Starting phenix.real_space_refine on Thu Dec 7 20:39:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgf_22325/12_2023/7jgf_22325.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgf_22325/12_2023/7jgf_22325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgf_22325/12_2023/7jgf_22325.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgf_22325/12_2023/7jgf_22325.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgf_22325/12_2023/7jgf_22325.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgf_22325/12_2023/7jgf_22325.pdb" } resolution = 4.69 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 30 5.16 5 C 2808 2.51 5 N 770 2.21 5 O 839 1.98 5 H 30 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 2064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2088": "OD1" <-> "OD2" Residue "A PHE 2118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2130": "OE1" <-> "OE2" Residue "A GLU 2132": "OE1" <-> "OE2" Residue "A TYR 2158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2188": "OE1" <-> "OE2" Residue "A GLU 2199": "OE1" <-> "OE2" Residue "A TYR 2203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2227": "OE1" <-> "OE2" Residue "A TYR 2231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2256": "OD1" <-> "OD2" Residue "A PHE 2374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2459": "OE1" <-> "OE2" Residue "A ASP 2466": "OD1" <-> "OD2" Residue "A TYR 2470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2481": "NH1" <-> "NH2" Residue "A GLU 2491": "OE1" <-> "OE2" Residue "A PHE 2495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2497": "OD1" <-> "OD2" Residue "A PHE 2504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2510": "OE1" <-> "OE2" Residue "A GLU 2513": "OE1" <-> "OE2" Residue "A ASP 2524": "OD1" <-> "OD2" Residue "A GLU 2534": "OE1" <-> "OE2" Residue "A TYR 2555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2564": "OE1" <-> "OE2" Residue "A ASP 2571": "OD1" <-> "OD2" Residue "A GLU 2573": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4477 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4477 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 532, 4455 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 516} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 532, 4455 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 516} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 4528 Conformer: "C" Number of residues, atoms: 532, 4439 Classifications: {'peptide': 532} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 516} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 4528 Time building chain proxies: 7.29, per 1000 atoms: 1.63 Number of scatterers: 4477 At special positions: 0 Unit cell: (74.06, 137.54, 93.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 O 839 8.00 N 770 7.00 C 2808 6.00 H 30 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A2208 " - pdb=" SG CYS A2224 " distance=2.03 Simple disulfide: pdb=" SG CYS A2331 " - pdb=" SG CYS A2478 " distance=2.03 Simple disulfide: pdb=" SG CYS A2516 " - pdb=" SG CYS A2599 " distance=2.03 Simple disulfide: pdb=" SG CYS A2530 " - pdb=" SG CYS A2545 " distance=2.03 Simple disulfide: pdb=" SG CYS A2592 " - pdb=" SG CYS A2597 " distance=2.03 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: 1.85 Conformation dependent library (CDL) restraints added in 2.2 seconds 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1024 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 65.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 2023 through 2032 Processing helix chain 'A' and resid 2060 through 2086 removed outlier: 4.283A pdb=" N LEU A2079 " --> pdb=" O GLU A2075 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY A2080 " --> pdb=" O GLY A2076 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN A2081 " --> pdb=" O LYS A2077 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS A2084 " --> pdb=" O GLY A2080 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU A2085 " --> pdb=" O ASN A2081 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS A2086 " --> pdb=" O TYR A2082 " (cutoff:3.500A) Processing helix chain 'A' and resid 2088 through 2110 removed outlier: 3.977A pdb=" N TYR A2103 " --> pdb=" O SER A2099 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLU A2104 " --> pdb=" O PHE A2100 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP A2105 " --> pdb=" O TYR A2101 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE A2106 " --> pdb=" O ASP A2102 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A2107 " --> pdb=" O TYR A2103 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A2110 " --> pdb=" O ILE A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2117 through 2130 removed outlier: 3.627A pdb=" N LYS A2122 " --> pdb=" O PHE A2118 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2157 removed outlier: 3.574A pdb=" N TRP A2143 " --> pdb=" O ALA A2139 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LYS A2148 " --> pdb=" O LYS A2144 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER A2149 " --> pdb=" O THR A2145 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TRP A2151 " --> pdb=" O LYS A2147 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET A2154 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A2155 " --> pdb=" O TRP A2151 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS A2156 " --> pdb=" O ASN A2152 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY A2157 " --> pdb=" O ALA A2153 " (cutoff:3.500A) Processing helix chain 'A' and resid 2183 through 2207 Processing helix chain 'A' and resid 2221 through 2252 removed outlier: 3.599A pdb=" N ILE A2240 " --> pdb=" O ARG A2236 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A2241 " --> pdb=" O LYS A2237 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TRP A2242 " --> pdb=" O ARG A2238 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU A2243 " --> pdb=" O SER A2239 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR A2244 " --> pdb=" O ILE A2240 " (cutoff:3.500A) Processing helix chain 'A' and resid 2294 through 2300 removed outlier: 4.137A pdb=" N PHE A2298 " --> pdb=" O GLU A2294 " (cutoff:3.500A) Processing helix chain 'A' and resid 2302 through 2310 removed outlier: 3.860A pdb=" N ILE A2307 " --> pdb=" O GLN A2304 " (cutoff:3.500A) Proline residue: A2308 - end of helix Processing helix chain 'A' and resid 2328 through 2337 removed outlier: 3.849A pdb=" N LYS A2333 " --> pdb=" O TYR A2329 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR A2334 " --> pdb=" O ILE A2330 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A2335 " --> pdb=" O CYS A2331 " (cutoff:3.500A) Processing helix chain 'A' and resid 2367 through 2372 removed outlier: 4.344A pdb=" N ASN A2372 " --> pdb=" O PRO A2368 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2380 No H-bonds generated for 'chain 'A' and resid 2378 through 2380' Processing helix chain 'A' and resid 2381 through 2388 removed outlier: 3.527A pdb=" N TYR A2385 " --> pdb=" O LYS A2381 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A2386 " --> pdb=" O ILE A2382 " (cutoff:3.500A) Processing helix chain 'A' and resid 2388 through 2411 removed outlier: 3.975A pdb=" N PHE A2392 " --> pdb=" O ASP A2388 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP A2394 " --> pdb=" O LYS A2390 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LYS A2408 " --> pdb=" O VAL A2404 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LYS A2409 " --> pdb=" O GLU A2405 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A2410 " --> pdb=" O ARG A2406 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR A2411 " --> pdb=" O LEU A2407 " (cutoff:3.500A) Processing helix chain 'A' and resid 2414 through 2433 Processing helix chain 'A' and resid 2441 through 2451 Processing helix chain 'A' and resid 2458 through 2484 removed outlier: 3.686A pdb=" N CYS A2478 " --> pdb=" O GLU A2474 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A2484 " --> pdb=" O TYR A2480 " (cutoff:3.500A) Processing helix chain 'A' and resid 2496 through 2501 removed outlier: 3.540A pdb=" N GLU A2499 " --> pdb=" O PRO A2496 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A2501 " --> pdb=" O ILE A2498 " (cutoff:3.500A) Processing helix chain 'A' and resid 2502 through 2513 Processing helix chain 'A' and resid 2515 through 2529 removed outlier: 3.726A pdb=" N TYR A2523 " --> pdb=" O ARG A2519 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN A2527 " --> pdb=" O TYR A2523 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A2528 " --> pdb=" O ASP A2524 " (cutoff:3.500A) Processing helix chain 'A' and resid 2546 through 2548 No H-bonds generated for 'chain 'A' and resid 2546 through 2548' Processing helix chain 'A' and resid 2549 through 2574 removed outlier: 4.107A pdb=" N LYS A2553 " --> pdb=" O CYS A2549 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP A2571 " --> pdb=" O THR A2567 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU A2573 " --> pdb=" O LYS A2569 " (cutoff:3.500A) Processing helix chain 'A' and resid 2583 through 2591 removed outlier: 3.894A pdb=" N LYS A2589 " --> pdb=" O PRO A2585 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2166 through 2167 210 hydrogen bonds defined for protein. 618 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: 1.10 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 30 1.05 - 1.24: 585 1.24 - 1.43: 1336 1.43 - 1.62: 2578 1.62 - 1.81: 42 Bond restraints: 4571 Sorted by residual: bond pdb=" CA PHE A2064 " pdb=" CB PHE A2064 " ideal model delta sigma weight residual 1.529 1.550 -0.021 1.74e-02 3.30e+03 1.41e+00 bond pdb=" CG MET A2422 " pdb=" SD MET A2422 " ideal model delta sigma weight residual 1.803 1.773 0.030 2.50e-02 1.60e+03 1.41e+00 bond pdb=" CA PHE A2574 " pdb=" C PHE A2574 " ideal model delta sigma weight residual 1.522 1.537 -0.014 1.51e-02 4.39e+03 9.22e-01 bond pdb=" CB GLU A2202 " pdb=" CG GLU A2202 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.16e-01 bond pdb=" CA PHE A2182 " pdb=" C PHE A2182 " ideal model delta sigma weight residual 1.526 1.540 -0.015 1.75e-02 3.27e+03 6.94e-01 ... (remaining 4566 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.91: 93 106.91 - 113.74: 2455 113.74 - 120.57: 1986 120.57 - 127.40: 1556 127.40 - 134.23: 53 Bond angle restraints: 6143 Sorted by residual: angle pdb=" C ALA A2421 " pdb=" N MET A2422 " pdb=" CA MET A2422 " ideal model delta sigma weight residual 121.14 114.07 7.07 1.75e+00 3.27e-01 1.63e+01 angle pdb=" C GLU A2063 " pdb=" N PHE A2064 " pdb=" CA PHE A2064 " ideal model delta sigma weight residual 120.72 115.30 5.42 1.67e+00 3.59e-01 1.05e+01 angle pdb=" N MET A2422 " pdb=" CA MET A2422 " pdb=" CB MET A2422 " ideal model delta sigma weight residual 110.40 115.64 -5.24 1.63e+00 3.76e-01 1.03e+01 angle pdb=" N GLY A2412 " pdb=" CA GLY A2412 " pdb=" C GLY A2412 " ideal model delta sigma weight residual 110.20 114.32 -4.12 1.32e+00 5.74e-01 9.74e+00 angle pdb=" CA MET A2422 " pdb=" CB MET A2422 " pdb=" CG MET A2422 " ideal model delta sigma weight residual 114.10 119.70 -5.60 2.00e+00 2.50e-01 7.83e+00 ... (remaining 6138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 2550 17.85 - 35.70: 223 35.70 - 53.55: 37 53.55 - 71.39: 5 71.39 - 89.24: 3 Dihedral angle restraints: 2818 sinusoidal: 1240 harmonic: 1578 Sorted by residual: dihedral pdb=" CB CYS A2208 " pdb=" SG CYS A2208 " pdb=" SG CYS A2224 " pdb=" CB CYS A2224 " ideal model delta sinusoidal sigma weight residual -86.00 3.24 -89.24 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CB CYS A2516 " pdb=" SG CYS A2516 " pdb=" SG CYS A2599 " pdb=" CB CYS A2599 " ideal model delta sinusoidal sigma weight residual -86.00 -14.43 -71.57 1 1.00e+01 1.00e-02 6.57e+01 dihedral pdb=" CB CYS A2530 " pdb=" SG CYS A2530 " pdb=" SG CYS A2545 " pdb=" CB CYS A2545 " ideal model delta sinusoidal sigma weight residual -86.00 -53.56 -32.44 1 1.00e+01 1.00e-02 1.50e+01 ... (remaining 2815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 409 0.033 - 0.065: 153 0.065 - 0.097: 43 0.097 - 0.130: 12 0.130 - 0.162: 3 Chirality restraints: 620 Sorted by residual: chirality pdb=" CA PHE A2064 " pdb=" N PHE A2064 " pdb=" C PHE A2064 " pdb=" CB PHE A2064 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" CG LEU A2113 " pdb=" CB LEU A2113 " pdb=" CD1 LEU A2113 " pdb=" CD2 LEU A2113 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CB VAL A2404 " pdb=" CA VAL A2404 " pdb=" CG1 VAL A2404 " pdb=" CG2 VAL A2404 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 617 not shown) Planarity restraints: 776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A2234 " 0.022 2.00e-02 2.50e+03 2.20e-02 1.21e+01 pdb=" CG TRP A2234 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP A2234 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A2234 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A2234 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A2234 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A2234 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2234 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2234 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A2234 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A2495 " -0.045 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO A2496 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A2496 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A2496 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A2584 " -0.039 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO A2585 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A2585 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A2585 " -0.034 5.00e-02 4.00e+02 ... (remaining 773 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.61: 64 2.61 - 3.11: 3665 3.11 - 3.60: 5373 3.60 - 4.10: 6676 4.10 - 4.60: 10272 Nonbonded interactions: 26050 Sorted by model distance: nonbonded pdb=" O ILE A2396 " pdb=" OG SER A2399 " model vdw 2.109 2.200 nonbonded pdb=" O TRP A2142 " pdb="HD21 ASN A2146 " model vdw 2.212 1.850 nonbonded pdb=" O ARG A2241 " pdb=" OG1 THR A2244 " model vdw 2.233 2.200 nonbonded pdb=" O MET A2467 " pdb=" ND1 HIS A2471 " model vdw 2.255 2.350 nonbonded pdb=" O GLY A2071 " pdb=" OG SER A2074 " model vdw 2.273 2.200 ... (remaining 26045 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=0.10 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: 0.830 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: 0.150 Extract box with map and model: 3.710 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 22.480 Find NCS groups from input model: 0.120 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4393 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 : 0.002 0.030 4541 Z= 0.154 Angle : 0.619 7.070 6089 Z= 0.364 Chirality : 0.039 0.162 620 Planarity : 0.005 0.069 776 Dihedral : 13.157 75.227 1767 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 26.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.41 % Allowed : 0.20 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.87 (0.33), residues: 524 helix: 0.10 (0.29), residues: 267 sheet: None (None), residues: 0 loop : -1.28 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A2234 HIS 0.004 0.001 HIS A2200 PHE 0.037 0.002 PHE A2078 TYR 0.018 0.001 TYR A2424 ARG 0.007 0.000 ARG A2506 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2589 time to fit residues: 16.8863 Evaluate side-chains 41 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.548 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2503 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4488 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 4541 Z= 0.136 Angle : 0.452 5.485 6089 Z= 0.258 Chirality : 0.036 0.111 620 Planarity : 0.004 0.062 776 Dihedral : 3.781 15.187 579 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 41.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.41 % Allowed : 0.61 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.16 (0.37), residues: 524 helix: 1.03 (0.31), residues: 283 sheet: None (None), residues: 0 loop : -1.00 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A2234 HIS 0.001 0.000 HIS A2420 PHE 0.015 0.001 PHE A2064 TYR 0.013 0.001 TYR A2249 ARG 0.005 0.001 ARG A2127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2395 time to fit residues: 16.1432 Evaluate side-chains 46 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.549 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 0.0570 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 42 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4517 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4541 Z= 0.111 Angle : 0.427 5.312 6089 Z= 0.240 Chirality : 0.035 0.108 620 Planarity : 0.004 0.056 776 Dihedral : 3.686 15.149 579 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 42.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.41 % Allowed : 1.22 % Favored : 98.38 % 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: 0.59 (0.38), residues: 524 helix: 1.34 (0.31), residues: 286 sheet: None (None), residues: 0 loop : -0.77 (0.43), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2234 HIS 0.002 0.000 HIS A2200 PHE 0.019 0.001 PHE A2078 TYR 0.008 0.001 TYR A2103 ARG 0.007 0.000 ARG A2127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.2263 time to fit residues: 15.8303 Evaluate side-chains 45 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.0060 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 5 optimal weight: 0.0060 chunk 23 optimal weight: 0.0670 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 0.0470 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.2248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4484 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.029 4541 Z= 0.083 Angle : 0.398 4.301 6089 Z= 0.221 Chirality : 0.035 0.107 620 Planarity : 0.004 0.053 776 Dihedral : 3.595 17.186 579 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 42.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.41 % Allowed : 0.61 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.82 (0.39), residues: 524 helix: 1.53 (0.31), residues: 286 sheet: None (None), residues: 0 loop : -0.66 (0.44), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A2465 HIS 0.001 0.000 HIS A2200 PHE 0.019 0.001 PHE A2078 TYR 0.007 0.001 TYR A2249 ARG 0.006 0.000 ARG A2127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2220 time to fit residues: 14.6507 Evaluate side-chains 47 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.534 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2232 GLN ** A2503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4822 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4541 Z= 0.211 Angle : 0.654 8.478 6089 Z= 0.363 Chirality : 0.041 0.140 620 Planarity : 0.006 0.058 776 Dihedral : 4.629 21.891 579 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 63.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.41 % Allowed : 1.83 % Favored : 97.77 % 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: -0.00 (0.37), residues: 524 helix: 0.91 (0.31), residues: 279 sheet: None (None), residues: 0 loop : -1.07 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A2511 HIS 0.007 0.002 HIS A2200 PHE 0.027 0.003 PHE A2064 TYR 0.019 0.002 TYR A2082 ARG 0.014 0.001 ARG A2127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2316 time to fit residues: 16.4642 Evaluate side-chains 46 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.589 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 51 optimal weight: 0.0070 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4762 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 4541 Z= 0.133 Angle : 0.479 6.537 6089 Z= 0.264 Chirality : 0.037 0.140 620 Planarity : 0.004 0.049 776 Dihedral : 4.221 19.726 579 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 52.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.41 % Allowed : 0.20 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.26 (0.37), residues: 524 helix: 1.11 (0.31), residues: 286 sheet: None (None), residues: 0 loop : -0.97 (0.42), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A2465 HIS 0.001 0.000 HIS A2086 PHE 0.026 0.002 PHE A2078 TYR 0.020 0.001 TYR A2470 ARG 0.009 0.001 ARG A2127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2343 time to fit residues: 15.9128 Evaluate side-chains 45 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.0770 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 0.0040 chunk 23 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 overall best weight: 0.4750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4713 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.024 4541 Z= 0.099 Angle : 0.435 5.870 6089 Z= 0.239 Chirality : 0.036 0.185 620 Planarity : 0.004 0.048 776 Dihedral : 3.850 17.664 579 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 50.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.41 % Allowed : 0.61 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.65 (0.38), residues: 524 helix: 1.38 (0.31), residues: 287 sheet: None (None), residues: 0 loop : -0.74 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.001 0.000 HIS A2471 PHE 0.025 0.001 PHE A2078 TYR 0.013 0.001 TYR A2470 ARG 0.005 0.001 ARG A2248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2265 time to fit residues: 15.3438 Evaluate side-chains 48 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.526 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4748 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 4541 Z= 0.119 Angle : 0.444 5.057 6089 Z= 0.248 Chirality : 0.036 0.142 620 Planarity : 0.004 0.048 776 Dihedral : 3.853 18.655 579 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 51.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.41 % Allowed : 0.61 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.75 (0.38), residues: 524 helix: 1.45 (0.31), residues: 293 sheet: None (None), residues: 0 loop : -0.74 (0.44), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.002 0.000 HIS A2338 PHE 0.026 0.002 PHE A2078 TYR 0.010 0.001 TYR A2470 ARG 0.007 0.001 ARG A2127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.2218 time to fit residues: 15.6847 Evaluate side-chains 44 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.563 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 30 optimal weight: 0.0170 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 0.0010 overall best weight: 0.4424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2232 GLN A2503 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4723 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.026 4541 Z= 0.099 Angle : 0.447 7.785 6089 Z= 0.246 Chirality : 0.037 0.151 620 Planarity : 0.004 0.048 776 Dihedral : 3.749 17.352 579 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 49.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.41 % Allowed : 0.61 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.38), residues: 524 helix: 1.53 (0.31), residues: 293 sheet: None (None), residues: 0 loop : -0.63 (0.44), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.001 0.000 HIS A2471 PHE 0.025 0.002 PHE A2078 TYR 0.011 0.001 TYR A2470 ARG 0.010 0.001 ARG A2248 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2049 time to fit residues: 13.7729 Evaluate side-chains 45 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.490 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 8.9990 chunk 48 optimal weight: 0.0980 chunk 42 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2232 GLN A2420 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4707 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4541 Z= 0.107 Angle : 0.443 6.021 6089 Z= 0.245 Chirality : 0.036 0.132 620 Planarity : 0.004 0.048 776 Dihedral : 3.732 17.224 579 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 50.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.41 % Allowed : 0.20 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.92 (0.39), residues: 524 helix: 1.54 (0.31), residues: 293 sheet: None (None), residues: 0 loop : -0.59 (0.45), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A2511 HIS 0.001 0.000 HIS A2338 PHE 0.026 0.002 PHE A2078 TYR 0.010 0.001 TYR A2470 ARG 0.008 0.001 ARG A2248 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2115 time to fit residues: 14.2629 Evaluate side-chains 46 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.520 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.0270 chunk 42 optimal weight: 0.0670 chunk 17 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 5 optimal weight: 0.0370 chunk 7 optimal weight: 0.6980 chunk 36 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 0.0370 chunk 28 optimal weight: 7.9990 overall best weight: 0.0732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.219333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.201768 restraints weight = 40513.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.205201 restraints weight = 32994.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.207042 restraints weight = 24340.432| |-----------------------------------------------------------------------------| r_work (final): 0.4720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4730 r_free = 0.4730 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4729 r_free = 0.4729 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4622 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.030 4541 Z= 0.099 Angle : 0.430 6.209 6089 Z= 0.235 Chirality : 0.036 0.131 620 Planarity : 0.004 0.047 776 Dihedral : 3.503 15.439 579 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 46.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.41 % Allowed : 0.41 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.10 (0.39), residues: 524 helix: 1.69 (0.31), residues: 291 sheet: None (None), residues: 0 loop : -0.48 (0.45), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.001 0.000 HIS A2338 PHE 0.024 0.001 PHE A2078 TYR 0.012 0.001 TYR A2470 ARG 0.008 0.000 ARG A2248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1396.03 seconds wall clock time: 26 minutes 6.74 seconds (1566.74 seconds total)