Starting phenix.real_space_refine on Sun Aug 4 07:10:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi3_23838/08_2024/7mi3_23838.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi3_23838/08_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_23838/08_2024/7mi3_23838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi3_23838/08_2024/7mi3_23838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi3_23838/08_2024/7mi3_23838.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi3_23838/08_2024/7mi3_23838.cif" } 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9682 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1192, 9590 Classifications: {'peptide': 1192} Link IDs: {'PTRANS': 39, 'TRANS': 1152} Chain breaks: 1 Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 92 Unusual residues: {' MG': 1, 'ATP': 1, 'ZG7': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.65, per 1000 atoms: 0.69 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: 4.00 Conformation dependent library (CDL) restraints added in 1.6 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... Secondary structure from input PDB file: 56 helices and 9 sheets defined 58.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 2031 through 2046 Processing helix chain 'A' and resid 2050 through 2064 Processing helix chain 'A' and resid 2079 through 2096 Processing helix chain 'A' and resid 2105 through 2109 Processing helix chain 'A' and resid 2110 through 2115 Processing helix chain 'A' and resid 2128 through 2140 removed outlier: 3.560A pdb=" N ASP A2140 " --> pdb=" O ARG A2136 " (cutoff:3.500A) Processing helix chain 'A' and resid 2159 through 2165 removed outlier: 3.706A pdb=" N VAL A2163 " --> pdb=" O ASP A2159 " (cutoff:3.500A) Processing helix chain 'A' and resid 2166 through 2171 removed outlier: 3.881A pdb=" N LEU A2170 " --> pdb=" O MET A2166 " (cutoff:3.500A) Processing helix chain 'A' and resid 2203 through 2208 Processing helix chain 'A' and resid 2221 through 2241 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 2242 through 2258 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 2259 through 2268 removed outlier: 3.978A pdb=" N THR A2263 " --> pdb=" O MET A2259 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2282 Processing helix chain 'A' and resid 2283 through 2297 Processing helix chain 'A' and resid 2298 through 2303 removed outlier: 4.231A pdb=" N GLN A2303 " --> pdb=" O ARG A2299 " (cutoff:3.500A) Processing helix chain 'A' and resid 2306 through 2328 Processing helix chain 'A' and resid 2332 through 2346 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 2381 through 2387 Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2435 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) removed outlier: 4.013A pdb=" N SER A2435 " --> pdb=" O ALA A2431 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2462 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 2500 through 2513 Processing helix chain 'A' and resid 2547 through 2552 Processing helix chain 'A' and resid 2564 through 2579 Processing helix chain 'A' and resid 2580 through 2587 Proline residue: A2583 - end of helix removed outlier: 4.799A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2588 through 2607 Processing helix chain 'A' and resid 2619 through 2635 Processing helix chain 'A' and resid 2640 through 2657 Processing helix chain 'A' and resid 2658 through 2660 No H-bonds generated for 'chain 'A' and resid 2658 through 2660' Processing helix chain 'A' and resid 2662 through 2681 Processing helix chain 'A' and resid 2708 through 2727 Processing helix chain 'A' and resid 2735 through 2750 Processing helix chain 'A' and resid 2765 through 2778 removed outlier: 3.526A pdb=" N ARG A2771 " --> pdb=" O THR A2767 " (cutoff:3.500A) Processing helix chain 'A' and resid 2791 through 2809 Processing helix chain 'A' and resid 2820 through 2822 No H-bonds generated for 'chain 'A' and resid 2820 through 2822' Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 3.957A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) Processing helix chain 'A' and resid 2840 through 2845 removed outlier: 4.112A pdb=" N GLN A2845 " --> pdb=" O ASP A2842 " (cutoff:3.500A) Processing helix chain 'A' and resid 2846 through 2863 Processing helix chain 'A' and resid 2869 through 2884 removed outlier: 3.608A pdb=" N LEU A2873 " --> pdb=" O THR A2869 " (cutoff:3.500A) Processing helix chain 'A' and resid 2896 through 2905 Processing helix chain 'A' and resid 2905 through 2910 Processing helix chain 'A' and resid 2921 through 2936 removed outlier: 3.994A pdb=" N VAL A2935 " --> pdb=" O ASN A2931 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE A2936 " --> pdb=" O MET A2932 " (cutoff:3.500A) Processing helix chain 'A' and resid 2941 through 2945 removed outlier: 3.933A pdb=" N VAL A2945 " --> pdb=" O ASP A2942 " (cutoff:3.500A) Processing helix chain 'A' and resid 2960 through 2980 Processing helix chain 'A' and resid 2989 through 3011 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 3318 through 3334 removed outlier: 4.525A pdb=" N GLY A3322 " --> pdb=" O GLN A3318 " (cutoff:3.500A) Processing helix chain 'A' and resid 3335 through 3337 No H-bonds generated for 'chain 'A' and resid 3335 through 3337' Processing helix chain 'A' and resid 3338 through 3356 removed outlier: 3.746A pdb=" N LEU A3352 " --> pdb=" O ILE A3348 " (cutoff:3.500A) Processing helix chain 'A' and resid 3365 through 3371 Processing helix chain 'A' and resid 3372 through 3382 removed outlier: 4.105A pdb=" N LEU A3380 " --> pdb=" O LYS A3376 " (cutoff:3.500A) Processing helix chain 'A' and resid 3387 through 3400 Processing helix chain 'A' and resid 3413 through 3423 removed outlier: 4.237A pdb=" N SER A3419 " --> pdb=" O ILE A3415 " (cutoff:3.500A) Processing helix chain 'A' and resid 3435 through 3447 Processing helix chain 'A' and resid 3459 through 3461 No H-bonds generated for 'chain 'A' and resid 3459 through 3461' Processing helix chain 'A' and resid 3462 through 3467 removed outlier: 3.589A pdb=" N ILE A3466 " --> pdb=" O ILE A3462 " (cutoff:3.500A) Processing helix chain 'A' and resid 3506 through 3511 Processing sheet with id=AA1, first strand: chain 'A' and resid 2098 through 2103 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) 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: 6.818A pdb=" N LEU A2070 " --> pdb=" O PHE A2194 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR A2196 " --> pdb=" O LEU A2070 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU A2072 " --> pdb=" O THR A2196 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2175 through 2177 Processing sheet with id=AA3, 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=AA4, first strand: chain 'A' and resid 2438 through 2444 removed outlier: 6.637A pdb=" N ASP A2439 " --> pdb=" O VAL A2483 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N PHE A2485 " --> pdb=" O ASP A2439 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A2441 " --> pdb=" O PHE A2485 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ASP A2487 " --> pdb=" O VAL A2441 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE A2443 " --> pdb=" O ASP A2487 " (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) removed outlier: 6.447A pdb=" N ILE A2414 " --> pdb=" O GLY A2533 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N CYS A2535 " --> pdb=" O ILE A2414 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU A2416 " --> pdb=" O CYS A2535 " (cutoff:3.500A) 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) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 2465 through 2467 removed outlier: 12.576A pdb=" N THR A2472 " --> pdb=" O GLU A2527 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLU A2527 " --> pdb=" O THR A2472 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR A2525 " --> pdb=" O LEU A2474 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2696 through 2697 Processing sheet with id=AA7, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 6.381A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ASP A2818 " --> pdb=" O VAL A2782 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N HIS A2755 " --> pdb=" O ILE A2913 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN A2915 " --> pdb=" O HIS A2755 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N MET A2757 " --> pdb=" O ASN A2915 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N MET A2917 " --> pdb=" O MET A2757 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE A2759 " --> pdb=" O MET A2917 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 3426 through 3430 removed outlier: 6.657A pdb=" N VAL A3427 " --> pdb=" O ILE A3451 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLN A3453 " --> pdb=" O VAL A3427 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU A3429 " --> pdb=" O GLN A3453 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 3471 through 3472 removed outlier: 3.591A pdb=" N HIS A3484 " --> pdb=" O ILE A3481 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1401 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: 3.71 Time building geometry restraints manager: 4.30 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: 8195 3.15 - 3.73: 14809 3.73 - 4.32: 20558 4.32 - 4.90: 33965 Nonbonded interactions: 77595 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 3.040 nonbonded pdb=" NH1 ARG A2763 " pdb=" O SER A3511 " model vdw 2.298 3.120 ... (remaining 77590 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: 2.250 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: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 30.700 Find NCS groups from input model: 0.110 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.290 ------------------------------------------------------------------------------- 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= 0.789 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 : 1.181 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: 0.2635 time to fit residues: 83.1601 Evaluate side-chains 117 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.8255 > 50: distance: 139 - 144: 28.521 distance: 144 - 145: 15.842 distance: 145 - 146: 68.571 distance: 145 - 148: 37.534 distance: 146 - 154: 40.450 distance: 148 - 149: 5.712 distance: 149 - 150: 39.869 distance: 149 - 151: 38.996 distance: 150 - 152: 9.601 distance: 151 - 153: 28.337 distance: 152 - 153: 16.299 distance: 154 - 155: 36.980 distance: 155 - 156: 15.458 distance: 155 - 158: 48.224 distance: 156 - 157: 52.852 distance: 156 - 162: 46.873 distance: 158 - 159: 59.735 distance: 158 - 160: 45.879 distance: 159 - 161: 46.659 distance: 162 - 163: 38.220 distance: 163 - 164: 45.054 distance: 163 - 166: 12.828 distance: 164 - 165: 53.401 distance: 164 - 169: 40.156 distance: 166 - 167: 29.815 distance: 166 - 168: 49.823 distance: 169 - 170: 42.547 distance: 170 - 171: 44.101 distance: 171 - 172: 28.940 distance: 171 - 173: 25.737 distance: 173 - 174: 56.247 distance: 174 - 177: 57.366 distance: 175 - 176: 39.988 distance: 175 - 178: 56.681 distance: 178 - 179: 41.114 distance: 179 - 180: 39.740 distance: 180 - 181: 18.200 distance: 180 - 184: 55.447 distance: 184 - 185: 40.403 distance: 185 - 186: 69.100 distance: 185 - 188: 56.623 distance: 186 - 187: 35.547 distance: 186 - 192: 57.507 distance: 188 - 189: 56.723 distance: 189 - 190: 57.197 distance: 189 - 191: 55.562 distance: 192 - 193: 57.316 distance: 192 - 198: 52.254 distance: 193 - 194: 57.295 distance: 193 - 196: 55.709 distance: 194 - 195: 57.259 distance: 194 - 199: 56.241 distance: 196 - 197: 57.327 distance: 197 - 198: 52.069 distance: 199 - 200: 41.430 distance: 199 - 205: 38.643 distance: 200 - 203: 41.144 distance: 201 - 206: 41.248 distance: 203 - 204: 54.172 distance: 204 - 205: 39.959 distance: 206 - 207: 19.053 distance: 207 - 208: 21.845 distance: 207 - 210: 58.466 distance: 208 - 209: 31.229 distance: 208 - 213: 35.499 distance: 210 - 211: 31.505 distance: 210 - 212: 63.681