Starting phenix.real_space_refine (version: dev) on Tue Feb 28 00:54:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpx_30434/02_2023/7cpx_30434_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpx_30434/02_2023/7cpx_30434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpx_30434/02_2023/7cpx_30434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpx_30434/02_2023/7cpx_30434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpx_30434/02_2023/7cpx_30434_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpx_30434/02_2023/7cpx_30434_neut_trim_updated.pdb" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.003 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 Process input model Symmetric amino acids flipped Residue "A PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 70068 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 34986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2262, 34986 Classifications: {'peptide': 2262} Link IDs: {'PCIS': 2, 'PTRANS': 124, 'TRANS': 2135} Chain breaks: 12 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 34986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2262, 34986 Classifications: {'peptide': 2262} Link IDs: {'PCIS': 2, 'PTRANS': 124, 'TRANS': 2135} Chain breaks: 12 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C1B NAP A3500 " occ=0.00 ... (46 atoms not shown) pdb=" PN NAP A3500 " occ=0.00 residue: pdb=" C1B NAP B3500 " occ=0.00 ... (46 atoms not shown) pdb=" PN NAP B3500 " occ=0.00 Time building chain proxies: 24.61, per 1000 atoms: 0.35 Number of scatterers: 70068 At special positions: 0 Unit cell: (151, 203, 164, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 178 16.00 P 6 15.00 O 6684 8.00 N 6136 7.00 C 22396 6.00 H 34668 1.00 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: 51.57 Conformation dependent library (CDL) restraints added in 5.3 seconds 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8484 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 176 helices and 26 sheets defined 37.1% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.09 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 97 through 113 Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 149 through 155 removed outlier: 4.361A pdb=" N ALA A 152 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR A 153 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 155 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 168 removed outlier: 4.679A pdb=" N ARG A 163 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 168 " --> pdb=" O SER A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 removed outlier: 4.808A pdb=" N SER A 184 " --> pdb=" O CYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 223 removed outlier: 3.621A pdb=" N LEU A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 325 through 339 Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 369 through 386 removed outlier: 4.380A pdb=" N GLY A 373 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE A 382 " --> pdb=" O LYS A 379 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 383 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Proline residue: A 404 - end of helix No H-bonds generated for 'chain 'A' and resid 400 through 405' Processing helix chain 'A' and resid 482 through 498 Processing helix chain 'A' and resid 504 through 513 Processing helix chain 'A' and resid 529 through 542 Processing helix chain 'A' and resid 575 through 578 No H-bonds generated for 'chain 'A' and resid 575 through 578' Processing helix chain 'A' and resid 582 through 597 Processing helix chain 'A' and resid 608 through 610 No H-bonds generated for 'chain 'A' and resid 608 through 610' Processing helix chain 'A' and resid 624 through 644 Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 656 through 665 removed outlier: 4.464A pdb=" N ALA A 661 " --> pdb=" O GLY A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 682 Processing helix chain 'A' and resid 765 through 779 Proline residue: A 769 - end of helix Proline residue: A 773 - end of helix removed outlier: 3.723A pdb=" N GLU A 779 " --> pdb=" O GLN A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 823 removed outlier: 4.143A pdb=" N LEU A 822 " --> pdb=" O TRP A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 838 Processing helix chain 'A' and resid 855 through 865 Processing helix chain 'A' and resid 883 through 898 Processing helix chain 'A' and resid 900 through 902 No H-bonds generated for 'chain 'A' and resid 900 through 902' Processing helix chain 'A' and resid 905 through 911 Processing helix chain 'A' and resid 921 through 923 No H-bonds generated for 'chain 'A' and resid 921 through 923' Processing helix chain 'A' and resid 941 through 946 Processing helix chain 'A' and resid 980 through 984 removed outlier: 3.699A pdb=" N ASP A 983 " --> pdb=" O GLU A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1012 Processing helix chain 'A' and resid 1117 through 1126 Processing helix chain 'A' and resid 1133 through 1136 Processing helix chain 'A' and resid 1170 through 1184 removed outlier: 3.669A pdb=" N VAL A1180 " --> pdb=" O ALA A1176 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A1181 " --> pdb=" O PHE A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1217 Processing helix chain 'A' and resid 1266 through 1268 No H-bonds generated for 'chain 'A' and resid 1266 through 1268' Processing helix chain 'A' and resid 1290 through 1292 No H-bonds generated for 'chain 'A' and resid 1290 through 1292' Processing helix chain 'A' and resid 1296 through 1309 Proline residue: A1303 - end of helix removed outlier: 3.592A pdb=" N VAL A1309 " --> pdb=" O ILE A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1325 removed outlier: 5.460A pdb=" N SER A1318 " --> pdb=" O ARG A1314 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLN A1319 " --> pdb=" O SER A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1333 No H-bonds generated for 'chain 'A' and resid 1330 through 1333' Processing helix chain 'A' and resid 1339 through 1354 removed outlier: 3.981A pdb=" N LYS A1347 " --> pdb=" O LEU A1343 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TRP A1353 " --> pdb=" O GLY A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1370 Processing helix chain 'A' and resid 1376 through 1386 Processing helix chain 'A' and resid 1390 through 1393 No H-bonds generated for 'chain 'A' and resid 1390 through 1393' Processing helix chain 'A' and resid 1409 through 1415 Processing helix chain 'A' and resid 1420 through 1436 Processing helix chain 'A' and resid 1451 through 1457 Processing helix chain 'A' and resid 1474 through 1483 removed outlier: 4.039A pdb=" N GLU A1478 " --> pdb=" O GLY A1475 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1505 No H-bonds generated for 'chain 'A' and resid 1503 through 1505' Processing helix chain 'A' and resid 1521 through 1523 No H-bonds generated for 'chain 'A' and resid 1521 through 1523' Processing helix chain 'A' and resid 1527 through 1537 Processing helix chain 'A' and resid 1558 through 1563 removed outlier: 3.987A pdb=" N LEU A1563 " --> pdb=" O PHE A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1571 through 1573 No H-bonds generated for 'chain 'A' and resid 1571 through 1573' Processing helix chain 'A' and resid 1583 through 1592 Processing helix chain 'A' and resid 1652 through 1664 Processing helix chain 'A' and resid 1676 through 1680 Processing helix chain 'A' and resid 1705 through 1707 No H-bonds generated for 'chain 'A' and resid 1705 through 1707' Processing helix chain 'A' and resid 1709 through 1719 Processing helix chain 'A' and resid 1730 through 1733 No H-bonds generated for 'chain 'A' and resid 1730 through 1733' Processing helix chain 'A' and resid 1735 through 1750 removed outlier: 3.735A pdb=" N ARG A1749 " --> pdb=" O ARG A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1776 through 1784 Processing helix chain 'A' and resid 1814 through 1823 removed outlier: 3.896A pdb=" N SER A1823 " --> pdb=" O ARG A1819 " (cutoff:3.500A) Processing helix chain 'A' and resid 1920 through 1922 No H-bonds generated for 'chain 'A' and resid 1920 through 1922' Processing helix chain 'A' and resid 1935 through 1953 removed outlier: 3.653A pdb=" N ILE A1953 " --> pdb=" O ALA A1949 " (cutoff:3.500A) Processing helix chain 'A' and resid 1972 through 1985 Processing helix chain 'A' and resid 2018 through 2024 Processing helix chain 'A' and resid 2039 through 2051 removed outlier: 3.827A pdb=" N GLY A2043 " --> pdb=" O SER A2040 " (cutoff:3.500A) Processing helix chain 'A' and resid 2061 through 2064 No H-bonds generated for 'chain 'A' and resid 2061 through 2064' Processing helix chain 'A' and resid 2085 through 2097 Processing helix chain 'A' and resid 2099 through 2101 No H-bonds generated for 'chain 'A' and resid 2099 through 2101' Processing helix chain 'A' and resid 2111 through 2117 Processing helix chain 'A' and resid 2135 through 2138 No H-bonds generated for 'chain 'A' and resid 2135 through 2138' Processing helix chain 'A' and resid 2167 through 2179 Processing helix chain 'A' and resid 2195 through 2203 Processing helix chain 'A' and resid 2218 through 2230 removed outlier: 3.540A pdb=" N LYS A2229 " --> pdb=" O LEU A2225 " (cutoff:3.500A) Processing helix chain 'A' and resid 2256 through 2277 Proline residue: A2265 - end of helix removed outlier: 3.764A pdb=" N GLY A2269 " --> pdb=" O PRO A2265 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2299 Processing helix chain 'A' and resid 2305 through 2323 Processing helix chain 'A' and resid 2341 through 2344 No H-bonds generated for 'chain 'A' and resid 2341 through 2344' Processing helix chain 'A' and resid 2348 through 2354 removed outlier: 3.513A pdb=" N ILE A2354 " --> pdb=" O ASP A2350 " (cutoff:3.500A) Processing helix chain 'A' and resid 2363 through 2385 Processing helix chain 'A' and resid 2393 through 2395 No H-bonds generated for 'chain 'A' and resid 2393 through 2395' Processing helix chain 'A' and resid 2410 through 2412 No H-bonds generated for 'chain 'A' and resid 2410 through 2412' Processing helix chain 'A' and resid 2422 through 2427 removed outlier: 5.172A pdb=" N ASN A2426 " --> pdb=" O ARG A2423 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 35 Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 97 through 113 Processing helix chain 'B' and resid 117 through 120 No H-bonds generated for 'chain 'B' and resid 117 through 120' Processing helix chain 'B' and resid 149 through 155 removed outlier: 4.360A pdb=" N ALA B 152 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR B 153 " --> pdb=" O TYR B 150 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 155 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 168 removed outlier: 4.680A pdb=" N ARG B 163 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE B 168 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.807A pdb=" N SER B 184 " --> pdb=" O CYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 223 removed outlier: 3.621A pdb=" N LEU B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 262 Processing helix chain 'B' and resid 289 through 302 Processing helix chain 'B' and resid 325 through 339 Proline residue: B 329 - end of helix Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'B' and resid 369 through 386 removed outlier: 4.380A pdb=" N GLY B 373 " --> pdb=" O GLY B 370 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE B 382 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA B 383 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Proline residue: B 404 - end of helix No H-bonds generated for 'chain 'B' and resid 400 through 405' Processing helix chain 'B' and resid 482 through 498 Processing helix chain 'B' and resid 504 through 513 Processing helix chain 'B' and resid 529 through 542 Processing helix chain 'B' and resid 575 through 578 No H-bonds generated for 'chain 'B' and resid 575 through 578' Processing helix chain 'B' and resid 582 through 597 Processing helix chain 'B' and resid 608 through 610 No H-bonds generated for 'chain 'B' and resid 608 through 610' Processing helix chain 'B' and resid 624 through 644 Proline residue: B 629 - end of helix Processing helix chain 'B' and resid 656 through 665 removed outlier: 4.464A pdb=" N ALA B 661 " --> pdb=" O GLY B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 682 Processing helix chain 'B' and resid 765 through 779 Proline residue: B 769 - end of helix Proline residue: B 773 - end of helix removed outlier: 3.724A pdb=" N GLU B 779 " --> pdb=" O GLN B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 823 removed outlier: 4.143A pdb=" N LEU B 822 " --> pdb=" O TRP B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 838 Processing helix chain 'B' and resid 855 through 865 Processing helix chain 'B' and resid 883 through 898 Processing helix chain 'B' and resid 900 through 902 No H-bonds generated for 'chain 'B' and resid 900 through 902' Processing helix chain 'B' and resid 905 through 911 Processing helix chain 'B' and resid 921 through 923 No H-bonds generated for 'chain 'B' and resid 921 through 923' Processing helix chain 'B' and resid 941 through 947 Processing helix chain 'B' and resid 980 through 984 removed outlier: 3.699A pdb=" N ASP B 983 " --> pdb=" O GLU B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1012 Processing helix chain 'B' and resid 1117 through 1126 Processing helix chain 'B' and resid 1133 through 1136 Processing helix chain 'B' and resid 1170 through 1184 removed outlier: 3.668A pdb=" N VAL B1180 " --> pdb=" O ALA B1176 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B1181 " --> pdb=" O PHE B1177 " (cutoff:3.500A) Processing helix chain 'B' and resid 1208 through 1217 Processing helix chain 'B' and resid 1266 through 1268 No H-bonds generated for 'chain 'B' and resid 1266 through 1268' Processing helix chain 'B' and resid 1290 through 1292 No H-bonds generated for 'chain 'B' and resid 1290 through 1292' Processing helix chain 'B' and resid 1296 through 1309 Proline residue: B1303 - end of helix removed outlier: 3.593A pdb=" N VAL B1309 " --> pdb=" O ILE B1305 " (cutoff:3.500A) Processing helix chain 'B' and resid 1313 through 1325 removed outlier: 5.459A pdb=" N SER B1318 " --> pdb=" O ARG B1314 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLN B1319 " --> pdb=" O SER B1315 " (cutoff:3.500A) Processing helix chain 'B' and resid 1330 through 1333 No H-bonds generated for 'chain 'B' and resid 1330 through 1333' Processing helix chain 'B' and resid 1339 through 1354 removed outlier: 3.981A pdb=" N LYS B1347 " --> pdb=" O LEU B1343 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TRP B1353 " --> pdb=" O GLY B1349 " (cutoff:3.500A) Processing helix chain 'B' and resid 1359 through 1370 Processing helix chain 'B' and resid 1376 through 1386 Processing helix chain 'B' and resid 1390 through 1393 No H-bonds generated for 'chain 'B' and resid 1390 through 1393' Processing helix chain 'B' and resid 1409 through 1415 Processing helix chain 'B' and resid 1420 through 1436 Processing helix chain 'B' and resid 1451 through 1457 Processing helix chain 'B' and resid 1474 through 1483 removed outlier: 4.039A pdb=" N GLU B1478 " --> pdb=" O GLY B1475 " (cutoff:3.500A) Processing helix chain 'B' and resid 1503 through 1505 No H-bonds generated for 'chain 'B' and resid 1503 through 1505' Processing helix chain 'B' and resid 1521 through 1523 No H-bonds generated for 'chain 'B' and resid 1521 through 1523' Processing helix chain 'B' and resid 1527 through 1537 Processing helix chain 'B' and resid 1558 through 1563 removed outlier: 3.987A pdb=" N LEU B1563 " --> pdb=" O PHE B1559 " (cutoff:3.500A) Processing helix chain 'B' and resid 1571 through 1573 No H-bonds generated for 'chain 'B' and resid 1571 through 1573' Processing helix chain 'B' and resid 1583 through 1592 Processing helix chain 'B' and resid 1652 through 1664 Processing helix chain 'B' and resid 1676 through 1680 Processing helix chain 'B' and resid 1705 through 1707 No H-bonds generated for 'chain 'B' and resid 1705 through 1707' Processing helix chain 'B' and resid 1709 through 1719 Processing helix chain 'B' and resid 1730 through 1733 No H-bonds generated for 'chain 'B' and resid 1730 through 1733' Processing helix chain 'B' and resid 1735 through 1750 removed outlier: 3.734A pdb=" N ARG B1749 " --> pdb=" O ARG B1745 " (cutoff:3.500A) Processing helix chain 'B' and resid 1776 through 1784 Processing helix chain 'B' and resid 1814 through 1823 removed outlier: 3.896A pdb=" N SER B1823 " --> pdb=" O ARG B1819 " (cutoff:3.500A) Processing helix chain 'B' and resid 1920 through 1922 No H-bonds generated for 'chain 'B' and resid 1920 through 1922' Processing helix chain 'B' and resid 1935 through 1953 removed outlier: 3.652A pdb=" N ILE B1953 " --> pdb=" O ALA B1949 " (cutoff:3.500A) Processing helix chain 'B' and resid 1972 through 1985 Processing helix chain 'B' and resid 2018 through 2024 Processing helix chain 'B' and resid 2039 through 2051 removed outlier: 3.826A pdb=" N GLY B2043 " --> pdb=" O SER B2040 " (cutoff:3.500A) Processing helix chain 'B' and resid 2061 through 2064 No H-bonds generated for 'chain 'B' and resid 2061 through 2064' Processing helix chain 'B' and resid 2085 through 2097 Processing helix chain 'B' and resid 2099 through 2101 No H-bonds generated for 'chain 'B' and resid 2099 through 2101' Processing helix chain 'B' and resid 2111 through 2117 Processing helix chain 'B' and resid 2135 through 2138 No H-bonds generated for 'chain 'B' and resid 2135 through 2138' Processing helix chain 'B' and resid 2167 through 2179 Processing helix chain 'B' and resid 2195 through 2203 Processing helix chain 'B' and resid 2218 through 2230 removed outlier: 3.540A pdb=" N LYS B2229 " --> pdb=" O LEU B2225 " (cutoff:3.500A) Processing helix chain 'B' and resid 2256 through 2277 Proline residue: B2265 - end of helix removed outlier: 3.764A pdb=" N GLY B2269 " --> pdb=" O PRO B2265 " (cutoff:3.500A) Processing helix chain 'B' and resid 2295 through 2299 Processing helix chain 'B' and resid 2305 through 2323 Processing helix chain 'B' and resid 2341 through 2344 No H-bonds generated for 'chain 'B' and resid 2341 through 2344' Processing helix chain 'B' and resid 2348 through 2354 removed outlier: 3.515A pdb=" N ILE B2354 " --> pdb=" O ASP B2350 " (cutoff:3.500A) Processing helix chain 'B' and resid 2363 through 2385 Processing helix chain 'B' and resid 2393 through 2395 No H-bonds generated for 'chain 'B' and resid 2393 through 2395' Processing helix chain 'B' and resid 2410 through 2412 No H-bonds generated for 'chain 'B' and resid 2410 through 2412' Processing helix chain 'B' and resid 2422 through 2427 removed outlier: 5.172A pdb=" N ASN B2426 " --> pdb=" O ARG B2423 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 174 through 177 removed outlier: 5.995A pdb=" N VAL A 127 " --> pdb=" O MET A 175 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE A 177 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N VAL A 129 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A 15 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LYS A 254 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL A 13 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE A 444 " --> pdb=" O ARG A 271 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR A 273 " --> pdb=" O HIS A 442 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N HIS A 442 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL A 275 " --> pdb=" O ASN A 440 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASN A 440 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE A 316 " --> pdb=" O SER A 430 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ASN A 432 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU A 318 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N PHE A 434 " --> pdb=" O GLU A 318 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 475 through 479 Processing sheet with id= C, first strand: chain 'A' and resid 649 through 652 removed outlier: 6.298A pdb=" N VAL A 559 " --> pdb=" O THR A 650 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL A 652 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLY A 561 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE A 844 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE A 562 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE A 846 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA A 872 " --> pdb=" O GLY A 845 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLU A 847 " --> pdb=" O ALA A 872 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR A 874 " --> pdb=" O GLU A 847 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 967 through 974 removed outlier: 6.407A pdb=" N THR A1059 " --> pdb=" O SER A1049 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASN A1051 " --> pdb=" O SER A1057 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N SER A1057 " --> pdb=" O ASN A1051 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N SER A1066 " --> pdb=" O LEU A1076 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU A1076 " --> pdb=" O SER A1066 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU A1087 " --> pdb=" O VAL A1017 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL A1017 " --> pdb=" O GLU A1087 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A1242 " --> pdb=" O LEU A1250 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN A1252 " --> pdb=" O ILE A1240 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE A1240 " --> pdb=" O GLN A1252 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N MET A1141 " --> pdb=" O VAL A1115 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1235 through 1238 removed outlier: 5.848A pdb=" N LYS A1259 " --> pdb=" O PRO A1198 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1275 through 1280 removed outlier: 7.041A pdb=" N GLU A1797 " --> pdb=" O PRO A1808 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL A1798 " --> pdb=" O VAL A1756 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL A1758 " --> pdb=" O VAL A1798 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TRP A1800 " --> pdb=" O VAL A1758 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASP A1760 " --> pdb=" O TRP A1800 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER A1689 " --> pdb=" O SER A1721 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N THR A1723 " --> pdb=" O SER A1689 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N PHE A1691 " --> pdb=" O THR A1723 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N TRP A1725 " --> pdb=" O PHE A1691 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N MET A1693 " --> pdb=" O TRP A1725 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR A1727 " --> pdb=" O MET A1693 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1614 through 1618 removed outlier: 6.938A pdb=" N ILE A1442 " --> pdb=" O ASN A1465 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR A1467 " --> pdb=" O ILE A1442 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU A1444 " --> pdb=" O TYR A1467 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TYR A1469 " --> pdb=" O GLU A1444 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1828 through 1832 Processing sheet with id= I, first strand: chain 'A' and resid 1838 through 1842 Processing sheet with id= J, first strand: chain 'A' and resid 1915 through 1918 removed outlier: 7.189A pdb=" N THR A1870 " --> pdb=" O GLN A1897 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLN A1897 " --> pdb=" O THR A1870 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLN A1893 " --> pdb=" O HIS A1874 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N SER A1876 " --> pdb=" O LEU A1891 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU A1891 " --> pdb=" O SER A1876 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1875 through 1877 Processing sheet with id= L, first strand: chain 'A' and resid 1988 through 1992 removed outlier: 6.283A pdb=" N ALA A2031 " --> pdb=" O LEU A1966 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU A1968 " --> pdb=" O ALA A2031 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL A2033 " --> pdb=" O LEU A1968 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA A2057 " --> pdb=" O LEU A2032 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASP A2034 " --> pdb=" O ALA A2057 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR A2059 " --> pdb=" O ASP A2034 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 2207 through 2210 removed outlier: 7.319A pdb=" N LEU A2160 " --> pdb=" O GLY A2237 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE A2239 " --> pdb=" O LEU A2160 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL A2162 " --> pdb=" O ILE A2239 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE A2241 " --> pdb=" O VAL A2162 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N PHE A2288 " --> pdb=" O ILE A2239 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE A2241 " --> pdb=" O PHE A2288 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A2290 " --> pdb=" O PHE A2241 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER A2329 " --> pdb=" O MET A2291 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N SER A2293 " --> pdb=" O SER A2329 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE A2331 " --> pdb=" O SER A2293 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 174 through 177 removed outlier: 5.995A pdb=" N VAL B 127 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE B 177 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL B 129 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY B 15 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LYS B 254 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL B 13 " --> pdb=" O LYS B 254 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 444 " --> pdb=" O ARG B 271 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR B 273 " --> pdb=" O HIS B 442 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N HIS B 442 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL B 275 " --> pdb=" O ASN B 440 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN B 440 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE B 316 " --> pdb=" O SER B 430 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ASN B 432 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLU B 318 " --> pdb=" O ASN B 432 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N PHE B 434 " --> pdb=" O GLU B 318 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 475 through 479 Processing sheet with id= P, first strand: chain 'B' and resid 649 through 652 removed outlier: 6.299A pdb=" N VAL B 559 " --> pdb=" O THR B 650 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL B 652 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLY B 561 " --> pdb=" O VAL B 652 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE B 844 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE B 562 " --> pdb=" O ILE B 844 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE B 846 " --> pdb=" O ILE B 562 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA B 872 " --> pdb=" O GLY B 845 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLU B 847 " --> pdb=" O ALA B 872 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR B 874 " --> pdb=" O GLU B 847 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'B' and resid 967 through 974 removed outlier: 6.407A pdb=" N THR B1059 " --> pdb=" O SER B1049 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASN B1051 " --> pdb=" O SER B1057 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N SER B1057 " --> pdb=" O ASN B1051 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N SER B1066 " --> pdb=" O LEU B1076 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU B1076 " --> pdb=" O SER B1066 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU B1087 " --> pdb=" O VAL B1017 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL B1017 " --> pdb=" O GLU B1087 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL B1242 " --> pdb=" O LEU B1250 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN B1252 " --> pdb=" O ILE B1240 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE B1240 " --> pdb=" O GLN B1252 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N MET B1141 " --> pdb=" O VAL B1115 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 1235 through 1238 removed outlier: 5.849A pdb=" N LYS B1259 " --> pdb=" O PRO B1198 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 1275 through 1280 removed outlier: 7.042A pdb=" N GLU B1797 " --> pdb=" O PRO B1808 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL B1798 " --> pdb=" O VAL B1756 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL B1758 " --> pdb=" O VAL B1798 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TRP B1800 " --> pdb=" O VAL B1758 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP B1760 " --> pdb=" O TRP B1800 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER B1689 " --> pdb=" O SER B1721 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N THR B1723 " --> pdb=" O SER B1689 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N PHE B1691 " --> pdb=" O THR B1723 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N TRP B1725 " --> pdb=" O PHE B1691 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N MET B1693 " --> pdb=" O TRP B1725 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N THR B1727 " --> pdb=" O MET B1693 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 1614 through 1618 removed outlier: 6.938A pdb=" N ILE B1442 " --> pdb=" O ASN B1465 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR B1467 " --> pdb=" O ILE B1442 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU B1444 " --> pdb=" O TYR B1467 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TYR B1469 " --> pdb=" O GLU B1444 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 1828 through 1832 Processing sheet with id= V, first strand: chain 'B' and resid 1838 through 1842 Processing sheet with id= W, first strand: chain 'B' and resid 1915 through 1918 removed outlier: 7.188A pdb=" N THR B1870 " --> pdb=" O GLN B1897 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLN B1897 " --> pdb=" O THR B1870 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLN B1893 " --> pdb=" O HIS B1874 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER B1876 " --> pdb=" O LEU B1891 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU B1891 " --> pdb=" O SER B1876 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 1875 through 1877 Processing sheet with id= Y, first strand: chain 'B' and resid 1988 through 1992 removed outlier: 6.282A pdb=" N ALA B2031 " --> pdb=" O LEU B1966 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU B1968 " --> pdb=" O ALA B2031 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B2033 " --> pdb=" O LEU B1968 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA B2057 " --> pdb=" O LEU B2032 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASP B2034 " --> pdb=" O ALA B2057 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR B2059 " --> pdb=" O ASP B2034 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 2207 through 2210 removed outlier: 7.319A pdb=" N LEU B2160 " --> pdb=" O GLY B2237 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE B2239 " --> pdb=" O LEU B2160 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B2162 " --> pdb=" O ILE B2239 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE B2241 " --> pdb=" O VAL B2162 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE B2288 " --> pdb=" O ILE B2239 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N PHE B2241 " --> pdb=" O PHE B2288 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL B2290 " --> pdb=" O PHE B2241 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER B2329 " --> pdb=" O MET B2291 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N SER B2293 " --> pdb=" O SER B2329 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE B2331 " --> pdb=" O SER B2293 " (cutoff:3.500A) 1299 hydrogen bonds defined for protein. 3333 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: 32.92 Time building geometry restraints manager: 53.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 34610 1.03 - 1.23: 66 1.23 - 1.42: 15286 1.42 - 1.62: 20644 1.62 - 1.81: 308 Bond restraints: 70914 Sorted by residual: bond pdb=" C5A NAP A3500 " pdb=" N7A NAP A3500 " ideal model delta sigma weight residual 1.370 1.519 -0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" C5A NAP B3500 " pdb=" N7A NAP B3500 " ideal model delta sigma weight residual 1.370 1.518 -0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" C1B NAP B3500 " pdb=" O4B NAP B3500 " ideal model delta sigma weight residual 1.400 1.527 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C1B NAP A3500 " pdb=" O4B NAP A3500 " ideal model delta sigma weight residual 1.400 1.527 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C6A NAP B3500 " pdb=" N6A NAP B3500 " ideal model delta sigma weight residual 1.335 1.451 -0.116 2.00e-02 2.50e+03 3.38e+01 ... (remaining 70909 not shown) Histogram of bond angle deviations from ideal: 60.23 - 76.05: 20 76.05 - 91.87: 6 91.87 - 107.69: 5239 107.69 - 123.51: 116115 123.51 - 139.33: 6620 Bond angle restraints: 128000 Sorted by residual: angle pdb=" C THR A 133 " pdb=" N HIS A 134 " pdb=" H HIS A 134 " ideal model delta sigma weight residual 124.38 70.27 54.11 3.00e+00 1.11e-01 3.25e+02 angle pdb=" CA HIS A 134 " pdb=" N HIS A 134 " pdb=" H HIS A 134 " ideal model delta sigma weight residual 114.08 60.23 53.85 3.00e+00 1.11e-01 3.22e+02 angle pdb=" C LEU A 947 " pdb=" N ARG A 948 " pdb=" H ARG A 948 " ideal model delta sigma weight residual 124.09 70.35 53.74 3.00e+00 1.11e-01 3.21e+02 angle pdb=" CA ARG A 948 " pdb=" N ARG A 948 " pdb=" H ARG A 948 " ideal model delta sigma weight residual 113.79 60.78 53.01 3.00e+00 1.11e-01 3.12e+02 angle pdb=" C ALA A1622 " pdb=" N THR A1623 " pdb=" H THR A1623 " ideal model delta sigma weight residual 124.38 71.41 52.97 3.00e+00 1.11e-01 3.12e+02 ... (remaining 127995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 27016 17.99 - 35.97: 1132 35.97 - 53.96: 284 53.96 - 71.95: 116 71.95 - 89.94: 58 Dihedral angle restraints: 28606 sinusoidal: 13086 harmonic: 15520 Sorted by residual: dihedral pdb=" CA HIS B1109 " pdb=" C HIS B1109 " pdb=" N PRO B1110 " pdb=" CA PRO B1110 " ideal model delta harmonic sigma weight residual -180.00 -154.58 -25.42 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA HIS A1109 " pdb=" C HIS A1109 " pdb=" N PRO A1110 " pdb=" CA PRO A1110 " ideal model delta harmonic sigma weight residual -180.00 -154.64 -25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA PHE B 649 " pdb=" C PHE B 649 " pdb=" N THR B 650 " pdb=" CA THR B 650 " ideal model delta harmonic sigma weight residual 180.00 157.05 22.95 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 28603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 5380 0.107 - 0.214: 146 0.214 - 0.321: 2 0.321 - 0.428: 2 0.428 - 0.535: 4 Chirality restraints: 5534 Sorted by residual: chirality pdb=" CB THR A 964 " pdb=" CA THR A 964 " pdb=" OG1 THR A 964 " pdb=" CG2 THR A 964 " both_signs ideal model delta sigma weight residual False 2.55 2.02 0.53 2.00e-01 2.50e+01 7.15e+00 chirality pdb=" CB THR B 964 " pdb=" CA THR B 964 " pdb=" OG1 THR B 964 " pdb=" CG2 THR B 964 " both_signs ideal model delta sigma weight residual False 2.55 2.02 0.53 2.00e-01 2.50e+01 7.10e+00 chirality pdb=" CB THR B 216 " pdb=" CA THR B 216 " pdb=" OG1 THR B 216 " pdb=" CG2 THR B 216 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 6.11e+00 ... (remaining 5531 not shown) Planarity restraints: 10658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B2429 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO B2430 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B2430 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B2430 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A2429 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO A2430 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A2430 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A2430 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 603 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO A 604 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 604 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 604 " 0.019 5.00e-02 4.00e+02 ... (remaining 10655 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 1833 2.07 - 2.70: 121221 2.70 - 3.33: 229694 3.33 - 3.97: 297519 3.97 - 4.60: 467774 Nonbonded interactions: 1118041 Sorted by model distance: nonbonded pdb=" H ARG A 948 " pdb=" HA ARG A 948 " model vdw 1.436 1.816 nonbonded pdb=" HB THR A 216 " pdb=" HG1 THR A 216 " model vdw 1.517 1.816 nonbonded pdb=" H HIS A 320 " pdb=" OE2 GLU A 331 " model vdw 1.523 1.850 nonbonded pdb=" H HIS B 320 " pdb=" OE2 GLU B 331 " model vdw 1.523 1.850 nonbonded pdb=" O LEU B2263 " pdb=" H VAL B2267 " model vdw 1.525 1.850 ... (remaining 1118036 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 178 5.16 5 C 22396 2.51 5 N 6136 2.21 5 O 6684 1.98 5 H 34668 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.810 Extract box with map and model: 12.910 Check model and map are aligned: 0.790 Process input model: 194.450 Find NCS groups from input model: 2.710 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.520 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 225.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5623 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 : 0.004 0.149 36246 Z= 0.268 Angle : 0.657 21.213 49334 Z= 0.324 Chirality : 0.043 0.535 5534 Planarity : 0.004 0.045 6412 Dihedral : 11.465 87.448 13148 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 4472 helix: 0.13 (0.13), residues: 1710 sheet: -0.86 (0.20), residues: 590 loop : -0.51 (0.14), residues: 2172 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1834 is missing expected H atoms. Skipping. Residue SER 1834 is missing expected H atoms. Skipping. Evaluate side-chains 1111 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 997 time to evaluate : 4.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 33 residues processed: 1061 average time/residue: 2.3748 time to fit residues: 3141.2978 Evaluate side-chains 639 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 606 time to evaluate : 4.165 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 24 residues processed: 9 average time/residue: 1.9977 time to fit residues: 28.6833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 381 optimal weight: 4.9990 chunk 342 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 231 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 354 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 chunk 410 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN A 425 GLN ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN A 972 ASN A1113 ASN ** A1270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1461 GLN ** A1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2192 GLN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN B 425 GLN ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 972 ASN B1113 ASN ** B1270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1461 GLN ** B1757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2192 GLN B2194 ASN B2219 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5852 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.102 36246 Z= 0.637 Angle : 0.825 26.140 49334 Z= 0.436 Chirality : 0.056 1.409 5534 Planarity : 0.006 0.064 6412 Dihedral : 5.982 40.435 4924 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.57 % Favored : 94.34 % Rotamer Outliers : 4.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.31 (0.12), residues: 4472 helix: -0.58 (0.12), residues: 1700 sheet: -1.39 (0.20), residues: 602 loop : -0.81 (0.14), residues: 2170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1834 is missing expected H atoms. Skipping. Residue SER 1834 is missing expected H atoms. Skipping. Evaluate side-chains 795 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 607 time to evaluate : 4.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 188 outliers final: 73 residues processed: 737 average time/residue: 2.2394 time to fit residues: 2086.3141 Evaluate side-chains 586 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 513 time to evaluate : 4.180 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 58 residues processed: 18 average time/residue: 1.0385 time to fit residues: 34.6684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 228 optimal weight: 0.3980 chunk 127 optimal weight: 9.9990 chunk 341 optimal weight: 0.6980 chunk 279 optimal weight: 9.9990 chunk 113 optimal weight: 0.2980 chunk 411 optimal weight: 2.9990 chunk 444 optimal weight: 3.9990 chunk 366 optimal weight: 3.9990 chunk 407 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 329 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1081 GLN ** A1270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2192 GLN A2219 ASN ** A2315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1081 GLN ** B1270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1376 HIS ** B1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2192 GLN B2219 ASN ** B2315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5823 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.102 36246 Z= 0.302 Angle : 0.668 25.218 49334 Z= 0.346 Chirality : 0.049 1.374 5534 Planarity : 0.005 0.052 6412 Dihedral : 5.657 35.965 4924 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.66 % Favored : 94.25 % Rotamer Outliers : 3.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.20 (0.13), residues: 4472 helix: -0.43 (0.12), residues: 1702 sheet: -1.54 (0.20), residues: 608 loop : -0.72 (0.14), residues: 2162 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1834 is missing expected H atoms. Skipping. Residue SER 1834 is missing expected H atoms. Skipping. Evaluate side-chains 684 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 538 time to evaluate : 4.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 146 outliers final: 80 residues processed: 643 average time/residue: 2.1141 time to fit residues: 1750.2421 Evaluate side-chains 579 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 499 time to evaluate : 4.182 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 67 residues processed: 13 average time/residue: 0.9916 time to fit residues: 26.0094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 406 optimal weight: 4.9990 chunk 309 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 196 optimal weight: 0.9990 chunk 276 optimal weight: 5.9990 chunk 412 optimal weight: 1.9990 chunk 436 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 391 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2192 GLN A2219 ASN ** A2315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2426 ASN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1757 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2192 GLN B2219 ASN ** B2315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2426 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5836 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 36246 Z= 0.338 Angle : 0.660 25.622 49334 Z= 0.341 Chirality : 0.050 1.370 5534 Planarity : 0.005 0.055 6412 Dihedral : 5.596 34.628 4924 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.72 % Favored : 94.19 % Rotamer Outliers : 4.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.22 (0.13), residues: 4472 helix: -0.46 (0.12), residues: 1704 sheet: -1.71 (0.19), residues: 630 loop : -0.64 (0.14), residues: 2138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1834 is missing expected H atoms. Skipping. Residue SER 1834 is missing expected H atoms. Skipping. Evaluate side-chains 677 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 517 time to evaluate : 4.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 160 outliers final: 95 residues processed: 633 average time/residue: 2.1318 time to fit residues: 1735.3996 Evaluate side-chains 596 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 501 time to evaluate : 4.195 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 79 residues processed: 16 average time/residue: 1.1688 time to fit residues: 33.6474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 363 optimal weight: 0.3980 chunk 248 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 325 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 372 optimal weight: 0.1980 chunk 302 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 223 optimal weight: 0.4980 chunk 392 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2192 GLN A2219 ASN ** A2315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2192 GLN B2219 ASN ** B2315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 36246 Z= 0.224 Angle : 0.627 25.762 49334 Z= 0.322 Chirality : 0.049 1.372 5534 Planarity : 0.004 0.060 6412 Dihedral : 5.412 33.847 4924 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.70 % Favored : 94.21 % Rotamer Outliers : 3.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.12 (0.13), residues: 4472 helix: -0.36 (0.12), residues: 1704 sheet: -1.62 (0.19), residues: 620 loop : -0.63 (0.14), residues: 2148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1834 is missing expected H atoms. Skipping. Residue SER 1834 is missing expected H atoms. Skipping. Evaluate side-chains 669 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 538 time to evaluate : 4.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 97 residues processed: 639 average time/residue: 2.1728 time to fit residues: 1801.1356 Evaluate side-chains 593 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 496 time to evaluate : 4.201 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 79 residues processed: 19 average time/residue: 1.3095 time to fit residues: 41.8064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 146 optimal weight: 7.9990 chunk 393 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 256 optimal weight: 2.9990 chunk 107 optimal weight: 0.3980 chunk 437 optimal weight: 1.9990 chunk 363 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 36 optimal weight: 0.1980 chunk 144 optimal weight: 5.9990 chunk 229 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2192 GLN A2219 ASN ** A2315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2192 GLN B2219 ASN ** B2315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5813 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 36246 Z= 0.237 Angle : 0.622 25.891 49334 Z= 0.318 Chirality : 0.049 1.381 5534 Planarity : 0.004 0.066 6412 Dihedral : 5.317 32.976 4924 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.61 % Favored : 94.30 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.06 (0.13), residues: 4472 helix: -0.30 (0.12), residues: 1706 sheet: -1.58 (0.20), residues: 612 loop : -0.62 (0.14), residues: 2154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1834 is missing expected H atoms. Skipping. Residue SER 1834 is missing expected H atoms. Skipping. Evaluate side-chains 650 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 518 time to evaluate : 4.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 132 outliers final: 96 residues processed: 621 average time/residue: 2.1871 time to fit residues: 1733.9152 Evaluate side-chains 602 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 506 time to evaluate : 4.232 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 80 residues processed: 17 average time/residue: 0.9820 time to fit residues: 32.1703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 421 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 319 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 chunk 368 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 435 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 265 optimal weight: 0.5980 chunk 201 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2192 GLN A2219 ASN ** A2315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2192 GLN B2219 ASN ** B2315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5825 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 36246 Z= 0.284 Angle : 0.635 25.917 49334 Z= 0.326 Chirality : 0.049 1.401 5534 Planarity : 0.004 0.056 6412 Dihedral : 5.332 33.292 4924 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.68 % Favored : 94.23 % Rotamer Outliers : 3.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.05 (0.13), residues: 4472 helix: -0.27 (0.12), residues: 1702 sheet: -1.55 (0.20), residues: 602 loop : -0.65 (0.14), residues: 2168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1834 is missing expected H atoms. Skipping. Residue SER 1834 is missing expected H atoms. Skipping. Evaluate side-chains 640 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 511 time to evaluate : 4.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 129 outliers final: 97 residues processed: 612 average time/residue: 2.1804 time to fit residues: 1704.5796 Evaluate side-chains 581 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 484 time to evaluate : 4.269 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 84 residues processed: 13 average time/residue: 1.2071 time to fit residues: 28.9033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 269 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 260 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 276 optimal weight: 4.9990 chunk 296 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 342 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2192 GLN A2219 ASN ** A2315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2192 GLN B2219 ASN ** B2315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5816 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 36246 Z= 0.242 Angle : 0.625 25.996 49334 Z= 0.319 Chirality : 0.049 1.405 5534 Planarity : 0.004 0.066 6412 Dihedral : 5.264 33.217 4924 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.86 % Favored : 94.05 % Rotamer Outliers : 3.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.02 (0.13), residues: 4472 helix: -0.24 (0.12), residues: 1702 sheet: -1.56 (0.20), residues: 602 loop : -0.62 (0.14), residues: 2168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1834 is missing expected H atoms. Skipping. Residue SER 1834 is missing expected H atoms. Skipping. Evaluate side-chains 629 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 506 time to evaluate : 4.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 94 residues processed: 601 average time/residue: 2.2406 time to fit residues: 1717.1118 Evaluate side-chains 581 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 487 time to evaluate : 4.212 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 83 residues processed: 11 average time/residue: 1.0549 time to fit residues: 23.5745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 396 optimal weight: 3.9990 chunk 417 optimal weight: 5.9990 chunk 380 optimal weight: 5.9990 chunk 405 optimal weight: 8.9990 chunk 244 optimal weight: 0.9990 chunk 176 optimal weight: 0.6980 chunk 318 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 366 optimal weight: 6.9990 chunk 383 optimal weight: 3.9990 chunk 404 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2192 GLN A2219 ASN ** A2315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2192 GLN B2219 ASN ** B2315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5863 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.074 36246 Z= 0.474 Angle : 0.714 25.890 49334 Z= 0.370 Chirality : 0.053 1.472 5534 Planarity : 0.005 0.060 6412 Dihedral : 5.645 35.337 4924 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.13 % Favored : 93.81 % Rotamer Outliers : 3.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.35 (0.12), residues: 4472 helix: -0.46 (0.12), residues: 1682 sheet: -1.84 (0.20), residues: 568 loop : -0.85 (0.14), residues: 2222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1834 is missing expected H atoms. Skipping. Residue SER 1834 is missing expected H atoms. Skipping. Evaluate side-chains 629 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 506 time to evaluate : 4.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 89 residues processed: 601 average time/residue: 2.2461 time to fit residues: 1722.9253 Evaluate side-chains 575 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 486 time to evaluate : 4.292 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 80 residues processed: 10 average time/residue: 1.1780 time to fit residues: 23.6823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 266 optimal weight: 0.6980 chunk 429 optimal weight: 1.9990 chunk 262 optimal weight: 0.0980 chunk 203 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 chunk 450 optimal weight: 0.9980 chunk 414 optimal weight: 0.7980 chunk 358 optimal weight: 7.9990 chunk 37 optimal weight: 0.5980 chunk 276 optimal weight: 1.9990 chunk 219 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2192 GLN A2219 ASN A2315 GLN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2192 GLN B2219 ASN ** B2315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5819 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 36246 Z= 0.221 Angle : 0.647 25.731 49334 Z= 0.331 Chirality : 0.050 1.412 5534 Planarity : 0.004 0.058 6412 Dihedral : 5.420 36.366 4924 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.86 % Favored : 94.07 % Rotamer Outliers : 2.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.25 (0.12), residues: 4472 helix: -0.36 (0.12), residues: 1702 sheet: -1.97 (0.20), residues: 586 loop : -0.73 (0.14), residues: 2184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8944 Ramachandran restraints generated. 4472 Oldfield, 0 Emsley, 4472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1834 is missing expected H atoms. Skipping. Residue SER 1834 is missing expected H atoms. Skipping. Evaluate side-chains 597 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 503 time to evaluate : 4.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 80 residues processed: 587 average time/residue: 2.2111 time to fit residues: 1659.8368 Evaluate side-chains 559 residues out of total 3812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 479 time to evaluate : 4.216 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 77 residues processed: 3 average time/residue: 0.7055 time to fit residues: 9.3750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 284 optimal weight: 10.0000 chunk 381 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 330 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 99 optimal weight: 0.6980 chunk 359 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 368 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 chunk 66 optimal weight: 0.0050 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1162 ASN A2192 GLN A2219 ASN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1162 ASN B2192 GLN B2219 ASN B2315 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.201173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.153826 restraints weight = 120909.874| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.70 r_work: 0.3507 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 36246 Z= 0.241 Angle : 0.642 26.272 49334 Z= 0.329 Chirality : 0.050 1.414 5534 Planarity : 0.004 0.057 6412 Dihedral : 5.329 34.268 4924 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.86 % Favored : 94.07 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.16 (0.13), residues: 4472 helix: -0.28 (0.12), residues: 1692 sheet: -1.96 (0.20), residues: 596 loop : -0.67 (0.14), residues: 2184 =============================================================================== Job complete usr+sys time: 26488.16 seconds wall clock time: 455 minutes 50.60 seconds (27350.60 seconds total)