Starting phenix.real_space_refine on Wed Sep 17 13:05:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mn8_48416/09_2025/9mn8_48416.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mn8_48416/09_2025/9mn8_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mn8_48416/09_2025/9mn8_48416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mn8_48416/09_2025/9mn8_48416.map" model { file = "/net/cci-nas-00/data/ceres_data/9mn8_48416/09_2025/9mn8_48416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mn8_48416/09_2025/9mn8_48416.cif" } 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-2.0-5805/lib/python3.9/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: 2.28, per 1000 atoms: 0.27 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: 1.03 Conformation dependent library (CDL) restraints added in 319.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.05 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: 1.71 Time building geometry restraints manager: 1.28 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=" N GLN E 238 " pdb=" CA GLN E 238 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.39e+00 bond pdb=" C LEU E 606 " pdb=" N TYR E 607 " ideal model delta sigma weight residual 1.331 1.362 -0.032 1.48e-02 4.57e+03 4.57e+00 bond pdb=" CB ASP E1151 " pdb=" CG ASP E1151 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.87e+00 bond pdb=" N THR E 315 " pdb=" CA THR E 315 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.70e+00 bond pdb=" CG LEU E 487 " pdb=" CD1 LEU E 487 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.58e+00 ... (remaining 8765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 11849 3.28 - 6.56: 178 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=" 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=" C SER E 736 " pdb=" N GLU E 737 " pdb=" CA GLU E 737 " ideal model delta sigma weight residual 122.61 130.60 -7.99 1.56e+00 4.11e-01 2.62e+01 angle pdb=" C ASP E1151 " pdb=" CA ASP E1151 " pdb=" CB ASP E1151 " ideal model delta sigma weight residual 110.04 102.66 7.38 1.51e+00 4.39e-01 2.39e+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: 1023 0.055 - 0.109: 254 0.109 - 0.164: 63 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=" CA THR E 315 " pdb=" N THR E 315 " pdb=" C THR E 315 " pdb=" CB THR E 315 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+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: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.820 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5441 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= 0.257 Angle : 0.998 16.399 12052 Z= 0.535 Chirality : 0.052 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 aren 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 covalent geometry : bond 0.00566 ( 8770) covalent geometry : angle 0.99838 (12052) hydrogen bonds : bond 0.14509 ( 471) hydrogen bonds : angle 6.22087 ( 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 : 0.242 Fit side-chains REVERT: E 372 LYS cc_start: 0.7238 (mtpt) cc_final: 0.6897 (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: 0.6823 time to fit residues: 97.8534 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 : 0.296 ------------------------------------------------------------------------------- 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: 6.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4155 r_free = 0.4155 target = 0.168598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.142230 restraints weight = 12031.422| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.59 r_work: 0.3726 rms_B_bonded: 2.23 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: 0.7476 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8770 Z= 0.163 Angle : 0.638 10.962 12052 Z= 0.330 Chirality : 0.039 0.192 1349 Planarity : 0.006 0.041 1426 Dihedral : 16.417 90.090 1494 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.71 % Allowed : 7.34 % Favored : 91.95 % 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 aren not related in a simple way. whole: 0.05 (0.26), residues: 963 helix: 0.49 (0.21), residues: 587 sheet: -1.62 (1.10), residues: 22 loop : -0.45 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 854 TYR 0.016 0.002 TYR E 552 PHE 0.020 0.002 PHE E 465 TRP 0.011 0.002 TRP E 441 HIS 0.007 0.001 HIS E1175 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8770) covalent geometry : angle 0.63831 (12052) hydrogen bonds : bond 0.04673 ( 471) hydrogen bonds : angle 4.27582 ( 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 139 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.316 Fit side-chains REVERT: E 264 TYR cc_start: 0.7323 (m-80) cc_final: 0.6992 (m-80) REVERT: E 268 MET cc_start: 0.7083 (mmm) cc_final: 0.6882 (mmm) REVERT: E 481 ARG cc_start: 0.6888 (mtm-85) cc_final: 0.6661 (mtm-85) REVERT: E 515 GLN cc_start: 0.7675 (tp-100) cc_final: 0.6961 (tp-100) REVERT: E 1082 TYR cc_start: 0.7524 (m-10) cc_final: 0.6858 (m-80) outliers start: 6 outliers final: 1 residues processed: 134 average time/residue: 0.7141 time to fit residues: 100.8087 Evaluate side-chains 131 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1147 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 81 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 369 ASN E 522 GLN E 524 GLN ** E1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.167126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.140577 restraints weight = 11922.909| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.58 r_work: 0.3692 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8770 Z= 0.180 Angle : 0.630 14.116 12052 Z= 0.325 Chirality : 0.040 0.192 1349 Planarity : 0.005 0.045 1426 Dihedral : 16.271 90.551 1494 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.89 % Allowed : 9.11 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.27), residues: 963 helix: 0.87 (0.21), residues: 588 sheet: -1.77 (1.15), residues: 22 loop : -0.34 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 803 TYR 0.018 0.002 TYR E 552 PHE 0.028 0.002 PHE E 509 TRP 0.012 0.002 TRP E 567 HIS 0.006 0.001 HIS E1175 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 8770) covalent geometry : angle 0.62984 (12052) hydrogen bonds : bond 0.04539 ( 471) hydrogen bonds : angle 4.11013 ( 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 147 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: E 482 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.8013 (ttm) REVERT: E 515 GLN cc_start: 0.7682 (tp-100) cc_final: 0.7010 (tp-100) REVERT: E 685 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: E 1082 TYR cc_start: 0.7642 (m-10) cc_final: 0.6906 (m-80) outliers start: 16 outliers final: 9 residues processed: 138 average time/residue: 0.6624 time to fit residues: 96.6712 Evaluate side-chains 142 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 268 MET 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 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 997 VAL 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: 0.6980 chunk 94 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 chunk 34 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 58 optimal weight: 0.0870 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 223 GLN E 331 GLN E 369 ASN E 522 GLN E 524 GLN E 836 HIS ** E1030 HIS ** 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 = 0.4145 r_free = 0.4145 target = 0.167639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.141159 restraints weight = 12087.859| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.59 r_work: 0.3713 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1726 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= 0.148 Angle : 0.592 15.031 12052 Z= 0.304 Chirality : 0.038 0.175 1349 Planarity : 0.005 0.044 1426 Dihedral : 16.146 88.790 1494 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.78 % Allowed : 10.77 % Favored : 87.46 % 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 aren not related in a simple way. whole: 0.83 (0.27), residues: 963 helix: 1.18 (0.22), residues: 588 sheet: -1.67 (1.16), residues: 22 loop : -0.24 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 803 TYR 0.014 0.002 TYR E 552 PHE 0.022 0.002 PHE E 229 TRP 0.012 0.001 TRP E 567 HIS 0.006 0.001 HIS E1175 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8770) covalent geometry : angle 0.59174 (12052) hydrogen bonds : bond 0.04203 ( 471) hydrogen bonds : angle 3.97294 ( 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 144 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: E 264 TYR cc_start: 0.7250 (m-80) cc_final: 0.6940 (m-80) REVERT: E 482 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.8014 (ttm) REVERT: E 515 GLN cc_start: 0.7627 (tp-100) cc_final: 0.6978 (tp-100) REVERT: E 685 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: E 1082 TYR cc_start: 0.7484 (m-10) cc_final: 0.6764 (m-80) outliers start: 15 outliers final: 7 residues processed: 135 average time/residue: 0.6896 time to fit residues: 98.3623 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 : 0.304 ------------------------------------------------------------------------------- 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 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 997 VAL 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: 0.5980 chunk 76 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 0.0870 chunk 16 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 223 GLN E 369 ASN E 522 GLN E 836 HIS E 926 ASN E1030 HIS E1221 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.166758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.140190 restraints weight = 12063.435| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.60 r_work: 0.3704 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1847 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= 0.167 Angle : 0.602 15.669 12052 Z= 0.310 Chirality : 0.039 0.180 1349 Planarity : 0.005 0.044 1426 Dihedral : 16.136 88.297 1494 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.13 % Allowed : 11.95 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.27), residues: 963 helix: 1.24 (0.22), residues: 588 sheet: -1.74 (1.13), residues: 22 loop : -0.20 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 776 TYR 0.014 0.002 TYR E 552 PHE 0.024 0.002 PHE E 509 TRP 0.011 0.001 TRP E1026 HIS 0.005 0.001 HIS E1175 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8770) covalent geometry : angle 0.60168 (12052) hydrogen bonds : bond 0.04246 ( 471) hydrogen bonds : angle 3.95339 ( 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: 18 poor density : 132 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: E 264 TYR cc_start: 0.7228 (m-80) cc_final: 0.6910 (m-80) REVERT: E 482 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7998 (ttm) REVERT: E 515 GLN cc_start: 0.7616 (tp-100) cc_final: 0.6979 (tp-100) REVERT: E 685 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7677 (mt-10) REVERT: E 1082 TYR cc_start: 0.7581 (m-10) cc_final: 0.6917 (m-80) outliers start: 18 outliers final: 11 residues processed: 140 average time/residue: 0.6365 time to fit residues: 94.2626 Evaluate side-chains 142 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 377 VAL 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 1211 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 69 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4125 r_free = 0.4125 target = 0.165951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.139510 restraints weight = 11874.245| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.59 r_work: 0.3689 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8770 Z= 0.199 Angle : 0.630 16.702 12052 Z= 0.323 Chirality : 0.040 0.187 1349 Planarity : 0.005 0.045 1426 Dihedral : 16.176 88.531 1494 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.55 % Allowed : 11.72 % Favored : 84.73 % 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 aren not related in a simple way. whole: 0.81 (0.27), residues: 963 helix: 1.15 (0.21), residues: 587 sheet: -1.59 (0.87), residues: 32 loop : -0.17 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 776 TYR 0.020 0.002 TYR E 552 PHE 0.020 0.002 PHE E 802 TRP 0.011 0.002 TRP E 707 HIS 0.006 0.001 HIS E 920 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 8770) covalent geometry : angle 0.63038 (12052) hydrogen bonds : bond 0.04452 ( 471) hydrogen bonds : angle 4.03066 ( 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 159 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: E 264 TYR cc_start: 0.7147 (m-80) cc_final: 0.6798 (m-80) REVERT: E 295 ASP cc_start: 0.7313 (t0) cc_final: 0.6917 (m-30) REVERT: E 481 ARG cc_start: 0.6915 (mtm-85) cc_final: 0.6638 (mtt180) REVERT: E 515 GLN cc_start: 0.7642 (tp-100) cc_final: 0.7011 (tp-100) REVERT: E 685 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: E 1082 TYR cc_start: 0.7719 (m-10) cc_final: 0.6974 (m-80) outliers start: 30 outliers final: 15 residues processed: 141 average time/residue: 0.6244 time to fit residues: 93.3301 Evaluate side-chains 143 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 377 VAL Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 488 GLN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 82 optimal weight: 0.1980 chunk 44 optimal weight: 0.0870 chunk 13 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 369 ASN E 522 GLN E 920 HIS E 926 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.167039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.140441 restraints weight = 12049.772| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.61 r_work: 0.3707 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8770 Z= 0.145 Angle : 0.585 15.285 12052 Z= 0.303 Chirality : 0.038 0.169 1349 Planarity : 0.005 0.046 1426 Dihedral : 16.103 87.694 1494 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.49 % Allowed : 13.25 % Favored : 84.26 % 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 aren not related in a simple way. whole: 1.04 (0.27), residues: 963 helix: 1.36 (0.21), residues: 587 sheet: -1.61 (0.87), residues: 32 loop : -0.13 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 776 TYR 0.013 0.001 TYR E 552 PHE 0.017 0.002 PHE E 229 TRP 0.010 0.001 TRP E 707 HIS 0.007 0.001 HIS E 680 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8770) covalent geometry : angle 0.58510 (12052) hydrogen bonds : bond 0.04030 ( 471) hydrogen bonds : angle 3.84980 ( 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 148 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: E 264 TYR cc_start: 0.7050 (m-80) cc_final: 0.6718 (m-80) REVERT: E 295 ASP cc_start: 0.7314 (t0) cc_final: 0.6912 (m-30) REVERT: E 481 ARG cc_start: 0.6932 (mtm-85) cc_final: 0.6692 (mtt180) REVERT: E 482 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.8015 (ttm) REVERT: E 515 GLN cc_start: 0.7634 (tp-100) cc_final: 0.7260 (tp-100) REVERT: E 685 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7491 (mt-10) REVERT: E 1082 TYR cc_start: 0.7489 (m-10) cc_final: 0.6854 (m-80) outliers start: 21 outliers final: 13 residues processed: 136 average time/residue: 0.6545 time to fit residues: 94.2937 Evaluate side-chains 140 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 49 optimal weight: 0.0970 chunk 35 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 369 ASN E 522 GLN E 920 HIS E1221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.166195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.139821 restraints weight = 11900.467| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.60 r_work: 0.3682 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8770 Z= 0.181 Angle : 0.617 14.609 12052 Z= 0.315 Chirality : 0.040 0.180 1349 Planarity : 0.005 0.046 1426 Dihedral : 16.120 87.822 1494 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.49 % Allowed : 13.25 % Favored : 84.26 % 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 aren not related in a simple way. whole: 0.95 (0.27), residues: 963 helix: 1.27 (0.21), residues: 588 sheet: -1.53 (0.86), residues: 32 loop : -0.13 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 455 TYR 0.017 0.002 TYR E 552 PHE 0.029 0.002 PHE E 509 TRP 0.010 0.001 TRP E 707 HIS 0.005 0.001 HIS E 920 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 8770) covalent geometry : angle 0.61683 (12052) hydrogen bonds : bond 0.04276 ( 471) hydrogen bonds : angle 3.94599 ( 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 148 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 264 TYR cc_start: 0.7118 (m-80) cc_final: 0.6795 (m-80) REVERT: E 295 ASP cc_start: 0.7340 (t0) cc_final: 0.6949 (m-30) REVERT: E 481 ARG cc_start: 0.6980 (mtm-85) cc_final: 0.6713 (mtt180) REVERT: E 515 GLN cc_start: 0.7649 (tp-100) cc_final: 0.7285 (tp-100) REVERT: E 685 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: E 1082 TYR cc_start: 0.7626 (m-10) cc_final: 0.6930 (m-80) outliers start: 21 outliers final: 15 residues processed: 137 average time/residue: 0.6179 time to fit residues: 89.7326 Evaluate side-chains 140 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 377 VAL Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 452 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 660 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 56 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.0370 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 369 ASN E 522 GLN E 920 HIS E1221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.167500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.140976 restraints weight = 11993.263| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.62 r_work: 0.3715 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8770 Z= 0.139 Angle : 0.599 15.930 12052 Z= 0.307 Chirality : 0.038 0.166 1349 Planarity : 0.005 0.047 1426 Dihedral : 16.068 88.169 1494 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.13 % Allowed : 13.02 % 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 aren not related in a simple way. whole: 1.17 (0.27), residues: 963 helix: 1.46 (0.21), residues: 587 sheet: -1.45 (0.87), residues: 32 loop : -0.07 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 455 TYR 0.011 0.001 TYR E 552 PHE 0.015 0.001 PHE E 229 TRP 0.010 0.001 TRP E 707 HIS 0.006 0.001 HIS E 920 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8770) covalent geometry : angle 0.59869 (12052) hydrogen bonds : bond 0.03996 ( 471) hydrogen bonds : angle 3.81599 ( 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 142 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: E 264 TYR cc_start: 0.7041 (m-80) cc_final: 0.6690 (m-80) REVERT: E 295 ASP cc_start: 0.7323 (t0) cc_final: 0.6936 (m-30) REVERT: E 481 ARG cc_start: 0.6921 (mtm-85) cc_final: 0.6720 (mtt180) REVERT: E 482 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7859 (ttm) REVERT: E 515 GLN cc_start: 0.7645 (tp-100) cc_final: 0.7259 (tp-100) REVERT: E 685 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: E 1082 TYR cc_start: 0.7429 (m-10) cc_final: 0.6827 (m-10) outliers start: 18 outliers final: 11 residues processed: 136 average time/residue: 0.6048 time to fit residues: 87.1753 Evaluate side-chains 139 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 452 THR 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 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 91 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 70 optimal weight: 0.0970 chunk 93 optimal weight: 0.4980 chunk 17 optimal weight: 0.4980 chunk 85 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 46 optimal weight: 0.3980 chunk 42 optimal weight: 0.0970 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 369 ASN E 522 GLN E 920 HIS E1221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.167768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141384 restraints weight = 11949.657| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.60 r_work: 0.3723 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8770 Z= 0.133 Angle : 0.607 15.190 12052 Z= 0.304 Chirality : 0.038 0.157 1349 Planarity : 0.005 0.046 1426 Dihedral : 15.993 86.882 1494 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.78 % Allowed : 13.49 % Favored : 84.73 % 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 aren not related in a simple way. whole: 1.21 (0.27), residues: 963 helix: 1.46 (0.21), residues: 589 sheet: -1.43 (0.87), residues: 32 loop : -0.01 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 455 TYR 0.010 0.001 TYR E 552 PHE 0.029 0.002 PHE E 509 TRP 0.009 0.001 TRP E 271 HIS 0.006 0.001 HIS E 920 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8770) covalent geometry : angle 0.60672 (12052) hydrogen bonds : bond 0.03874 ( 471) hydrogen bonds : angle 3.78002 ( 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 137 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.217 Fit side-chains REVERT: E 264 TYR cc_start: 0.7045 (m-80) cc_final: 0.6684 (m-80) REVERT: E 286 MET cc_start: 0.6482 (mtt) cc_final: 0.6145 (mtt) REVERT: E 481 ARG cc_start: 0.6920 (mtm-85) cc_final: 0.6706 (mtt180) REVERT: E 515 GLN cc_start: 0.7594 (tp-100) cc_final: 0.7203 (tp-100) REVERT: E 685 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7451 (mt-10) REVERT: E 1003 ARG cc_start: 0.6302 (mmp-170) cc_final: 0.3629 (tpt170) REVERT: E 1082 TYR cc_start: 0.7370 (m-10) cc_final: 0.6790 (m-10) REVERT: E 1116 LYS cc_start: 0.7910 (ttpm) cc_final: 0.7702 (ttpt) outliers start: 15 outliers final: 12 residues processed: 130 average time/residue: 0.6491 time to fit residues: 89.3460 Evaluate side-chains 130 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 377 VAL Chi-restraints excluded: chain E residue 452 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 660 SER 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: 0.9980 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 369 ASN E 522 GLN E 920 HIS E1221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.167557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.141264 restraints weight = 11844.224| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.59 r_work: 0.3716 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8770 Z= 0.153 Angle : 0.623 14.978 12052 Z= 0.314 Chirality : 0.039 0.162 1349 Planarity : 0.005 0.047 1426 Dihedral : 15.946 85.784 1494 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.13 % Allowed : 13.37 % Favored : 84.50 % 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 aren not related in a simple way. whole: 1.17 (0.27), residues: 963 helix: 1.45 (0.21), residues: 589 sheet: -1.50 (0.87), residues: 32 loop : -0.05 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 854 TYR 0.013 0.002 TYR E 552 PHE 0.016 0.001 PHE E 802 TRP 0.010 0.001 TRP E 707 HIS 0.007 0.001 HIS E 920 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8770) covalent geometry : angle 0.62314 (12052) hydrogen bonds : bond 0.03994 ( 471) hydrogen bonds : angle 3.81666 ( 1342) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3754.50 seconds wall clock time: 64 minutes 38.44 seconds (3878.44 seconds total)