb=" C6 DT T 13 " ideal model delta sigma weight residual 1.339 1.320 0.019 7.00e-03 2.04e+04 7.57e+00 bond pdb=" N1 DT T 13 " pdb=" C6 DT T 13 " ideal model delta sigma weight residual 1.378 1.360 0.018 7.00e-03 2.04e+04 6.97e+00 ... (remaining 8765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 11846 3.28 - 6.56: 181 6.56 - 9.84: 19 9.84 - 13.12: 5 13.12 - 16.40: 1 Bond angle restraints: 12052 Sorted by residual: angle pdb=" N VAL E 351 " pdb=" CA VAL E 351 " pdb=" C VAL E 351 " ideal model delta sigma weight residual 112.29 105.66 6.63 9.40e-01 1.13e+00 4.97e+01 angle pdb=" O4' DT T 13 " pdb=" C1' DT T 13 " pdb=" N1 DT T 13 " ideal model delta sigma weight residual 108.00 112.23 -4.23 7.00e-01 2.04e+00 3.65e+01 angle pdb=" C HIS E1150 " pdb=" N ASP E1151 " pdb=" CA ASP E1151 " ideal model delta sigma weight residual 126.32 135.97 -9.65 1.74e+00 3.30e-01 3.08e+01 angle pdb=" C GLY E 314 " pdb=" N THR E 315 " pdb=" CA THR E 315 " ideal model delta sigma weight residual 121.54 131.65 -10.11 1.91e+00 2.74e-01 2.80e+01 angle pdb=" O4' DT T 9 " pdb=" C4' DT T 9 " pdb=" C3' DT T 9 " ideal model delta sigma weight residual 106.00 102.85 3.15 6.00e-01 2.78e+00 2.76e+01 ... (remaining 12047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 4687 17.60 - 35.21: 382 35.21 - 52.81: 125 52.81 - 70.42: 71 70.42 - 88.02: 14 Dihedral angle restraints: 5279 sinusoidal: 2438 harmonic: 2841 Sorted by residual: dihedral pdb=" CA VAL E1033 " pdb=" C VAL E1033 " pdb=" N ARG E1034 " pdb=" CA ARG E1034 " ideal model delta harmonic sigma weight residual 180.00 155.36 24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA CYS E 687 " pdb=" C CYS E 687 " pdb=" N PRO E 688 " pdb=" CA PRO E 688 " ideal model delta harmonic sigma weight residual 180.00 156.02 23.98 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA MET E 800 " pdb=" C MET E 800 " pdb=" N ASP E 801 " pdb=" CA ASP E 801 " ideal model delta harmonic sigma weight residual 180.00 157.16 22.84 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 5276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1001 0.055 - 0.109: 264 0.109 - 0.164: 75 0.164 - 0.218: 7 0.218 - 0.273: 2 Chirality restraints: 1349 Sorted by residual: chirality pdb=" CB VAL E 354 " pdb=" CA VAL E 354 " pdb=" CG1 VAL E 354 " pdb=" CG2 VAL E 354 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB VAL E 990 " pdb=" CA VAL E 990 " pdb=" CG1 VAL E 990 " pdb=" CG2 VAL E 990 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C1' G R 8 " pdb=" O4' G R 8 " pdb=" C2' G R 8 " pdb=" N9 G R 8 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1346 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS E1150 " -0.019 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C HIS E1150 " 0.068 2.00e-02 2.50e+03 pdb=" O HIS E1150 " -0.026 2.00e-02 2.50e+03 pdb=" N ASP E1151 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 477 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.67e+00 pdb=" C ARG E 477 " 0.045 2.00e-02 2.50e+03 pdb=" O ARG E 477 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU E 478 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E1154 " 0.007 2.00e-02 2.50e+03 1.63e-02 6.67e+00 pdb=" CG TRP E1154 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP E1154 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP E1154 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E1154 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP E1154 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP E1154 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E1154 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP E1154 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP E1154 " 0.001 2.00e-02 2.50e+03 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 42 2.56 - 3.15: 6356 3.15 - 3.73: 13753 3.73 - 4.32: 18955 4.32 - 4.90: 30466 Nonbonded interactions: 69572 Sorted by model distance: nonbonded pdb=" O1G ATP E1301 " pdb="MG MG E1302 " model vdw 1.979 2.170 nonbonded pdb=" OD2 ASP E 922 " pdb="MG MG E1302 " model vdw 1.994 2.170 nonbonded pdb=" O2A ATP E1301 " pdb="MG MG E1302 " model vdw 2.199 2.170 nonbonded pdb=" OH TYR E 530 " pdb=" O PRO E 651 " model vdw 2.261 3.040 nonbonded pdb=" OG SER E 938 " pdb=" O ALA E1216 " model vdw 2.261 3.040 ... (remaining 69567 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.390 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.300 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:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5819 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 0.062 8770 Z= 0.332 Angle : 1.027 16.399 12052 Z= 0.618 Chirality : 0.054 0.273 1349 Planarity : 0.008 0.089 1426 Dihedral : 16.709 88.020 3429 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -1.28 (0.25), residues: 963 helix: -0.66 (0.20), residues: 583 sheet: -1.99 (0.95), residues: 27 loop : -0.81 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG E 803 TYR 0.023 0.003 TYR E 607 PHE 0.041 0.004 PHE E 465 TRP 0.038 0.004 TRP E1154 HIS 0.020 0.003 HIS E 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.33 ( 8770) covalent geometry : angle 1.02653 / 0.62 (12052) hydrogen bonds : bond 0.14509 / 9.93 ( 471) hydrogen bonds : angle 6.22087 / 4.41 ( 1342) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.195 Fit side-chains REVERT: E 372 LYS cc_start: 0.7237 (mtpt) cc_final: 0.6896 (mtmt) REVERT: E 410 SER cc_start: 0.6694 (t) cc_final: 0.6491 (t) REVERT: E 554 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6516 (mm-30) REVERT: E 682 GLU cc_start: 0.6466 (mt-10) cc_final: 0.6194 (mt-10) REVERT: E 781 TYR cc_start: 0.7324 (m-80) cc_final: 0.7124 (m-80) REVERT: E 816 LEU cc_start: 0.8026 (mp) cc_final: 0.7820 (mp) REVERT: E 1151 ASP cc_start: 0.5544 (p0) cc_final: 0.5279 (p0) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.6089 time to fit residues: 87.4193 Evaluate side-chains 126 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.0870 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 304 GLN E 369 ASN E 524 GLN E 773 HIS E 953 GLN ** E1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1035 GLN E1041 GLN E1063 HIS E1125 HIS E1138 HIS E1221 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.168822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.142358 restraints weight = 12038.210| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.60 r_work: 0.3732 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8770 Z= 0.169 Angle : 0.662 12.083 12052 Z= 0.352 Chirality : 0.041 0.171 1349 Planarity : 0.006 0.043 1426 Dihedral : 16.458 86.532 1494 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.59 % Allowed : 7.22 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.26), residues: 963 helix: 0.37 (0.21), residues: 586 sheet: -1.69 (1.12), residues: 22 loop : -0.48 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 803 TYR 0.016 0.002 TYR E 552 PHE 0.020 0.002 PHE E 465 TRP 0.011 0.002 TRP E 567 HIS 0.009 0.001 HIS E1175 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 ( 8770) covalent geometry : angle 0.66193 / 0.35 (12052) hydrogen bonds : bond 0.05078 / 3.43 ( 471) hydrogen bonds : angle 4.44373 / 3.10 ( 1342) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.295 Fit side-chains REVERT: E 264 TYR cc_start: 0.7324 (m-80) cc_final: 0.6991 (m-80) REVERT: E 515 GLN cc_start: 0.7657 (tp-100) cc_final: 0.6943 (tp-100) REVERT: E 1082 TYR cc_start: 0.7499 (m-10) cc_final: 0.6792 (m-80) outliers start: 5 outliers final: 1 residues processed: 128 average time/residue: 0.6535 time to fit residues: 88.3749 Evaluate side-chains 127 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 908 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 81 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 78 optimal weight: 0.0770 chunk 51 optimal weight: 3.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 369 ASN E 522 GLN E 524 GLN E1030 HIS E1221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.168387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.141849 restraints weight = 11948.816| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.58 r_work: 0.3720 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8770 Z= 0.162 Angle : 0.623 12.467 12052 Z= 0.332 Chirality : 0.041 0.168 1349 Planarity : 0.005 0.044 1426 Dihedral : 16.367 88.907 1494 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.42 % Allowed : 9.47 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.27), residues: 963 helix: 0.83 (0.21), residues: 588 sheet: -1.73 (1.11), residues: 22 loop : -0.33 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 455 TYR 0.017 0.002 TYR E 552 PHE 0.023 0.002 PHE E 509 TRP 0.013 0.002 TRP E 567 HIS 0.006 0.001 HIS E1175 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 8770) covalent geometry : angle 0.62327 / 0.33 (12052) hydrogen bonds : bond 0.04623 / 3.12 ( 471) hydrogen bonds : angle 4.15740 / 2.90 ( 1342) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.295 Fit side-chains REVERT: E 264 TYR cc_start: 0.7307 (m-80) cc_final: 0.6970 (m-80) REVERT: E 478 GLU cc_start: 0.7192 (mp0) cc_final: 0.6964 (mp0) REVERT: E 515 GLN cc_start: 0.7645 (tp-100) cc_final: 0.6945 (tp-100) REVERT: E 685 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7513 (mt-10) REVERT: E 1082 TYR cc_start: 0.7541 (m-10) cc_final: 0.6791 (m-80) outliers start: 12 outliers final: 5 residues processed: 133 average time/residue: 0.6596 time to fit residues: 92.8735 Evaluate side-chains 132 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 659 HIS Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 1132 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 17 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 58 optimal weight: 0.0980 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 369 ASN E 522 GLN E 524 GLN E1221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.168005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.141391 restraints weight = 12120.721| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.61 r_work: 0.3716 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8770 Z= 0.157 Angle : 0.604 15.219 12052 Z= 0.320 Chirality : 0.040 0.172 1349 Planarity : 0.005 0.044 1426 Dihedral : 16.296 88.177 1494 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.78 % Allowed : 10.30 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.27), residues: 963 helix: 1.04 (0.22), residues: 588 sheet: -1.57 (1.15), residues: 22 loop : -0.26 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 776 TYR 0.014 0.002 TYR E 552 PHE 0.016 0.002 PHE E 465 TRP 0.010 0.001 TRP E 707 HIS 0.005 0.001 HIS E1175 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 8770) covalent geometry : angle 0.60426 / 0.32 (12052) hydrogen bonds : bond 0.04436 / 3.01 ( 471) hydrogen bonds : angle 4.05425 / 2.83 ( 1342) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.261 Fit side-chains REVERT: E 264 TYR cc_start: 0.7283 (m-80) cc_final: 0.6957 (m-80) REVERT: E 268 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6851 (mmm) REVERT: E 482 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7971 (ttm) REVERT: E 515 GLN cc_start: 0.7650 (tp-100) cc_final: 0.6959 (tp-100) REVERT: E 685 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: E 1082 TYR cc_start: 0.7518 (m-10) cc_final: 0.6882 (m-80) outliers start: 15 outliers final: 8 residues processed: 137 average time/residue: 0.6617 time to fit residues: 95.9200 Evaluate side-chains 141 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 482 MET Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 659 HIS Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 1132 MET Chi-restraints excluded: chain E residue 1211 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 67 optimal weight: 0.0980 chunk 28 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 369 ASN E 522 GLN E 524 GLN E1221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.167831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.141226 restraints weight = 12096.652| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.61 r_work: 0.3711 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8770 Z= 0.158 Angle : 0.613 15.836 12052 Z= 0.322 Chirality : 0.040 0.170 1349 Planarity : 0.005 0.044 1426 Dihedral : 16.277 87.519 1494 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.60 % Allowed : 11.01 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.27), residues: 963 helix: 1.16 (0.22), residues: 588 sheet: -1.78 (1.11), residues: 22 loop : -0.22 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 455 TYR 0.014 0.002 TYR E 552 PHE 0.014 0.002 PHE E 465 TRP 0.012 0.001 TRP E 567 HIS 0.005 0.001 HIS E1175 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 ( 8770) covalent geometry : angle 0.61291 / 0.32 (12052) hydrogen bonds : bond 0.04377 / 2.97 ( 471) hydrogen bonds : angle 3.98829 / 2.79 ( 1342) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.241 Fit side-chains REVERT: E 264 TYR cc_start: 0.7241 (m-80) cc_final: 0.6916 (m-80) REVERT: E 482 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.8005 (ttm) REVERT: E 515 GLN cc_start: 0.7644 (tp-100) cc_final: 0.6981 (tp-100) REVERT: E 685 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7542 (mt-10) REVERT: E 1082 TYR cc_start: 0.7516 (m-10) cc_final: 0.6881 (m-80) outliers start: 22 outliers final: 14 residues processed: 137 average time/residue: 0.6039 time to fit residues: 87.9842 Evaluate side-chains 142 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 482 MET Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 659 HIS Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 791 ASP Chi-restraints excluded: chain E residue 908 SER Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1069 GLU Chi-restraints excluded: chain E residue 1132 MET Chi-restraints excluded: chain E residue 1211 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 69 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 66 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 71 optimal weight: 0.0070 chunk 1 optimal weight: 0.5980 chunk 32 optimal weight: 0.0770 chunk 49 optimal weight: 0.5980 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 223 GLN E 331 GLN E 369 ASN E 522 GLN E 524 GLN E 926 ASN E1221 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.168742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.142230 restraints weight = 11975.837| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.59 r_work: 0.3727 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8770 Z= 0.134 Angle : 0.575 16.209 12052 Z= 0.306 Chirality : 0.039 0.166 1349 Planarity : 0.005 0.044 1426 Dihedral : 16.232 86.582 1494 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.13 % Allowed : 12.31 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.27), residues: 963 helix: 1.32 (0.22), residues: 588 sheet: -1.97 (0.98), residues: 27 loop : -0.13 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 776 TYR 0.010 0.001 TYR E 552 PHE 0.027 0.002 PHE E 509 TRP 0.012 0.001 TRP E 567 HIS 0.005 0.001 HIS E1175 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 8770) covalent geometry : angle 0.57470 / 0.31 (12052) hydrogen bonds : bond 0.04141 / 2.80 ( 471) hydrogen bonds : angle 3.91267 / 2.73 ( 1342) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.298 Fit side-chains REVERT: E 264 TYR cc_start: 0.7087 (m-80) cc_final: 0.6797 (m-80) REVERT: E 268 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6983 (mmm) REVERT: E 481 ARG cc_start: 0.6862 (mtm-85) cc_final: 0.6637 (mtt180) REVERT: E 482 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.8009 (ttm) REVERT: E 515 GLN cc_start: 0.7629 (tp-100) cc_final: 0.6966 (tp-100) REVERT: E 685 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: E 1082 TYR cc_start: 0.7438 (m-10) cc_final: 0.6770 (m-80) outliers start: 18 outliers final: 6 residues processed: 136 average time/residue: 0.6113 time to fit residues: 88.2869 Evaluate side-chains 136 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 482 MET Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 659 HIS Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 671 MET Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 791 ASP Chi-restraints excluded: chain E residue 997 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 17 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 82 optimal weight: 0.0770 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 223 GLN E 369 ASN E 522 GLN E 524 GLN E 920 HIS E1221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.167284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.140676 restraints weight = 12065.990| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.60 r_work: 0.3703 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8770 Z= 0.169 Angle : 0.608 16.794 12052 Z= 0.321 Chirality : 0.041 0.175 1349 Planarity : 0.005 0.045 1426 Dihedral : 16.272 86.336 1494 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.13 % Allowed : 12.07 % Favored : 85.80 % 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: 1.01 (0.27), residues: 963 helix: 1.30 (0.21), residues: 588 sheet: -1.69 (1.13), residues: 22 loop : -0.13 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 776 TYR 0.015 0.002 TYR E 552 PHE 0.017 0.002 PHE E 802 TRP 0.016 0.001 TRP E 567 HIS 0.006 0.001 HIS E 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 ( 8770) covalent geometry : angle 0.60788 / 0.32 (12052) hydrogen bonds : bond 0.04321 / 2.93 ( 471) hydrogen bonds : angle 3.94282 / 2.75 ( 1342) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: E 264 TYR cc_start: 0.7062 (m-80) cc_final: 0.6742 (m-80) REVERT: E 268 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.7026 (mmm) REVERT: E 481 ARG cc_start: 0.6870 (mtm-85) cc_final: 0.6625 (mtt180) REVERT: E 482 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.8030 (ttm) REVERT: E 515 GLN cc_start: 0.7634 (tp-100) cc_final: 0.7001 (tp-100) REVERT: E 685 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: E 1082 TYR cc_start: 0.7549 (m-10) cc_final: 0.6892 (m-80) REVERT: E 1151 ASP cc_start: 0.6266 (OUTLIER) cc_final: 0.6026 (p0) outliers start: 18 outliers final: 7 residues processed: 138 average time/residue: 0.6393 time to fit residues: 93.5444 Evaluate side-chains 140 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 482 MET Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 659 HIS Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 908 SER Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1151 ASP Chi-restraints excluded: chain E residue 1211 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.0070 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 223 GLN E 369 ASN E 522 GLN E 524 GLN E 920 HIS E1221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.167125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.140699 restraints weight = 11953.176| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.59 r_work: 0.3709 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8770 Z= 0.160 Angle : 0.602 17.352 12052 Z= 0.317 Chirality : 0.040 0.173 1349 Planarity : 0.005 0.045 1426 Dihedral : 16.292 85.940 1494 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.78 % Allowed : 12.54 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.27), residues: 963 helix: 1.35 (0.21), residues: 588 sheet: -1.79 (1.10), residues: 22 loop : -0.11 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 455 TYR 0.015 0.002 TYR E 552 PHE 0.017 0.001 PHE E 802 TRP 0.014 0.001 TRP E 567 HIS 0.005 0.001 HIS E 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 8770) covalent geometry : angle 0.60239 / 0.32 (12052) hydrogen bonds : bond 0.04243 / 2.88 ( 471) hydrogen bonds : angle 3.90392 / 2.72 ( 1342) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: E 264 TYR cc_start: 0.7079 (m-80) cc_final: 0.6743 (m-80) REVERT: E 268 MET cc_start: 0.7253 (mmm) cc_final: 0.7015 (mmm) REVERT: E 295 ASP cc_start: 0.7283 (t0) cc_final: 0.6870 (m-30) REVERT: E 482 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8059 (ttm) REVERT: E 515 GLN cc_start: 0.7618 (tp-100) cc_final: 0.6965 (tp-100) REVERT: E 685 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: E 1082 TYR cc_start: 0.7524 (m-10) cc_final: 0.6896 (m-80) outliers start: 15 outliers final: 8 residues processed: 134 average time/residue: 0.6433 time to fit residues: 91.2818 Evaluate side-chains 137 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 452 THR Chi-restraints excluded: chain E residue 482 MET Chi-restraints excluded: chain E residue 607 TYR Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 659 HIS Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 995 MET Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1211 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 84 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 223 GLN E 369 ASN E 522 GLN E 524 GLN E 836 HIS E 920 HIS ** E1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1221 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.167006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.140502 restraints weight = 12031.799| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.59 r_work: 0.3703 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8770 Z= 0.166 Angle : 0.614 16.558 12052 Z= 0.322 Chirality : 0.041 0.214 1349 Planarity : 0.005 0.045 1426 Dihedral : 16.282 85.669 1494 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.01 % Allowed : 13.14 % Favored : 84.85 % 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: 1.06 (0.27), residues: 963 helix: 1.35 (0.21), residues: 588 sheet: -1.86 (1.08), residues: 22 loop : -0.11 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 776 TYR 0.015 0.002 TYR E 552 PHE 0.032 0.002 PHE E 509 TRP 0.013 0.001 TRP E 567 HIS 0.006 0.001 HIS E 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 8770) covalent geometry : angle 0.61376 / 0.32 (12052) hydrogen bonds : bond 0.04253 / 2.89 ( 471) hydrogen bonds : angle 3.91771 / 2.75 ( 1342) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: E 264 TYR cc_start: 0.7080 (m-80) cc_final: 0.6725 (m-80) REVERT: E 295 ASP cc_start: 0.7284 (t0) cc_final: 0.6874 (m-30) REVERT: E 481 ARG cc_start: 0.6877 (mtm-85) cc_final: 0.6642 (mtt180) REVERT: E 482 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.8033 (ttm) REVERT: E 515 GLN cc_start: 0.7624 (tp-100) cc_final: 0.6968 (tp-100) REVERT: E 671 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8558 (mmm) REVERT: E 685 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: E 1082 TYR cc_start: 0.7546 (m-10) cc_final: 0.6883 (m-80) outliers start: 17 outliers final: 11 residues processed: 133 average time/residue: 0.6322 time to fit residues: 89.2258 Evaluate side-chains 139 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 482 MET Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 607 TYR Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 659 HIS Chi-restraints excluded: chain E residue 660 SER Chi-restraints excluded: chain E residue 671 MET Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 908 SER Chi-restraints excluded: chain E residue 995 MET Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1211 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 91 optimal weight: 0.0270 chunk 47 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 17 optimal weight: 0.0010 chunk 85 optimal weight: 0.9980 chunk 80 optimal weight: 0.0170 chunk 58 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 46 optimal weight: 0.0000 chunk 42 optimal weight: 0.7980 overall best weight: 0.1286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 223 GLN E 369 ASN E 522 GLN E 836 HIS E 920 HIS E1221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.169567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.143176 restraints weight = 12039.798| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.60 r_work: 0.3746 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8770 Z= 0.122 Angle : 0.594 15.727 12052 Z= 0.312 Chirality : 0.039 0.184 1349 Planarity : 0.005 0.044 1426 Dihedral : 16.150 84.077 1494 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.07 % Allowed : 13.96 % Favored : 84.97 % 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: 1.29 (0.27), residues: 963 helix: 1.53 (0.22), residues: 588 sheet: -1.84 (1.10), residues: 22 loop : -0.01 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 455 TYR 0.011 0.001 TYR E 999 PHE 0.016 0.001 PHE E 229 TRP 0.013 0.001 TRP E 567 HIS 0.008 0.001 HIS E1150 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 ( 8770) covalent geometry : angle 0.59392 / 0.31 (12052) hydrogen bonds : bond 0.03916 / 2.64 ( 471) hydrogen bonds : angle 3.74318 / 2.61 ( 1342) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.317 Fit side-chains REVERT: E 264 TYR cc_start: 0.7002 (m-80) cc_final: 0.6704 (m-80) REVERT: E 295 ASP cc_start: 0.7265 (t0) cc_final: 0.6865 (m-30) REVERT: E 515 GLN cc_start: 0.7610 (tp-100) cc_final: 0.7199 (tp-100) REVERT: E 685 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: E 1116 LYS cc_start: 0.7873 (ttpm) cc_final: 0.7665 (ttpt) outliers start: 9 outliers final: 9 residues processed: 134 average time/residue: 0.6164 time to fit residues: 87.7477 Evaluate side-chains 136 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 237 ASP Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 607 TYR Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 659 HIS Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1211 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 89 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 31 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 369 ASN E 522 GLN E 836 HIS E 920 HIS E1221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.167391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.140957 restraints weight = 11915.009| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.59 r_work: 0.3710 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8770 Z= 0.180 Angle : 0.640 15.888 12052 Z= 0.332 Chirality : 0.042 0.203 1349 Planarity : 0.005 0.045 1426 Dihedral : 16.183 84.187 1494 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.42 % Allowed : 13.73 % Favored : 84.85 % 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: 1.11 (0.27), residues: 963 helix: 1.41 (0.21), residues: 587 sheet: -1.83 (1.08), residues: 22 loop : -0.12 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 854 TYR 0.015 0.002 TYR E 552 PHE 0.030 0.002 PHE E 509 TRP 0.017 0.002 TRP E 567 HIS 0.006 0.001 HIS E 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 8770) covalent geometry : angle 0.64033 / 0.33 (12052) hydrogen bonds : bond 0.04184 / 2.84 ( 471) hydrogen bonds : angle 3.89660 / 2.73 ( 1342) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3592.31 seconds wall clock time: 61 minutes 53.17 seconds (3713.17 seconds total)