Starting phenix.real_space_refine on Wed Feb 14 16:23:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi3_23838/02_2024/7mi3_23838_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi3_23838/02_2024/7mi3_23838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi3_23838/02_2024/7mi3_23838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi3_23838/02_2024/7mi3_23838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi3_23838/02_2024/7mi3_23838_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi3_23838/02_2024/7mi3_23838_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 8 Type Number sf(0) Gaussians Br 2 7.06 5 P 3 5.49 5 Mg 1 5.21 5 S 49 5.16 5 Cl 2 4.86 5 C 6197 2.51 5 N 1624 2.21 5 O 1804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 2112": "OE1" <-> "OE2" Residue "A GLU 2124": "OE1" <-> "OE2" Residue "A PHE 2368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2520": "OE1" <-> "OE2" Residue "A ARG 2528": "NH1" <-> "NH2" Residue "A ARG 2552": "NH1" <-> "NH2" Residue "A TYR 2650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2939": "OE1" <-> "OE2" Residue "A GLU 2947": "OE1" <-> "OE2" Residue "A ARG 2974": "NH1" <-> "NH2" Residue "A ARG 2997": "NH1" <-> "NH2" Residue "A TYR 3364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3365": "NH1" <-> "NH2" Residue "A TYR 3389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3434": "OE1" <-> "OE2" Residue "A ARG 3445": "NH1" <-> "NH2" Residue "A PHE 3457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3464": "NH1" <-> "NH2" Residue "A GLU 3469": "OE1" <-> "OE2" Residue "A PHE 3470": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9682 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1196, 9682 Unusual residues: {' MG': 1, 'ATP': 1, 'ZG7': 2} Classifications: {'peptide': 1192, 'undetermined': 4} Link IDs: {'PTRANS': 39, 'TRANS': 1152, None: 4} Not linked: pdbres="GLU A3523 " pdbres="ZG7 A4201 " Not linked: pdbres="ZG7 A4201 " pdbres="ZG7 A4202 " Not linked: pdbres="ZG7 A4202 " pdbres="ATP A4203 " Not linked: pdbres="ATP A4203 " pdbres=" MG A4204 " Chain breaks: 1 Time building chain proxies: 5.72, per 1000 atoms: 0.59 Number of scatterers: 9682 At special positions: 0 Unit cell: (89.096, 137.27, 103.082, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Br 2 34.99 Cl 2 17.00 S 49 16.00 P 3 15.00 Mg 1 11.99 O 1804 8.00 N 1624 7.00 C 6197 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 - 3.50 Amino acid : False - 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: 3.98 Conformation dependent library (CDL) restraints added in 1.8 seconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 8 sheets defined 51.5% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 2032 through 2045 Processing helix chain 'A' and resid 2051 through 2065 removed outlier: 3.928A pdb=" N LYS A2065 " --> pdb=" O TYR A2061 " (cutoff:3.500A) Processing helix chain 'A' and resid 2080 through 2095 Processing helix chain 'A' and resid 2106 through 2108 No H-bonds generated for 'chain 'A' and resid 2106 through 2108' Processing helix chain 'A' and resid 2111 through 2114 No H-bonds generated for 'chain 'A' and resid 2111 through 2114' Processing helix chain 'A' and resid 2129 through 2139 Processing helix chain 'A' and resid 2160 through 2170 removed outlier: 3.564A pdb=" N MET A2166 " --> pdb=" O TYR A2162 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N SER A2168 " --> pdb=" O GLU A2164 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A2169 " --> pdb=" O ALA A2165 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A2170 " --> pdb=" O MET A2166 " (cutoff:3.500A) Processing helix chain 'A' and resid 2204 through 2209 removed outlier: 3.689A pdb=" N ARG A2209 " --> pdb=" O ALA A2205 " (cutoff:3.500A) Processing helix chain 'A' and resid 2222 through 2240 removed outlier: 3.803A pdb=" N ALA A2236 " --> pdb=" O LYS A2232 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN A2239 " --> pdb=" O GLU A2235 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS A2240 " --> pdb=" O ALA A2236 " (cutoff:3.500A) Processing helix chain 'A' and resid 2243 through 2257 removed outlier: 4.074A pdb=" N LYS A2248 " --> pdb=" O PHE A2244 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP A2255 " --> pdb=" O ASP A2251 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N SER A2256 " --> pdb=" O LEU A2252 " (cutoff:3.500A) Processing helix chain 'A' and resid 2260 through 2267 Processing helix chain 'A' and resid 2280 through 2282 No H-bonds generated for 'chain 'A' and resid 2280 through 2282' Processing helix chain 'A' and resid 2284 through 2304 removed outlier: 3.805A pdb=" N TYR A2298 " --> pdb=" O LEU A2294 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG A2299 " --> pdb=" O ILE A2295 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLN A2300 " --> pdb=" O SER A2296 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TRP A2301 " --> pdb=" O SER A2297 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN A2303 " --> pdb=" O ARG A2299 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASN A2304 " --> pdb=" O GLN A2300 " (cutoff:3.500A) Processing helix chain 'A' and resid 2307 through 2327 Processing helix chain 'A' and resid 2333 through 2345 removed outlier: 3.857A pdb=" N GLN A2340 " --> pdb=" O ARG A2336 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR A2341 " --> pdb=" O ALA A2337 " (cutoff:3.500A) Processing helix chain 'A' and resid 2382 through 2386 Processing helix chain 'A' and resid 2395 through 2409 Processing helix chain 'A' and resid 2424 through 2434 removed outlier: 3.842A pdb=" N MET A2428 " --> pdb=" O LYS A2424 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2451 through 2461 removed outlier: 4.234A pdb=" N ARG A2460 " --> pdb=" O SER A2456 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N HIS A2461 " --> pdb=" O ALA A2457 " (cutoff:3.500A) Processing helix chain 'A' and resid 2501 through 2512 Processing helix chain 'A' and resid 2548 through 2553 removed outlier: 4.521A pdb=" N HIS A2553 " --> pdb=" O ARG A2549 " (cutoff:3.500A) Processing helix chain 'A' and resid 2565 through 2581 removed outlier: 4.569A pdb=" N LEU A2581 " --> pdb=" O ALA A2577 " (cutoff:3.500A) Processing helix chain 'A' and resid 2583 through 2606 removed outlier: 4.799A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A2590 " --> pdb=" O SER A2587 " (cutoff:3.500A) Proline residue: A2591 - end of helix Processing helix chain 'A' and resid 2619 through 2634 removed outlier: 3.525A pdb=" N ARG A2624 " --> pdb=" O GLU A2621 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A2629 " --> pdb=" O VAL A2626 " (cutoff:3.500A) Processing helix chain 'A' and resid 2641 through 2659 removed outlier: 4.906A pdb=" N ASP A2658 " --> pdb=" O ARG A2654 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ARG A2659 " --> pdb=" O ILE A2655 " (cutoff:3.500A) Processing helix chain 'A' and resid 2663 through 2680 Processing helix chain 'A' and resid 2709 through 2726 Processing helix chain 'A' and resid 2736 through 2750 Processing helix chain 'A' and resid 2766 through 2777 removed outlier: 3.526A pdb=" N ARG A2771 " --> pdb=" O THR A2767 " (cutoff:3.500A) Processing helix chain 'A' and resid 2792 through 2808 Processing helix chain 'A' and resid 2819 through 2821 No H-bonds generated for 'chain 'A' and resid 2819 through 2821' Processing helix chain 'A' and resid 2825 through 2836 Processing helix chain 'A' and resid 2841 through 2844 Processing helix chain 'A' and resid 2846 through 2863 removed outlier: 3.557A pdb=" N LYS A2851 " --> pdb=" O GLU A2848 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A2860 " --> pdb=" O ARG A2857 " (cutoff:3.500A) Processing helix chain 'A' and resid 2870 through 2884 Processing helix chain 'A' and resid 2897 through 2904 Processing helix chain 'A' and resid 2906 through 2909 No H-bonds generated for 'chain 'A' and resid 2906 through 2909' Processing helix chain 'A' and resid 2922 through 2935 removed outlier: 3.994A pdb=" N VAL A2935 " --> pdb=" O ASN A2931 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2944 No H-bonds generated for 'chain 'A' and resid 2942 through 2944' Processing helix chain 'A' and resid 2961 through 2979 Processing helix chain 'A' and resid 2990 through 3010 removed outlier: 3.600A pdb=" N VAL A3000 " --> pdb=" O LEU A2996 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A3001 " --> pdb=" O ARG A2997 " (cutoff:3.500A) Processing helix chain 'A' and resid 3317 through 3336 removed outlier: 3.789A pdb=" N ILE A3321 " --> pdb=" O GLN A3318 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR A3333 " --> pdb=" O TYR A3330 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N PHE A3334 " --> pdb=" O GLU A3331 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLY A3335 " --> pdb=" O THR A3332 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N HIS A3336 " --> pdb=" O TYR A3333 " (cutoff:3.500A) Processing helix chain 'A' and resid 3339 through 3355 removed outlier: 3.746A pdb=" N LEU A3352 " --> pdb=" O ILE A3348 " (cutoff:3.500A) Processing helix chain 'A' and resid 3366 through 3370 Processing helix chain 'A' and resid 3373 through 3381 removed outlier: 4.105A pdb=" N LEU A3380 " --> pdb=" O LYS A3376 " (cutoff:3.500A) Processing helix chain 'A' and resid 3388 through 3399 Processing helix chain 'A' and resid 3414 through 3425 removed outlier: 4.237A pdb=" N SER A3419 " --> pdb=" O ILE A3415 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASN A3424 " --> pdb=" O ASN A3420 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LYS A3425 " --> pdb=" O TYR A3421 " (cutoff:3.500A) Processing helix chain 'A' and resid 3436 through 3446 Processing helix chain 'A' and resid 3460 through 3466 removed outlier: 4.394A pdb=" N ARG A3464 " --> pdb=" O ILE A3461 " (cutoff:3.500A) Processing helix chain 'A' and resid 3507 through 3510 No H-bonds generated for 'chain 'A' and resid 3507 through 3510' Processing sheet with id= A, first strand: chain 'A' and resid 2211 through 2215 removed outlier: 8.827A pdb=" N LEU A2070 " --> pdb=" O PHE A2190 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE A2192 " --> pdb=" O LEU A2070 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU A2072 " --> pdb=" O ILE A2192 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE A2194 " --> pdb=" O LEU A2072 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLY A2074 " --> pdb=" O PHE A2194 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR A2196 " --> pdb=" O GLY A2074 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ARG A2191 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE A2150 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU A2193 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A2152 " --> pdb=" O LEU A2193 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLU A2195 " --> pdb=" O VAL A2152 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA A2098 " --> pdb=" O ARG A2149 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N TRP A2151 " --> pdb=" O ALA A2098 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A2100 " --> pdb=" O TRP A2151 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL A2153 " --> pdb=" O VAL A2100 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TYR A2102 " --> pdb=" O VAL A2153 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 2175 through 2177 Processing sheet with id= C, first strand: chain 'A' and resid 2358 through 2361 removed outlier: 3.589A pdb=" N THR A2358 " --> pdb=" O PHE A2371 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 2554 through 2559 removed outlier: 6.762A pdb=" N GLY A2413 " --> pdb=" O ALA A2555 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU A2557 " --> pdb=" O GLY A2413 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE A2415 " --> pdb=" O LEU A2557 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU A2559 " --> pdb=" O ILE A2415 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N CYS A2417 " --> pdb=" O LEU A2559 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A2414 " --> pdb=" O ILE A2531 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU A2482 " --> pdb=" O HIS A2530 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL A2532 " --> pdb=" O LEU A2482 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU A2484 " --> pdb=" O VAL A2532 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ALA A2534 " --> pdb=" O LEU A2484 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N CYS A2486 " --> pdb=" O ALA A2534 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 2465 through 2467 Processing sheet with id= F, first strand: chain 'A' and resid 2780 through 2783 removed outlier: 6.863A pdb=" N MET A2756 " --> pdb=" O PHE A2889 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ILE A2891 " --> pdb=" O MET A2756 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A2758 " --> pdb=" O ILE A2891 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 3514 through 3517 removed outlier: 7.538A pdb=" N LEU A3494 " --> pdb=" O PRO A3405 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N LEU A3407 " --> pdb=" O LEU A3494 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE A3496 " --> pdb=" O LEU A3407 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 3478 through 3481 removed outlier: 3.591A pdb=" N HIS A3484 " --> pdb=" O ILE A3481 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1110 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.41 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.29: 1587 1.29 - 1.46: 3126 1.46 - 1.62: 5093 1.62 - 1.78: 18 1.78 - 1.94: 65 Bond restraints: 9889 Sorted by residual: bond pdb=" C14 ZG7 A4202 " pdb=" N15 ZG7 A4202 " ideal model delta sigma weight residual 1.328 1.531 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C14 ZG7 A4201 " pdb=" N15 ZG7 A4201 " ideal model delta sigma weight residual 1.328 1.520 -0.192 2.00e-02 2.50e+03 9.21e+01 bond pdb=" C5 ATP A4203 " pdb=" C6 ATP A4203 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.87e+01 bond pdb=" C26 ZG7 A4202 " pdb=" O27 ZG7 A4202 " ideal model delta sigma weight residual 1.305 1.166 0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C16 ZG7 A4202 " pdb=" N15 ZG7 A4202 " ideal model delta sigma weight residual 1.312 1.450 -0.138 2.00e-02 2.50e+03 4.77e+01 ... (remaining 9884 not shown) Histogram of bond angle deviations from ideal: 59.63 - 83.58: 6 83.58 - 107.53: 456 107.53 - 131.48: 12908 131.48 - 155.43: 31 155.43 - 179.38: 2 Bond angle restraints: 13403 Sorted by residual: angle pdb=" PA ATP A4203 " pdb=" O3A ATP A4203 " pdb=" PB ATP A4203 " ideal model delta sigma weight residual 136.83 121.50 15.33 1.00e+00 1.00e+00 2.35e+02 angle pdb=" PB ATP A4203 " pdb=" O3B ATP A4203 " pdb=" PG ATP A4203 " ideal model delta sigma weight residual 139.87 128.63 11.24 1.00e+00 1.00e+00 1.26e+02 angle pdb=" C5 ATP A4203 " pdb=" C4 ATP A4203 " pdb=" N3 ATP A4203 " ideal model delta sigma weight residual 126.80 118.41 8.39 1.00e+00 1.00e+00 7.04e+01 angle pdb=" N TYR A2115 " pdb=" CA TYR A2115 " pdb=" C TYR A2115 " ideal model delta sigma weight residual 110.17 99.76 10.41 1.51e+00 4.39e-01 4.75e+01 angle pdb=" N3 ATP A4203 " pdb=" C4 ATP A4203 " pdb=" N9 ATP A4203 " ideal model delta sigma weight residual 127.04 134.67 -7.63 1.15e+00 7.59e-01 4.41e+01 ... (remaining 13398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 5544 17.88 - 35.76: 309 35.76 - 53.64: 55 53.64 - 71.53: 26 71.53 - 89.41: 14 Dihedral angle restraints: 5948 sinusoidal: 2446 harmonic: 3502 Sorted by residual: dihedral pdb=" CA ASP A2105 " pdb=" C ASP A2105 " pdb=" N THR A2106 " pdb=" CA THR A2106 " ideal model delta harmonic sigma weight residual -180.00 -153.51 -26.49 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA GLN A2639 " pdb=" C GLN A2639 " pdb=" N THR A2640 " pdb=" CA THR A2640 " ideal model delta harmonic sigma weight residual 180.00 154.29 25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA GLU A2810 " pdb=" C GLU A2810 " pdb=" N SER A2811 " pdb=" CA SER A2811 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 5945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1157 0.085 - 0.169: 315 0.169 - 0.254: 37 0.254 - 0.338: 7 0.338 - 0.423: 4 Chirality restraints: 1520 Sorted by residual: chirality pdb=" CB ILE A2226 " pdb=" CA ILE A2226 " pdb=" CG1 ILE A2226 " pdb=" CG2 ILE A2226 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CB ILE A2141 " pdb=" CA ILE A2141 " pdb=" CG1 ILE A2141 " pdb=" CG2 ILE A2141 " both_signs ideal model delta sigma weight residual False 2.64 3.00 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA LEU A2366 " pdb=" N LEU A2366 " pdb=" C LEU A2366 " pdb=" CB LEU A2366 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 1517 not shown) Planarity restraints: 1686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 ZG7 A4202 " -0.014 2.00e-02 2.50e+03 2.73e-02 2.61e+01 pdb=" C11 ZG7 A4202 " 0.067 2.00e-02 2.50e+03 pdb=" C14 ZG7 A4202 " -0.009 2.00e-02 2.50e+03 pdb=" C16 ZG7 A4202 " -0.015 2.00e-02 2.50e+03 pdb=" C17 ZG7 A4202 " -0.012 2.00e-02 2.50e+03 pdb=" C26 ZG7 A4202 " 0.002 2.00e-02 2.50e+03 pdb=" C28 ZG7 A4202 " -0.018 2.00e-02 2.50e+03 pdb=" C29 ZG7 A4202 " 0.003 2.00e-02 2.50e+03 pdb=" N12 ZG7 A4202 " -0.005 2.00e-02 2.50e+03 pdb=" N13 ZG7 A4202 " -0.029 2.00e-02 2.50e+03 pdb=" N15 ZG7 A4202 " -0.009 2.00e-02 2.50e+03 pdb=" N30 ZG7 A4202 " 0.010 2.00e-02 2.50e+03 pdb=" O18 ZG7 A4202 " 0.056 2.00e-02 2.50e+03 pdb=" O27 ZG7 A4202 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A2728 " -0.018 2.00e-02 2.50e+03 3.57e-02 1.28e+01 pdb=" C LEU A2728 " 0.062 2.00e-02 2.50e+03 pdb=" O LEU A2728 " -0.023 2.00e-02 2.50e+03 pdb=" N GLU A2729 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 ZG7 A4202 " -0.003 2.00e-02 2.50e+03 2.42e-02 1.17e+01 pdb=" C03 ZG7 A4202 " -0.003 2.00e-02 2.50e+03 pdb=" C04 ZG7 A4202 " -0.006 2.00e-02 2.50e+03 pdb=" C05 ZG7 A4202 " 0.059 2.00e-02 2.50e+03 pdb=" C06 ZG7 A4202 " -0.002 2.00e-02 2.50e+03 pdb=" C07 ZG7 A4202 " -0.005 2.00e-02 2.50e+03 pdb=" C08 ZG7 A4202 " -0.034 2.00e-02 2.50e+03 pdb="CL01 ZG7 A4202 " -0.004 2.00e-02 2.50e+03 ... (remaining 1683 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 68 2.56 - 3.15: 8279 3.15 - 3.73: 14789 3.73 - 4.32: 20691 4.32 - 4.90: 33976 Nonbonded interactions: 77803 Sorted by model distance: nonbonded pdb=" O3G ATP A4203 " pdb="MG MG A4204 " model vdw 1.978 2.170 nonbonded pdb=" OG1 THR A2081 " pdb="MG MG A4204 " model vdw 2.003 2.170 nonbonded pdb=" O1B ATP A4203 " pdb="MG MG A4204 " model vdw 2.038 2.170 nonbonded pdb=" OD1 ASN A2832 " pdb=" OG SER A2905 " model vdw 2.263 2.440 nonbonded pdb=" NH1 ARG A2763 " pdb=" O SER A3511 " model vdw 2.298 2.520 ... (remaining 77798 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.520 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: 11.120 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 30.230 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 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 : 0.012 0.203 9889 Z= 0.793 Angle : 1.474 19.050 13403 Z= 0.824 Chirality : 0.078 0.423 1520 Planarity : 0.008 0.054 1686 Dihedral : 13.199 89.407 3676 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.82 % Favored : 92.85 % Rotamer: Outliers : 1.94 % Allowed : 4.52 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.22), residues: 1188 helix: -0.54 (0.19), residues: 584 sheet: -1.71 (0.43), residues: 125 loop : -1.75 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP A3379 HIS 0.025 0.003 HIS A3517 PHE 0.050 0.004 PHE A2266 TYR 0.057 0.006 TYR A3330 ARG 0.036 0.004 ARG A2830 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 222 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2105 ASP cc_start: 0.8023 (m-30) cc_final: 0.7510 (m-30) REVERT: A 2180 ASN cc_start: 0.8596 (t0) cc_final: 0.8357 (t0) REVERT: A 2202 THR cc_start: 0.8417 (m) cc_final: 0.8216 (t) REVERT: A 2218 ASP cc_start: 0.7822 (m-30) cc_final: 0.7612 (m-30) REVERT: A 2411 LYS cc_start: 0.9360 (mtmm) cc_final: 0.9124 (mmmt) REVERT: A 2707 VAL cc_start: 0.9216 (t) cc_final: 0.8640 (m) REVERT: A 2792 LEU cc_start: 0.8765 (tp) cc_final: 0.8417 (tp) REVERT: A 2849 TYR cc_start: 0.9283 (t80) cc_final: 0.9021 (t80) REVERT: A 2960 THR cc_start: 0.7673 (OUTLIER) cc_final: 0.6231 (p) REVERT: A 3344 ASP cc_start: 0.8986 (m-30) cc_final: 0.8674 (m-30) REVERT: A 3358 VAL cc_start: 0.9000 (t) cc_final: 0.8722 (p) REVERT: A 3369 TYR cc_start: 0.8303 (t80) cc_final: 0.7940 (t80) REVERT: A 3394 MET cc_start: 0.9073 (tpt) cc_final: 0.8458 (tmm) REVERT: A 3438 LYS cc_start: 0.8734 (ttpp) cc_final: 0.8342 (tptp) REVERT: A 3486 VAL cc_start: 0.8615 (t) cc_final: 0.8397 (m) outliers start: 21 outliers final: 7 residues processed: 239 average time/residue: 0.2652 time to fit residues: 83.6667 Evaluate side-chains 117 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2131 THR Chi-restraints excluded: chain A residue 2295 ILE Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2702 LEU Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2958 ILE Chi-restraints excluded: chain A residue 2960 THR Chi-restraints excluded: chain A residue 3385 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 0.0020 chunk 30 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2099 ASN A2274 HIS ** A2300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2363 ASN A2481 ASN A2508 GLN A2536 ASN A2569 GLN A2854 ASN ** A3399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3471 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9889 Z= 0.174 Angle : 0.656 8.834 13403 Z= 0.338 Chirality : 0.044 0.174 1520 Planarity : 0.004 0.040 1686 Dihedral : 8.402 88.820 1351 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.95 % Favored : 96.89 % Rotamer: Outliers : 2.31 % Allowed : 11.25 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.24), residues: 1188 helix: 0.86 (0.21), residues: 599 sheet: -1.11 (0.43), residues: 140 loop : -1.08 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A2084 HIS 0.006 0.001 HIS A3517 PHE 0.013 0.001 PHE A2992 TYR 0.016 0.001 TYR A2571 ARG 0.009 0.001 ARG A2646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2105 ASP cc_start: 0.8025 (m-30) cc_final: 0.7697 (m-30) REVERT: A 2411 LYS cc_start: 0.9335 (mtmm) cc_final: 0.9110 (mmmt) REVERT: A 2590 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8575 (tm-30) REVERT: A 2849 TYR cc_start: 0.9319 (t80) cc_final: 0.9106 (t80) REVERT: A 2904 SER cc_start: 0.9365 (m) cc_final: 0.8986 (p) REVERT: A 3377 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8484 (ptp) REVERT: A 3438 LYS cc_start: 0.8653 (ttpp) cc_final: 0.8434 (tptp) REVERT: A 3480 GLU cc_start: 0.7458 (mp0) cc_final: 0.7207 (pm20) outliers start: 25 outliers final: 15 residues processed: 169 average time/residue: 0.2322 time to fit residues: 54.4924 Evaluate side-chains 133 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2148 SER Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2509 LEU Chi-restraints excluded: chain A residue 2590 GLU Chi-restraints excluded: chain A residue 2728 LEU Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2866 LEU Chi-restraints excluded: chain A residue 2872 GLU Chi-restraints excluded: chain A residue 2942 ASP Chi-restraints excluded: chain A residue 3002 LEU Chi-restraints excluded: chain A residue 3320 LEU Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3377 MET Chi-restraints excluded: chain A residue 3425 LYS Chi-restraints excluded: chain A residue 3459 ASP Chi-restraints excluded: chain A residue 3469 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2300 GLN A2500 GLN A2598 HIS A3471 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 9889 Z= 0.298 Angle : 0.631 8.106 13403 Z= 0.329 Chirality : 0.044 0.154 1520 Planarity : 0.005 0.045 1686 Dihedral : 8.203 89.962 1341 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.62 % Favored : 96.30 % Rotamer: Outliers : 4.06 % Allowed : 12.92 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.25), residues: 1188 helix: 1.16 (0.22), residues: 589 sheet: -0.78 (0.43), residues: 141 loop : -0.97 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A2084 HIS 0.008 0.001 HIS A3517 PHE 0.014 0.002 PHE A2992 TYR 0.020 0.002 TYR A3360 ARG 0.006 0.001 ARG A2646 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 107 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2105 ASP cc_start: 0.8144 (m-30) cc_final: 0.7940 (m-30) REVERT: A 2209 ARG cc_start: 0.7833 (mtm-85) cc_final: 0.7438 (mtm-85) REVERT: A 2305 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8555 (tp) REVERT: A 2411 LYS cc_start: 0.9383 (mtmm) cc_final: 0.9157 (mmmt) REVERT: A 2623 THR cc_start: 0.9490 (OUTLIER) cc_final: 0.9089 (p) REVERT: A 2849 TYR cc_start: 0.9394 (t80) cc_final: 0.9183 (t80) REVERT: A 3340 ARG cc_start: 0.8418 (tpp-160) cc_final: 0.8194 (tpp80) REVERT: A 3438 LYS cc_start: 0.8667 (ttpp) cc_final: 0.8447 (tptp) outliers start: 44 outliers final: 28 residues processed: 142 average time/residue: 0.2398 time to fit residues: 47.1774 Evaluate side-chains 124 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 94 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2127 ASP Chi-restraints excluded: chain A residue 2139 ASP Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2237 LEU Chi-restraints excluded: chain A residue 2270 ASN Chi-restraints excluded: chain A residue 2300 GLN Chi-restraints excluded: chain A residue 2305 LEU Chi-restraints excluded: chain A residue 2396 ASP Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2509 LEU Chi-restraints excluded: chain A residue 2623 THR Chi-restraints excluded: chain A residue 2658 ASP Chi-restraints excluded: chain A residue 2711 ASP Chi-restraints excluded: chain A residue 2728 LEU Chi-restraints excluded: chain A residue 2769 LEU Chi-restraints excluded: chain A residue 2825 THR Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2866 LEU Chi-restraints excluded: chain A residue 2872 GLU Chi-restraints excluded: chain A residue 2942 ASP Chi-restraints excluded: chain A residue 2984 VAL Chi-restraints excluded: chain A residue 3002 LEU Chi-restraints excluded: chain A residue 3320 LEU Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3332 THR Chi-restraints excluded: chain A residue 3338 ASN Chi-restraints excluded: chain A residue 3425 LYS Chi-restraints excluded: chain A residue 3450 VAL Chi-restraints excluded: chain A residue 3459 ASP Chi-restraints excluded: chain A residue 3469 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2300 GLN ** A3399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3471 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9889 Z= 0.173 Angle : 0.572 8.914 13403 Z= 0.293 Chirality : 0.042 0.181 1520 Planarity : 0.004 0.039 1686 Dihedral : 7.934 87.605 1341 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.32 % Allowed : 13.93 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1188 helix: 1.30 (0.22), residues: 589 sheet: -0.48 (0.44), residues: 144 loop : -0.76 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A2084 HIS 0.006 0.001 HIS A3517 PHE 0.019 0.001 PHE A2992 TYR 0.013 0.001 TYR A2571 ARG 0.006 0.000 ARG A2299 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 106 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2209 ARG cc_start: 0.7809 (mtm-85) cc_final: 0.7411 (mtm-85) REVERT: A 2305 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8578 (tp) REVERT: A 2411 LYS cc_start: 0.9376 (mtmm) cc_final: 0.9161 (mmmt) REVERT: A 2623 THR cc_start: 0.9422 (OUTLIER) cc_final: 0.9061 (p) REVERT: A 2679 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9140 (ttpp) REVERT: A 2819 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8201 (tm-30) REVERT: A 2849 TYR cc_start: 0.9387 (t80) cc_final: 0.9187 (t80) REVERT: A 3340 ARG cc_start: 0.8334 (tpp-160) cc_final: 0.8061 (tpp80) REVERT: A 3469 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7394 (mp0) outliers start: 36 outliers final: 23 residues processed: 134 average time/residue: 0.2462 time to fit residues: 45.8735 Evaluate side-chains 117 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2127 ASP Chi-restraints excluded: chain A residue 2139 ASP Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2305 LEU Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2396 ASP Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2509 LEU Chi-restraints excluded: chain A residue 2623 THR Chi-restraints excluded: chain A residue 2658 ASP Chi-restraints excluded: chain A residue 2679 LYS Chi-restraints excluded: chain A residue 2692 THR Chi-restraints excluded: chain A residue 2711 ASP Chi-restraints excluded: chain A residue 2728 LEU Chi-restraints excluded: chain A residue 2769 LEU Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2866 LEU Chi-restraints excluded: chain A residue 2872 GLU Chi-restraints excluded: chain A residue 2942 ASP Chi-restraints excluded: chain A residue 2984 VAL Chi-restraints excluded: chain A residue 3002 LEU Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3353 LEU Chi-restraints excluded: chain A residue 3425 LYS Chi-restraints excluded: chain A residue 3459 ASP Chi-restraints excluded: chain A residue 3469 GLU Chi-restraints excluded: chain A residue 3491 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9889 Z= 0.412 Angle : 0.670 7.938 13403 Z= 0.347 Chirality : 0.045 0.171 1520 Planarity : 0.005 0.057 1686 Dihedral : 8.298 87.938 1339 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.52 % Allowed : 13.93 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.24), residues: 1188 helix: 1.14 (0.22), residues: 590 sheet: -0.37 (0.43), residues: 140 loop : -0.93 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A2084 HIS 0.010 0.001 HIS A3517 PHE 0.037 0.002 PHE A2371 TYR 0.017 0.002 TYR A2571 ARG 0.004 0.001 ARG A2209 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 90 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2209 ARG cc_start: 0.7784 (mtm-85) cc_final: 0.7503 (mtm-85) REVERT: A 2305 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8572 (tp) REVERT: A 2371 PHE cc_start: 0.7694 (t80) cc_final: 0.7494 (t80) REVERT: A 2428 MET cc_start: 0.8920 (tmm) cc_final: 0.8695 (tmm) REVERT: A 2623 THR cc_start: 0.9453 (OUTLIER) cc_final: 0.9079 (p) REVERT: A 2819 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8312 (tm-30) REVERT: A 2849 TYR cc_start: 0.9465 (t80) cc_final: 0.9240 (t80) REVERT: A 3330 TYR cc_start: 0.9302 (OUTLIER) cc_final: 0.8604 (t80) outliers start: 49 outliers final: 31 residues processed: 133 average time/residue: 0.2166 time to fit residues: 40.8979 Evaluate side-chains 117 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 83 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2139 ASP Chi-restraints excluded: chain A residue 2142 THR Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2270 ASN Chi-restraints excluded: chain A residue 2305 LEU Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2396 ASP Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2509 LEU Chi-restraints excluded: chain A residue 2526 ILE Chi-restraints excluded: chain A residue 2623 THR Chi-restraints excluded: chain A residue 2658 ASP Chi-restraints excluded: chain A residue 2692 THR Chi-restraints excluded: chain A residue 2694 LEU Chi-restraints excluded: chain A residue 2728 LEU Chi-restraints excluded: chain A residue 2769 LEU Chi-restraints excluded: chain A residue 2825 THR Chi-restraints excluded: chain A residue 2866 LEU Chi-restraints excluded: chain A residue 2872 GLU Chi-restraints excluded: chain A residue 2935 VAL Chi-restraints excluded: chain A residue 2942 ASP Chi-restraints excluded: chain A residue 2945 VAL Chi-restraints excluded: chain A residue 2984 VAL Chi-restraints excluded: chain A residue 3002 LEU Chi-restraints excluded: chain A residue 3320 LEU Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3332 THR Chi-restraints excluded: chain A residue 3338 ASN Chi-restraints excluded: chain A residue 3385 ASP Chi-restraints excluded: chain A residue 3425 LYS Chi-restraints excluded: chain A residue 3459 ASP Chi-restraints excluded: chain A residue 3469 GLU Chi-restraints excluded: chain A residue 3486 VAL Chi-restraints excluded: chain A residue 3491 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 67 optimal weight: 0.0980 chunk 28 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9889 Z= 0.224 Angle : 0.586 9.301 13403 Z= 0.298 Chirality : 0.042 0.172 1520 Planarity : 0.004 0.055 1686 Dihedral : 8.044 88.542 1339 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.06 % Allowed : 15.22 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.25), residues: 1188 helix: 1.26 (0.22), residues: 590 sheet: -0.15 (0.41), residues: 154 loop : -0.80 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A3379 HIS 0.007 0.001 HIS A3517 PHE 0.024 0.001 PHE A3436 TYR 0.013 0.001 TYR A3330 ARG 0.003 0.000 ARG A2646 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 99 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2222 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.8058 (mt) REVERT: A 2305 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8617 (tp) REVERT: A 2371 PHE cc_start: 0.7593 (t80) cc_final: 0.7333 (t80) REVERT: A 2428 MET cc_start: 0.8913 (tmm) cc_final: 0.8692 (tmm) REVERT: A 2623 THR cc_start: 0.9393 (OUTLIER) cc_final: 0.9110 (p) REVERT: A 2651 GLU cc_start: 0.9360 (mm-30) cc_final: 0.9054 (mm-30) REVERT: A 2819 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8266 (tm-30) REVERT: A 2849 TYR cc_start: 0.9458 (t80) cc_final: 0.9257 (t80) REVERT: A 3330 TYR cc_start: 0.9246 (OUTLIER) cc_final: 0.8541 (t80) outliers start: 44 outliers final: 31 residues processed: 137 average time/residue: 0.2261 time to fit residues: 43.8864 Evaluate side-chains 128 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 93 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2106 THR Chi-restraints excluded: chain A residue 2142 THR Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2222 ILE Chi-restraints excluded: chain A residue 2270 ASN Chi-restraints excluded: chain A residue 2305 LEU Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2396 ASP Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2623 THR Chi-restraints excluded: chain A residue 2658 ASP Chi-restraints excluded: chain A residue 2692 THR Chi-restraints excluded: chain A residue 2728 LEU Chi-restraints excluded: chain A residue 2739 VAL Chi-restraints excluded: chain A residue 2769 LEU Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2825 THR Chi-restraints excluded: chain A residue 2866 LEU Chi-restraints excluded: chain A residue 2872 GLU Chi-restraints excluded: chain A residue 2935 VAL Chi-restraints excluded: chain A residue 2942 ASP Chi-restraints excluded: chain A residue 2945 VAL Chi-restraints excluded: chain A residue 2959 GLN Chi-restraints excluded: chain A residue 2965 VAL Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 2984 VAL Chi-restraints excluded: chain A residue 3002 LEU Chi-restraints excluded: chain A residue 3316 THR Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3353 LEU Chi-restraints excluded: chain A residue 3385 ASP Chi-restraints excluded: chain A residue 3425 LYS Chi-restraints excluded: chain A residue 3469 GLU Chi-restraints excluded: chain A residue 3486 VAL Chi-restraints excluded: chain A residue 3491 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2097 HIS ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9889 Z= 0.294 Angle : 0.618 14.294 13403 Z= 0.311 Chirality : 0.043 0.172 1520 Planarity : 0.004 0.061 1686 Dihedral : 8.006 88.333 1339 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.07 % Allowed : 14.48 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1188 helix: 1.22 (0.22), residues: 590 sheet: -0.12 (0.41), residues: 155 loop : -0.81 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A3379 HIS 0.007 0.001 HIS A3517 PHE 0.019 0.002 PHE A3436 TYR 0.015 0.001 TYR A2571 ARG 0.003 0.000 ARG A3365 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 93 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2222 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8078 (mt) REVERT: A 2305 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8587 (tp) REVERT: A 2371 PHE cc_start: 0.7456 (t80) cc_final: 0.7143 (t80) REVERT: A 2428 MET cc_start: 0.8956 (tmm) cc_final: 0.8746 (tmm) REVERT: A 2623 THR cc_start: 0.9408 (OUTLIER) cc_final: 0.9169 (p) REVERT: A 2679 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9206 (ttpp) REVERT: A 2819 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8306 (tm-30) REVERT: A 2849 TYR cc_start: 0.9482 (t80) cc_final: 0.9276 (t80) REVERT: A 3330 TYR cc_start: 0.9241 (OUTLIER) cc_final: 0.8576 (t80) outliers start: 55 outliers final: 37 residues processed: 137 average time/residue: 0.2284 time to fit residues: 44.4398 Evaluate side-chains 130 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 88 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2106 THR Chi-restraints excluded: chain A residue 2142 THR Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2222 ILE Chi-restraints excluded: chain A residue 2270 ASN Chi-restraints excluded: chain A residue 2305 LEU Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2396 ASP Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2526 ILE Chi-restraints excluded: chain A residue 2613 SER Chi-restraints excluded: chain A residue 2623 THR Chi-restraints excluded: chain A residue 2641 LEU Chi-restraints excluded: chain A residue 2658 ASP Chi-restraints excluded: chain A residue 2679 LYS Chi-restraints excluded: chain A residue 2692 THR Chi-restraints excluded: chain A residue 2694 LEU Chi-restraints excluded: chain A residue 2728 LEU Chi-restraints excluded: chain A residue 2769 LEU Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2825 THR Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2866 LEU Chi-restraints excluded: chain A residue 2872 GLU Chi-restraints excluded: chain A residue 2935 VAL Chi-restraints excluded: chain A residue 2942 ASP Chi-restraints excluded: chain A residue 2945 VAL Chi-restraints excluded: chain A residue 2959 GLN Chi-restraints excluded: chain A residue 2965 VAL Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 2984 VAL Chi-restraints excluded: chain A residue 3002 LEU Chi-restraints excluded: chain A residue 3316 THR Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3353 LEU Chi-restraints excluded: chain A residue 3385 ASP Chi-restraints excluded: chain A residue 3425 LYS Chi-restraints excluded: chain A residue 3445 ARG Chi-restraints excluded: chain A residue 3450 VAL Chi-restraints excluded: chain A residue 3469 GLU Chi-restraints excluded: chain A residue 3486 VAL Chi-restraints excluded: chain A residue 3491 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 4.9990 chunk 34 optimal weight: 0.0670 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9889 Z= 0.237 Angle : 0.604 16.333 13403 Z= 0.299 Chirality : 0.042 0.167 1520 Planarity : 0.004 0.060 1686 Dihedral : 7.891 88.939 1339 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.52 % Allowed : 14.85 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.25), residues: 1188 helix: 1.32 (0.22), residues: 585 sheet: -0.00 (0.41), residues: 155 loop : -0.70 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A2084 HIS 0.006 0.001 HIS A3517 PHE 0.019 0.001 PHE A3436 TYR 0.016 0.001 TYR A2571 ARG 0.002 0.000 ARG A2646 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 99 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2222 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8076 (mt) REVERT: A 2305 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8590 (tp) REVERT: A 2371 PHE cc_start: 0.7372 (t80) cc_final: 0.7052 (t80) REVERT: A 2428 MET cc_start: 0.8945 (tmm) cc_final: 0.8734 (tmm) REVERT: A 2679 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9219 (ttpp) REVERT: A 2819 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8275 (tm-30) REVERT: A 3330 TYR cc_start: 0.9226 (OUTLIER) cc_final: 0.8606 (t80) REVERT: A 3446 PHE cc_start: 0.1733 (OUTLIER) cc_final: 0.1247 (m-80) outliers start: 49 outliers final: 37 residues processed: 141 average time/residue: 0.2228 time to fit residues: 44.4603 Evaluate side-chains 131 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 89 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2106 THR Chi-restraints excluded: chain A residue 2142 THR Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2217 THR Chi-restraints excluded: chain A residue 2222 ILE Chi-restraints excluded: chain A residue 2259 MET Chi-restraints excluded: chain A residue 2270 ASN Chi-restraints excluded: chain A residue 2305 LEU Chi-restraints excluded: chain A residue 2329 ASP Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2396 ASP Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2613 SER Chi-restraints excluded: chain A residue 2658 ASP Chi-restraints excluded: chain A residue 2679 LYS Chi-restraints excluded: chain A residue 2686 LEU Chi-restraints excluded: chain A residue 2692 THR Chi-restraints excluded: chain A residue 2694 LEU Chi-restraints excluded: chain A residue 2769 LEU Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2825 THR Chi-restraints excluded: chain A residue 2866 LEU Chi-restraints excluded: chain A residue 2872 GLU Chi-restraints excluded: chain A residue 2935 VAL Chi-restraints excluded: chain A residue 2942 ASP Chi-restraints excluded: chain A residue 2945 VAL Chi-restraints excluded: chain A residue 2959 GLN Chi-restraints excluded: chain A residue 2965 VAL Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 2984 VAL Chi-restraints excluded: chain A residue 3002 LEU Chi-restraints excluded: chain A residue 3316 THR Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3353 LEU Chi-restraints excluded: chain A residue 3385 ASP Chi-restraints excluded: chain A residue 3425 LYS Chi-restraints excluded: chain A residue 3445 ARG Chi-restraints excluded: chain A residue 3446 PHE Chi-restraints excluded: chain A residue 3450 VAL Chi-restraints excluded: chain A residue 3469 GLU Chi-restraints excluded: chain A residue 3486 VAL Chi-restraints excluded: chain A residue 3491 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9889 Z= 0.211 Angle : 0.601 16.437 13403 Z= 0.298 Chirality : 0.042 0.166 1520 Planarity : 0.004 0.060 1686 Dihedral : 7.794 88.919 1339 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.15 % Allowed : 15.68 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1188 helix: 1.40 (0.22), residues: 577 sheet: 0.17 (0.42), residues: 156 loop : -0.67 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A3379 HIS 0.006 0.001 HIS A3517 PHE 0.021 0.001 PHE A2244 TYR 0.015 0.001 TYR A2571 ARG 0.003 0.000 ARG A3365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 99 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2305 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8577 (tp) REVERT: A 2371 PHE cc_start: 0.7289 (t80) cc_final: 0.6989 (t80) REVERT: A 2428 MET cc_start: 0.8943 (tmm) cc_final: 0.8732 (tmm) REVERT: A 2819 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8256 (tm-30) REVERT: A 2872 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8367 (pt0) REVERT: A 3330 TYR cc_start: 0.9181 (OUTLIER) cc_final: 0.8602 (t80) REVERT: A 3446 PHE cc_start: 0.1707 (OUTLIER) cc_final: 0.1226 (m-80) outliers start: 45 outliers final: 35 residues processed: 136 average time/residue: 0.2166 time to fit residues: 42.2297 Evaluate side-chains 131 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 92 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2040 ASP Chi-restraints excluded: chain A residue 2106 THR Chi-restraints excluded: chain A residue 2142 THR Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2217 THR Chi-restraints excluded: chain A residue 2259 MET Chi-restraints excluded: chain A residue 2270 ASN Chi-restraints excluded: chain A residue 2305 LEU Chi-restraints excluded: chain A residue 2329 ASP Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2396 ASP Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2613 SER Chi-restraints excluded: chain A residue 2658 ASP Chi-restraints excluded: chain A residue 2692 THR Chi-restraints excluded: chain A residue 2694 LEU Chi-restraints excluded: chain A residue 2769 LEU Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2866 LEU Chi-restraints excluded: chain A residue 2872 GLU Chi-restraints excluded: chain A residue 2935 VAL Chi-restraints excluded: chain A residue 2942 ASP Chi-restraints excluded: chain A residue 2945 VAL Chi-restraints excluded: chain A residue 2965 VAL Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 2984 VAL Chi-restraints excluded: chain A residue 3002 LEU Chi-restraints excluded: chain A residue 3316 THR Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3353 LEU Chi-restraints excluded: chain A residue 3385 ASP Chi-restraints excluded: chain A residue 3425 LYS Chi-restraints excluded: chain A residue 3445 ARG Chi-restraints excluded: chain A residue 3446 PHE Chi-restraints excluded: chain A residue 3450 VAL Chi-restraints excluded: chain A residue 3469 GLU Chi-restraints excluded: chain A residue 3486 VAL Chi-restraints excluded: chain A residue 3491 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 9 optimal weight: 0.0970 chunk 72 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9889 Z= 0.187 Angle : 0.617 16.973 13403 Z= 0.305 Chirality : 0.043 0.225 1520 Planarity : 0.004 0.060 1686 Dihedral : 7.709 88.544 1339 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.51 % Allowed : 15.96 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1188 helix: 1.43 (0.22), residues: 575 sheet: 0.30 (0.43), residues: 156 loop : -0.59 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A3379 HIS 0.005 0.001 HIS A3517 PHE 0.020 0.001 PHE A3436 TYR 0.014 0.001 TYR A2571 ARG 0.002 0.000 ARG A2209 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 100 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2209 ARG cc_start: 0.7712 (mtm-85) cc_final: 0.7464 (mtm-85) REVERT: A 2305 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8554 (tp) REVERT: A 2371 PHE cc_start: 0.7265 (t80) cc_final: 0.6963 (t80) REVERT: A 2428 MET cc_start: 0.8922 (tmm) cc_final: 0.8710 (tmm) REVERT: A 2819 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8235 (tm-30) REVERT: A 2872 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8399 (pt0) REVERT: A 3002 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9249 (tp) REVERT: A 3330 TYR cc_start: 0.9150 (OUTLIER) cc_final: 0.8530 (t80) REVERT: A 3446 PHE cc_start: 0.1670 (OUTLIER) cc_final: 0.1135 (m-80) outliers start: 38 outliers final: 31 residues processed: 132 average time/residue: 0.2143 time to fit residues: 40.7708 Evaluate side-chains 130 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 94 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2040 ASP Chi-restraints excluded: chain A residue 2106 THR Chi-restraints excluded: chain A residue 2142 THR Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2270 ASN Chi-restraints excluded: chain A residue 2305 LEU Chi-restraints excluded: chain A residue 2329 ASP Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2396 ASP Chi-restraints excluded: chain A residue 2476 LYS Chi-restraints excluded: chain A residue 2613 SER Chi-restraints excluded: chain A residue 2658 ASP Chi-restraints excluded: chain A residue 2692 THR Chi-restraints excluded: chain A residue 2694 LEU Chi-restraints excluded: chain A residue 2716 ILE Chi-restraints excluded: chain A residue 2769 LEU Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2842 ASP Chi-restraints excluded: chain A residue 2866 LEU Chi-restraints excluded: chain A residue 2872 GLU Chi-restraints excluded: chain A residue 2935 VAL Chi-restraints excluded: chain A residue 2942 ASP Chi-restraints excluded: chain A residue 2945 VAL Chi-restraints excluded: chain A residue 2965 VAL Chi-restraints excluded: chain A residue 2984 VAL Chi-restraints excluded: chain A residue 3002 LEU Chi-restraints excluded: chain A residue 3316 THR Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3353 LEU Chi-restraints excluded: chain A residue 3425 LYS Chi-restraints excluded: chain A residue 3445 ARG Chi-restraints excluded: chain A residue 3446 PHE Chi-restraints excluded: chain A residue 3450 VAL Chi-restraints excluded: chain A residue 3469 GLU Chi-restraints excluded: chain A residue 3486 VAL Chi-restraints excluded: chain A residue 3491 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 11 optimal weight: 0.0030 chunk 17 optimal weight: 5.9990 chunk 83 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.073343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.057273 restraints weight = 31507.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.059633 restraints weight = 15371.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.061289 restraints weight = 9731.574| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9889 Z= 0.147 Angle : 0.624 17.342 13403 Z= 0.304 Chirality : 0.042 0.229 1520 Planarity : 0.004 0.058 1686 Dihedral : 7.560 88.114 1339 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.86 % Allowed : 16.97 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.25), residues: 1188 helix: 1.47 (0.22), residues: 575 sheet: 0.47 (0.44), residues: 156 loop : -0.56 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A3379 HIS 0.004 0.000 HIS A3517 PHE 0.022 0.001 PHE A2244 TYR 0.014 0.001 TYR A3330 ARG 0.003 0.000 ARG A2620 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2636.14 seconds wall clock time: 48 minutes 35.74 seconds (2915.74 seconds total)