Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 14 08:14:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye1_33761/07_2023/7ye1_33761_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye1_33761/07_2023/7ye1_33761.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye1_33761/07_2023/7ye1_33761_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye1_33761/07_2023/7ye1_33761_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye1_33761/07_2023/7ye1_33761_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye1_33761/07_2023/7ye1_33761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye1_33761/07_2023/7ye1_33761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye1_33761/07_2023/7ye1_33761_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye1_33761/07_2023/7ye1_33761_updated.pdb" } resolution = 3.7 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 3 6.06 5 P 114 5.49 5 Mg 1 5.21 5 S 112 5.16 5 C 18782 2.51 5 N 5029 2.21 5 O 5911 1.98 5 H 12 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A ARG 36": "NH1" <-> "NH2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "C GLU 387": "OE1" <-> "OE2" Residue "C ARG 426": "NH1" <-> "NH2" Residue "C GLU 480": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 596": "OE1" <-> "OE2" Residue "C GLU 746": "OE1" <-> "OE2" Residue "C ARG 751": "NH1" <-> "NH2" Residue "C GLU 796": "OE1" <-> "OE2" Residue "C GLU 840": "OE1" <-> "OE2" Residue "C GLU 873": "OE1" <-> "OE2" Residue "C GLU 882": "OE1" <-> "OE2" Residue "C GLU 914": "OE1" <-> "OE2" Residue "C ARG 966": "NH1" <-> "NH2" Residue "C GLU 983": "OE1" <-> "OE2" Residue "C GLU 1233": "OE1" <-> "OE2" Residue "C GLU 1288": "OE1" <-> "OE2" Residue "C GLU 1293": "OE1" <-> "OE2" Residue "C GLU 1330": "OE1" <-> "OE2" Residue "C GLU 1343": "OE1" <-> "OE2" Residue "D GLU 149": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D GLU 286": "OE1" <-> "OE2" Residue "D PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 600": "OE1" <-> "OE2" Residue "D GLU 631": "OE1" <-> "OE2" Residue "D GLU 862": "OE1" <-> "OE2" Residue "D GLU 869": "OE1" <-> "OE2" Residue "D GLU 1223": "OE1" <-> "OE2" Residue "D GLU 1250": "OE1" <-> "OE2" Residue "D GLU 1280": "OE1" <-> "OE2" Residue "D GLU 1330": "OE1" <-> "OE2" Residue "F GLU 142": "OE1" <-> "OE2" Residue "F GLU 371": "OE1" <-> "OE2" Residue "F GLU 447": "OE1" <-> "OE2" Residue "F GLU 543": "OE1" <-> "OE2" Residue "F GLU 554": "OE1" <-> "OE2" Residue "F GLU 555": "OE1" <-> "OE2" Residue "F GLU 564": "OE1" <-> "OE2" Residue "F ARG 624": "NH1" <-> "NH2" Residue "G ARG 42": "NH1" <-> "NH2" Residue "G GLU 128": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 29964 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2208 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 19, 'TRANS': 287} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 132 Chain: "B" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1675 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 10, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 9879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1312, 9879 Classifications: {'peptide': 1312} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 61, 'TRANS': 1250} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 443 Unresolved non-hydrogen angles: 608 Unresolved non-hydrogen dihedrals: 320 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 11, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 82} Unresolved non-hydrogen planarities: 348 Chain: "D" Number of atoms: 8723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 8723 Classifications: {'peptide': 1144} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 52, 'TRANS': 1091} Chain breaks: 3 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 73, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 195 Chain: "E" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 518 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3851 Classifications: {'peptide': 497} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 484} Chain breaks: 1 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 41} Unresolved non-hydrogen planarities: 114 Chain: "G" Number of atoms: 754 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 103, 745 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 103, 745 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 748 Chain: "H" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1178 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "I" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1174 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14207 SG CYS D 71 109.392 81.251 68.315 1.00 96.66 S ATOM 14221 SG CYS D 73 110.679 81.121 63.435 1.00 98.64 S ATOM 14319 SG CYS D 86 112.978 80.884 66.280 1.00 91.81 S ATOM 19846 SG CYS D 810 82.521 97.575 127.904 1.00 87.13 S ATOM 20372 SG CYS D 884 82.795 99.418 124.051 1.00 82.67 S ATOM 20420 SG CYS D 891 81.529 96.080 124.891 1.00 77.69 S ATOM 20435 SG CYS D 894 79.128 98.696 126.448 1.00 75.45 S ATOM 27304 SG CYS G 118 119.424 146.216 55.086 1.00141.87 S ATOM 27421 SG CYS G 133 120.720 147.904 52.024 1.00142.98 S ATOM 27488 SG CYS G 143 116.662 148.828 54.459 1.00133.19 S Time building chain proxies: 14.51, per 1000 atoms: 0.48 Number of scatterers: 29964 At special positions: 0 Unit cell: (169.338, 188.604, 161.226, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 S 112 16.00 P 114 15.00 Mg 1 11.99 O 5911 8.00 N 5029 7.00 C 18782 6.00 H 12 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: 13.24 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 86 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 71 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 73 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 894 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 884 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 810 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 891 " pdb=" ZN G2001 " pdb="ZN ZN G2001 " - pdb=" ND1 HIS G 146 " pdb="ZN ZN G2001 " - pdb=" SG CYS G 118 " pdb="ZN ZN G2001 " - pdb=" SG CYS G 133 " pdb="ZN ZN G2001 " - pdb=" SG CYS G 143 " Number of angles added : 9 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6754 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 130 helices and 22 sheets defined 37.8% alpha, 4.4% beta 39 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 9.94 Creating SS restraints... Processing helix chain 'A' and resid 39 through 50 removed outlier: 3.658A pdb=" N GLY A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 88 removed outlier: 3.561A pdb=" N ASN A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 230 removed outlier: 3.506A pdb=" N VAL A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 218 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 265 through 274 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 288 through 291 No H-bonds generated for 'chain 'A' and resid 288 through 291' Processing helix chain 'A' and resid 298 through 310 removed outlier: 4.060A pdb=" N ASN A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'B' and resid 38 through 50 removed outlier: 3.642A pdb=" N GLY B 43 " --> pdb=" O GLY B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 212 through 226 Processing helix chain 'C' and resid 29 through 38 removed outlier: 3.531A pdb=" N GLN C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 59 Processing helix chain 'C' and resid 86 through 92 removed outlier: 4.035A pdb=" N GLN C 91 " --> pdb=" O GLU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 212 through 218 Processing helix chain 'C' and resid 223 through 228 removed outlier: 3.775A pdb=" N ILE C 226 " --> pdb=" O GLY C 223 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR C 228 " --> pdb=" O GLU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 330 through 334 removed outlier: 4.310A pdb=" N ALA C 334 " --> pdb=" O ILE C 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 330 through 334' Processing helix chain 'C' and resid 354 through 360 removed outlier: 3.715A pdb=" N LEU C 359 " --> pdb=" O MET C 355 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG C 360 " --> pdb=" O ARG C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 378 Processing helix chain 'C' and resid 386 through 396 removed outlier: 3.630A pdb=" N ALA C 391 " --> pdb=" O GLU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 416 Processing helix chain 'C' and resid 430 through 445 removed outlier: 4.077A pdb=" N LEU C 434 " --> pdb=" O LYS C 430 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 458 No H-bonds generated for 'chain 'C' and resid 456 through 458' Processing helix chain 'C' and resid 464 through 486 Processing helix chain 'C' and resid 507 through 515 removed outlier: 3.720A pdb=" N PHE C 513 " --> pdb=" O ALA C 509 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE C 514 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 533 removed outlier: 3.701A pdb=" N ILE C 532 " --> pdb=" O PRO C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 550 No H-bonds generated for 'chain 'C' and resid 548 through 550' Processing helix chain 'C' and resid 618 through 621 removed outlier: 3.772A pdb=" N LYS C 621 " --> pdb=" O GLU C 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 618 through 621' Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.830A pdb=" N LEU C 674 " --> pdb=" O VAL C 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 670 through 674' Processing helix chain 'C' and resid 683 through 695 removed outlier: 3.559A pdb=" N MET C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG C 694 " --> pdb=" O SER C 690 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN C 695 " --> pdb=" O ASN C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 718 Processing helix chain 'C' and resid 826 through 830 removed outlier: 3.524A pdb=" N ARG C 830 " --> pdb=" O ARG C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 868 No H-bonds generated for 'chain 'C' and resid 866 through 868' Processing helix chain 'C' and resid 903 through 912 Processing helix chain 'C' and resid 952 through 985 Processing helix chain 'C' and resid 1013 through 1015 No H-bonds generated for 'chain 'C' and resid 1013 through 1015' Processing helix chain 'C' and resid 1024 through 1056 removed outlier: 4.473A pdb=" N GLU C1028 " --> pdb=" O LYS C1024 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU C1035 " --> pdb=" O SER C1031 " (cutoff:3.500A) Processing helix chain 'C' and resid 1107 through 1109 No H-bonds generated for 'chain 'C' and resid 1107 through 1109' Processing helix chain 'C' and resid 1118 through 1123 removed outlier: 3.809A pdb=" N VAL C1121 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Proline residue: C1122 - end of helix No H-bonds generated for 'chain 'C' and resid 1118 through 1123' Processing helix chain 'C' and resid 1128 through 1152 removed outlier: 3.613A pdb=" N LEU C1149 " --> pdb=" O GLN C1145 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C1150 " --> pdb=" O ILE C1146 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP C1152 " --> pdb=" O ASN C1148 " (cutoff:3.500A) Processing helix chain 'C' and resid 1157 through 1166 Processing helix chain 'C' and resid 1181 through 1192 removed outlier: 3.924A pdb=" N GLY C1191 " --> pdb=" O ARG C1188 " (cutoff:3.500A) Processing helix chain 'C' and resid 1206 through 1216 Processing helix chain 'C' and resid 1286 through 1294 removed outlier: 3.573A pdb=" N LEU C1292 " --> pdb=" O GLU C1288 " (cutoff:3.500A) Processing helix chain 'C' and resid 1299 through 1306 removed outlier: 3.644A pdb=" N LEU C1305 " --> pdb=" O LEU C1301 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C1306 " --> pdb=" O GLN C1302 " (cutoff:3.500A) Processing helix chain 'C' and resid 1315 through 1324 removed outlier: 3.853A pdb=" N TYR C1319 " --> pdb=" O ARG C1315 " (cutoff:3.500A) Processing helix chain 'C' and resid 1335 through 1346 Processing helix chain 'D' and resid 28 through 34 Processing helix chain 'D' and resid 60 through 63 No H-bonds generated for 'chain 'D' and resid 60 through 63' Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 116 through 119 No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 124 through 130 removed outlier: 3.690A pdb=" N MET D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LEU D 129 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 124 through 130' Processing helix chain 'D' and resid 133 through 140 removed outlier: 3.700A pdb=" N ARG D 138 " --> pdb=" O LYS D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 168 Processing helix chain 'D' and resid 184 through 193 Processing helix chain 'D' and resid 197 through 207 Processing helix chain 'D' and resid 215 through 231 removed outlier: 4.158A pdb=" N LYS D 221 " --> pdb=" O LYS D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 238 No H-bonds generated for 'chain 'D' and resid 236 through 238' Processing helix chain 'D' and resid 267 through 287 Processing helix chain 'D' and resid 291 through 309 removed outlier: 3.666A pdb=" N PHE D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 333 removed outlier: 3.666A pdb=" N LEU D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 329 through 333' Processing helix chain 'D' and resid 372 through 378 removed outlier: 3.525A pdb=" N GLU D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 390 Processing helix chain 'D' and resid 396 through 405 removed outlier: 3.604A pdb=" N GLU D 404 " --> pdb=" O LYS D 400 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG D 405 " --> pdb=" O ARG D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 417 removed outlier: 3.534A pdb=" N TRP D 411 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP D 412 " --> pdb=" O GLN D 409 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU D 415 " --> pdb=" O ASP D 412 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 417 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 435 No H-bonds generated for 'chain 'D' and resid 433 through 435' Processing helix chain 'D' and resid 455 through 459 Processing helix chain 'D' and resid 476 through 483 removed outlier: 3.606A pdb=" N ARG D 483 " --> pdb=" O GLN D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 516 Processing helix chain 'D' and resid 532 through 541 Processing helix chain 'D' and resid 578 through 580 No H-bonds generated for 'chain 'D' and resid 578 through 580' Processing helix chain 'D' and resid 589 through 593 removed outlier: 3.661A pdb=" N GLU D 593 " --> pdb=" O ARG D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 611 removed outlier: 3.519A pdb=" N ASP D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 632 removed outlier: 3.688A pdb=" N GLY D 626 " --> pdb=" O ASP D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 667 removed outlier: 3.671A pdb=" N THR D 651 " --> pdb=" O VAL D 648 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL D 654 " --> pdb=" O THR D 651 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU D 663 " --> pdb=" O LEU D 660 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN D 666 " --> pdb=" O GLU D 663 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN D 667 " --> pdb=" O TYR D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 removed outlier: 3.741A pdb=" N VAL D 682 " --> pdb=" O LYS D 678 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP D 684 " --> pdb=" O ASN D 680 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA D 685 " --> pdb=" O LYS D 681 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP D 686 " --> pdb=" O VAL D 682 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA D 687 " --> pdb=" O VAL D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 724 Processing helix chain 'D' and resid 730 through 737 Processing helix chain 'D' and resid 765 through 799 removed outlier: 3.735A pdb=" N ASN D 770 " --> pdb=" O GLN D 766 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER D 771 " --> pdb=" O GLU D 767 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D 784 " --> pdb=" O ALA D 780 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR D 786 " --> pdb=" O THR D 782 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA D 787 " --> pdb=" O ALA D 783 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN D 788 " --> pdb=" O LEU D 784 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP D 798 " --> pdb=" O ARG D 794 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL D 799 " --> pdb=" O ARG D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 835 Processing helix chain 'D' and resid 862 through 870 Processing helix chain 'D' and resid 892 through 895 No H-bonds generated for 'chain 'D' and resid 892 through 895' Processing helix chain 'D' and resid 911 through 921 Processing helix chain 'D' and resid 1129 through 1137 Processing helix chain 'D' and resid 1213 through 1219 Processing helix chain 'D' and resid 1222 through 1238 Processing helix chain 'D' and resid 1246 through 1256 Processing helix chain 'D' and resid 1276 through 1289 removed outlier: 3.775A pdb=" N GLU D1280 " --> pdb=" O LEU D1276 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU D1284 " --> pdb=" O GLU D1280 " (cutoff:3.500A) Processing helix chain 'D' and resid 1305 through 1308 No H-bonds generated for 'chain 'D' and resid 1305 through 1308' Processing helix chain 'D' and resid 1315 through 1321 removed outlier: 4.157A pdb=" N PHE D1321 " --> pdb=" O SER D1317 " (cutoff:3.500A) Processing helix chain 'D' and resid 1324 through 1334 removed outlier: 3.618A pdb=" N VAL D1333 " --> pdb=" O THR D1329 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS D1334 " --> pdb=" O GLU D1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 1343 through 1349 Processing helix chain 'D' and resid 1357 through 1379 removed outlier: 3.678A pdb=" N GLN D1378 " --> pdb=" O GLN D1374 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG D1379 " --> pdb=" O LEU D1375 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 12 Processing helix chain 'E' and resid 18 through 30 Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.621A pdb=" N ALA E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP E 55 " --> pdb=" O ARG E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 67 Processing helix chain 'F' and resid 115 through 126 removed outlier: 3.595A pdb=" N VAL F 126 " --> pdb=" O GLU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 152 Processing helix chain 'F' and resid 159 through 168 removed outlier: 3.685A pdb=" N VAL F 164 " --> pdb=" O GLU F 160 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TRP F 165 " --> pdb=" O ALA F 161 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU F 168 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 188 Processing helix chain 'F' and resid 242 through 259 removed outlier: 4.360A pdb=" N SER F 256 " --> pdb=" O ASP F 252 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU F 257 " --> pdb=" O ALA F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 274 removed outlier: 4.580A pdb=" N ASP F 266 " --> pdb=" O ARG F 262 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS F 267 " --> pdb=" O LYS F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 298 removed outlier: 4.153A pdb=" N GLY F 288 " --> pdb=" O LYS F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 332 Processing helix chain 'F' and resid 339 through 348 Processing helix chain 'F' and resid 355 through 362 removed outlier: 4.124A pdb=" N LYS F 360 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA F 361 " --> pdb=" O GLU F 357 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET F 362 " --> pdb=" O GLN F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 368 removed outlier: 4.184A pdb=" N LYS F 368 " --> pdb=" O ARG F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 391 removed outlier: 4.683A pdb=" N ASP F 379 " --> pdb=" O GLN F 375 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR F 391 " --> pdb=" O LEU F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 422 removed outlier: 3.978A pdb=" N VAL F 405 " --> pdb=" O ILE F 401 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN F 406 " --> pdb=" O VAL F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 433 removed outlier: 3.618A pdb=" N VAL F 427 " --> pdb=" O LEU F 424 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA F 431 " --> pdb=" O ILE F 428 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS F 432 " --> pdb=" O SER F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 455 Processing helix chain 'F' and resid 467 through 486 removed outlier: 4.512A pdb=" N TRP F 473 " --> pdb=" O THR F 469 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TRP F 474 " --> pdb=" O TYR F 470 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA F 484 " --> pdb=" O THR F 480 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP F 485 " --> pdb=" O ARG F 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 513 Processing helix chain 'F' and resid 520 through 527 removed outlier: 3.699A pdb=" N ALA F 524 " --> pdb=" O PRO F 520 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU F 525 " --> pdb=" O GLU F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 537 Processing helix chain 'F' and resid 571 through 587 removed outlier: 3.706A pdb=" N THR F 585 " --> pdb=" O ARG F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 593 through 602 Processing helix chain 'F' and resid 613 through 619 removed outlier: 3.647A pdb=" N GLN F 619 " --> pdb=" O GLU F 615 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 638 removed outlier: 3.813A pdb=" N GLN F 629 " --> pdb=" O GLU F 625 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 651 removed outlier: 3.669A pdb=" N SER F 649 " --> pdb=" O LYS F 646 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE F 650 " --> pdb=" O LEU F 647 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 17 Processing helix chain 'G' and resid 21 through 28 removed outlier: 4.156A pdb=" N ALA G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS G 26 " --> pdb=" O SER G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 43 Processing helix chain 'G' and resid 144 through 150 removed outlier: 4.172A pdb=" N ARG G 148 " --> pdb=" O VAL G 144 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N VAL G 149 " --> pdb=" O GLU G 145 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 26 through 31 removed outlier: 3.678A pdb=" N ALA A 27 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 104 through 107 removed outlier: 3.738A pdb=" N ALA A 107 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 142 " --> pdb=" O ALA A 107 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 179 through 182 removed outlier: 7.110A pdb=" N GLU A 206 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 26 through 28 Processing sheet with id= E, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= F, first strand: chain 'C' and resid 12 through 14 No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 126 through 130 removed outlier: 3.899A pdb=" N LEU C 100 " --> pdb=" O MET C 130 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER C 76 " --> pdb=" O LYS C 103 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG C 105 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N TYR C 74 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 154 through 157 Processing sheet with id= I, first strand: chain 'C' and resid 162 through 164 Processing sheet with id= J, first strand: chain 'C' and resid 611 through 615 Processing sheet with id= K, first strand: chain 'C' and resid 739 through 741 Processing sheet with id= L, first strand: chain 'C' and resid 805 through 809 removed outlier: 3.632A pdb=" N ALA C 806 " --> pdb=" O ILE C1244 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 822 through 824 removed outlier: 3.571A pdb=" N LEU C 823 " --> pdb=" O VAL C1115 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 836 through 839 Processing sheet with id= O, first strand: chain 'C' and resid 842 through 845 Processing sheet with id= P, first strand: chain 'C' and resid 893 through 895 Processing sheet with id= Q, first strand: chain 'C' and resid 642 through 646 removed outlier: 3.915A pdb=" N GLY C 643 " --> pdb=" O THR C 650 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 645 " --> pdb=" O GLU C 648 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU C 648 " --> pdb=" O ILE C 645 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 104 through 107 Processing sheet with id= S, first strand: chain 'D' and resid 146 through 148 removed outlier: 3.603A pdb=" N THR D 179 " --> pdb=" O THR D 148 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 352 through 356 Processing sheet with id= U, first strand: chain 'D' and resid 551 through 553 Processing sheet with id= V, first strand: chain 'D' and resid 816 through 818 removed outlier: 3.624A pdb=" N LEU D 818 " --> pdb=" O VAL D 876 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL D 876 " --> pdb=" O LEU D 818 " (cutoff:3.500A) 858 hydrogen bonds defined for protein. 2419 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 198 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 13.10 Time building geometry restraints manager: 13.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 12 1.05 - 1.24: 3887 1.24 - 1.43: 8428 1.43 - 1.62: 18150 1.62 - 1.81: 201 Bond restraints: 30678 Sorted by residual: bond pdb=" C4' 6MA I 19 " pdb=" C3' 6MA I 19 " ideal model delta sigma weight residual 1.672 1.314 0.358 2.00e-02 2.50e+03 3.21e+02 bond pdb=" C3' 6MA H -21 " pdb=" C2' 6MA H -21 " ideal model delta sigma weight residual 1.232 1.587 -0.355 2.00e-02 2.50e+03 3.15e+02 bond pdb=" C4' 6MA H -21 " pdb=" C3' 6MA H -21 " ideal model delta sigma weight residual 1.672 1.318 0.354 2.00e-02 2.50e+03 3.13e+02 bond pdb=" C3' 6MA I 19 " pdb=" C2' 6MA I 19 " ideal model delta sigma weight residual 1.232 1.579 -0.347 2.00e-02 2.50e+03 3.01e+02 bond pdb=" C4' 6MA I 19 " pdb=" O4' 6MA I 19 " ideal model delta sigma weight residual 1.291 1.623 -0.332 2.00e-02 2.50e+03 2.76e+02 ... (remaining 30673 not shown) Histogram of bond angle deviations from ideal: 98.69 - 108.80: 2594 108.80 - 118.91: 23691 118.91 - 129.02: 15415 129.02 - 139.13: 176 139.13 - 149.24: 2 Bond angle restraints: 41878 Sorted by residual: angle pdb=" C1' 6MA I 19 " pdb=" N9 6MA I 19 " pdb=" C8 6MA I 19 " ideal model delta sigma weight residual 132.95 101.91 31.04 3.00e+00 1.11e-01 1.07e+02 angle pdb=" C1' 6MA I 19 " pdb=" N9 6MA I 19 " pdb=" C4 6MA I 19 " ideal model delta sigma weight residual 118.25 149.24 -30.99 3.00e+00 1.11e-01 1.07e+02 angle pdb=" C1' 6MA H -21 " pdb=" N9 6MA H -21 " pdb=" C4 6MA H -21 " ideal model delta sigma weight residual 118.25 148.49 -30.24 3.00e+00 1.11e-01 1.02e+02 angle pdb=" C1' 6MA H -21 " pdb=" N9 6MA H -21 " pdb=" C8 6MA H -21 " ideal model delta sigma weight residual 132.95 103.14 29.81 3.00e+00 1.11e-01 9.87e+01 angle pdb=" C GLY B 111 " pdb=" N PRO B 112 " pdb=" CA PRO B 112 " ideal model delta sigma weight residual 119.90 114.30 5.60 1.05e+00 9.07e-01 2.84e+01 ... (remaining 41873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 17863 35.82 - 71.63: 495 71.63 - 107.45: 15 107.45 - 143.26: 5 143.26 - 179.08: 4 Dihedral angle restraints: 18382 sinusoidal: 7971 harmonic: 10411 Sorted by residual: dihedral pdb=" C4' DA I 35 " pdb=" C3' DA I 35 " pdb=" O3' DA I 35 " pdb=" P DC I 36 " ideal model delta sinusoidal sigma weight residual 220.00 40.92 179.08 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' 6MA H -21 " pdb=" C3' 6MA H -21 " pdb=" O3' 6MA H -21 " pdb=" P DA H -20 " ideal model delta sinusoidal sigma weight residual 220.00 43.51 176.49 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT I 0 " pdb=" C3' DT I 0 " pdb=" O3' DT I 0 " pdb=" P DC I 1 " ideal model delta sinusoidal sigma weight residual 220.00 43.51 176.49 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 18379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 4062 0.046 - 0.092: 602 0.092 - 0.137: 208 0.137 - 0.183: 3 0.183 - 0.229: 2 Chirality restraints: 4877 Sorted by residual: chirality pdb=" C1' 6MA H -21 " pdb=" O4' 6MA H -21 " pdb=" C2' 6MA H -21 " pdb=" N9 6MA H -21 " both_signs ideal model delta sigma weight residual False 2.54 2.31 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C1' 6MA I 19 " pdb=" O4' 6MA I 19 " pdb=" C2' 6MA I 19 " pdb=" N9 6MA I 19 " both_signs ideal model delta sigma weight residual False 2.54 2.34 0.19 2.00e-01 2.50e+01 9.15e-01 chirality pdb=" CB ILE D 755 " pdb=" CA ILE D 755 " pdb=" CG1 ILE D 755 " pdb=" CG2 ILE D 755 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 4874 not shown) Planarity restraints: 4959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 1 " 0.024 2.00e-02 2.50e+03 1.36e-02 4.16e+00 pdb=" N1 DC I 1 " -0.015 2.00e-02 2.50e+03 pdb=" C2 DC I 1 " 0.009 2.00e-02 2.50e+03 pdb=" O2 DC I 1 " -0.020 2.00e-02 2.50e+03 pdb=" N3 DC I 1 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DC I 1 " 0.010 2.00e-02 2.50e+03 pdb=" N4 DC I 1 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC I 1 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DC I 1 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 111 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO A 112 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 3 " 0.024 2.00e-02 2.50e+03 1.10e-02 3.35e+00 pdb=" N9 DA I 3 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA I 3 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 3 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 3 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 3 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 3 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 3 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 3 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 3 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 3 " -0.003 2.00e-02 2.50e+03 ... (remaining 4956 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.58: 196 2.58 - 3.08: 22130 3.08 - 3.59: 34764 3.59 - 4.09: 46869 4.09 - 4.60: 70122 Nonbonded interactions: 174081 Sorted by model distance: nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D2001 " model vdw 2.071 2.050 nonbonded pdb=" O ARG C 307 " pdb=" H ALA C 309 " model vdw 2.101 1.850 nonbonded pdb=" OD1 ASP C 308 " pdb=" H ASP C 308 " model vdw 2.131 1.850 nonbonded pdb=" N ALA C 306 " pdb=" O VAL C 343 " model vdw 2.225 2.350 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D2001 " model vdw 2.247 2.050 ... (remaining 174076 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.36 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.840 Extract box with map and model: 8.640 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 84.300 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.358 30666 Z= 0.305 Angle : 0.526 31.039 41848 Z= 0.250 Chirality : 0.037 0.229 4877 Planarity : 0.002 0.046 4953 Dihedral : 14.641 179.080 11628 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 26.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.12), residues: 3620 helix: -0.90 (0.13), residues: 1393 sheet: -2.24 (0.31), residues: 241 loop : -3.01 (0.11), residues: 1986 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 309 is missing expected H atoms. Skipping. Residue ALA 1011 is missing expected H atoms. Skipping. Residue SER 1012 is missing expected H atoms. Skipping. Residue LEU 1014 is missing expected H atoms. Skipping. Evaluate side-chains 621 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 621 time to evaluate : 3.475 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 outliers start: 0 outliers final: 0 residues processed: 621 average time/residue: 0.4676 time to fit residues: 456.8646 Evaluate side-chains 382 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 3.256 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 20.0000 chunk 281 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 291 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 177 optimal weight: 6.9990 chunk 217 optimal weight: 0.0970 chunk 337 optimal weight: 7.9990 overall best weight: 3.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 128 ASN A 269 ASN ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS C 331 GLN ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 HIS ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 HIS ** C 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 884 GLN C 943 HIS ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS C1134 HIS C1155 GLN ** C1223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1251 HIS C1258 HIS C1271 GLN ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN D 234 ASN D 278 ASN ** D 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN D 450 GLN ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 917 GLN ** D1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS ** F 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 440 GLN F 577 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 30666 Z= 0.387 Angle : 0.626 9.102 41848 Z= 0.328 Chirality : 0.041 0.205 4877 Planarity : 0.004 0.045 4953 Dihedral : 17.285 179.352 4833 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 39.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer Outliers : 3.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.13), residues: 3620 helix: 0.46 (0.14), residues: 1409 sheet: -1.81 (0.29), residues: 287 loop : -2.61 (0.13), residues: 1924 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 309 is missing expected H atoms. Skipping. Residue ALA 1011 is missing expected H atoms. Skipping. Residue SER 1012 is missing expected H atoms. Skipping. Residue LEU 1014 is missing expected H atoms. Skipping. Evaluate side-chains 457 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 357 time to evaluate : 3.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 67 residues processed: 430 average time/residue: 0.4192 time to fit residues: 290.7617 Evaluate side-chains 378 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 311 time to evaluate : 3.135 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.2758 time to fit residues: 38.5517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 281 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 338 optimal weight: 9.9990 chunk 365 optimal weight: 4.9990 chunk 301 optimal weight: 3.9990 chunk 335 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 271 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 862 ASN ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1212 HIS ** C1223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1365 GLN ** F 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 30666 Z= 0.289 Angle : 0.506 7.618 41848 Z= 0.269 Chirality : 0.038 0.142 4877 Planarity : 0.003 0.060 4953 Dihedral : 17.348 177.834 4833 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 39.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.41 (0.14), residues: 3620 helix: 1.04 (0.14), residues: 1401 sheet: -1.83 (0.28), residues: 304 loop : -2.44 (0.13), residues: 1915 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 309 is missing expected H atoms. Skipping. Residue ALA 1011 is missing expected H atoms. Skipping. Residue SER 1012 is missing expected H atoms. Skipping. Residue LEU 1014 is missing expected H atoms. Skipping. Evaluate side-chains 391 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 334 time to evaluate : 3.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 37 residues processed: 368 average time/residue: 0.4328 time to fit residues: 261.9051 Evaluate side-chains 345 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 308 time to evaluate : 3.349 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 1 residues processed: 37 average time/residue: 0.3373 time to fit residues: 26.4006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 2.9990 chunk 254 optimal weight: 3.9990 chunk 175 optimal weight: 0.2980 chunk 37 optimal weight: 20.0000 chunk 161 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 339 optimal weight: 0.0980 chunk 359 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 321 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 HIS ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1212 HIS ** C1223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 30666 Z= 0.224 Angle : 0.462 8.472 41848 Z= 0.246 Chirality : 0.037 0.139 4877 Planarity : 0.003 0.045 4953 Dihedral : 17.342 175.410 4833 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 40.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3620 helix: 1.36 (0.15), residues: 1401 sheet: -1.66 (0.29), residues: 304 loop : -2.31 (0.13), residues: 1915 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 309 is missing expected H atoms. Skipping. Residue ALA 1011 is missing expected H atoms. Skipping. Residue SER 1012 is missing expected H atoms. Skipping. Residue LEU 1014 is missing expected H atoms. Skipping. Evaluate side-chains 382 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 322 time to evaluate : 3.348 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 37 residues processed: 353 average time/residue: 0.4105 time to fit residues: 239.2449 Evaluate side-chains 343 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 306 time to evaluate : 3.256 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 1 residues processed: 37 average time/residue: 0.2638 time to fit residues: 23.0051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 267 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 306 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 322 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 HIS ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1374 GLN ** F 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.099 30666 Z= 0.716 Angle : 0.904 16.190 41848 Z= 0.465 Chirality : 0.048 0.213 4877 Planarity : 0.005 0.074 4953 Dihedral : 18.142 178.226 4833 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 53.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 14.10 % Favored : 85.87 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.13), residues: 3620 helix: 0.27 (0.14), residues: 1385 sheet: -2.27 (0.26), residues: 329 loop : -2.79 (0.13), residues: 1906 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 309 is missing expected H atoms. Skipping. Residue ALA 1011 is missing expected H atoms. Skipping. Residue SER 1012 is missing expected H atoms. Skipping. Residue LEU 1014 is missing expected H atoms. Skipping. Evaluate side-chains 365 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 288 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 51 residues processed: 348 average time/residue: 0.3998 time to fit residues: 229.9360 Evaluate side-chains 319 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 268 time to evaluate : 3.256 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 4 residues processed: 51 average time/residue: 0.3104 time to fit residues: 32.5786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 2.9990 chunk 323 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 359 optimal weight: 9.9990 chunk 298 optimal weight: 0.6980 chunk 166 optimal weight: 0.6980 chunk 29 optimal weight: 20.0000 chunk 119 optimal weight: 0.9980 chunk 188 optimal weight: 7.9990 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 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 GLN D 409 GLN ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 ASN ** F 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 30666 Z= 0.159 Angle : 0.472 9.003 41848 Z= 0.253 Chirality : 0.037 0.137 4877 Planarity : 0.003 0.064 4953 Dihedral : 17.823 174.639 4833 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 42.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3620 helix: 1.18 (0.15), residues: 1380 sheet: -1.95 (0.28), residues: 300 loop : -2.43 (0.13), residues: 1940 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 309 is missing expected H atoms. Skipping. Residue ALA 1011 is missing expected H atoms. Skipping. Residue SER 1012 is missing expected H atoms. Skipping. Residue LEU 1014 is missing expected H atoms. Skipping. Evaluate side-chains 339 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 311 time to evaluate : 3.621 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 14 residues processed: 329 average time/residue: 0.4215 time to fit residues: 229.7181 Evaluate side-chains 298 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 284 time to evaluate : 3.316 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 5 residues processed: 14 average time/residue: 0.3512 time to fit residues: 12.5686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 262 optimal weight: 0.0170 chunk 203 optimal weight: 0.0470 chunk 302 optimal weight: 0.6980 chunk 200 optimal weight: 6.9990 chunk 358 optimal weight: 10.0000 chunk 224 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 165 optimal weight: 0.0770 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 GLN ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 ASN ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 30666 Z= 0.124 Angle : 0.419 6.801 41848 Z= 0.224 Chirality : 0.036 0.134 4877 Planarity : 0.003 0.054 4953 Dihedral : 17.622 179.922 4833 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 41.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3620 helix: 1.72 (0.15), residues: 1391 sheet: -1.31 (0.32), residues: 258 loop : -2.20 (0.13), residues: 1971 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 309 is missing expected H atoms. Skipping. Residue ALA 1011 is missing expected H atoms. Skipping. Residue SER 1012 is missing expected H atoms. Skipping. Residue LEU 1014 is missing expected H atoms. Skipping. Evaluate side-chains 335 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 316 time to evaluate : 3.626 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 331 average time/residue: 0.4140 time to fit residues: 225.3285 Evaluate side-chains 309 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 297 time to evaluate : 3.370 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 12 average time/residue: 0.4278 time to fit residues: 12.8819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 281 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.077 30666 Z= 0.491 Angle : 0.667 11.898 41848 Z= 0.348 Chirality : 0.042 0.163 4877 Planarity : 0.004 0.062 4953 Dihedral : 17.907 177.089 4833 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 47.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.02 % Favored : 86.98 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.14), residues: 3620 helix: 1.16 (0.14), residues: 1376 sheet: -1.84 (0.29), residues: 297 loop : -2.49 (0.13), residues: 1947 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 309 is missing expected H atoms. Skipping. Residue ALA 1011 is missing expected H atoms. Skipping. Residue SER 1012 is missing expected H atoms. Skipping. Residue LEU 1014 is missing expected H atoms. Skipping. Evaluate side-chains 334 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 291 time to evaluate : 3.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 35 residues processed: 318 average time/residue: 0.4221 time to fit residues: 220.4405 Evaluate side-chains 319 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 284 time to evaluate : 3.349 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 6 residues processed: 35 average time/residue: 0.3109 time to fit residues: 23.9484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 0.0050 chunk 343 optimal weight: 4.9990 chunk 313 optimal weight: 20.0000 chunk 334 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 262 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 301 optimal weight: 4.9990 chunk 316 optimal weight: 1.9990 chunk 332 optimal weight: 0.6980 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 30666 Z= 0.159 Angle : 0.451 8.042 41848 Z= 0.241 Chirality : 0.037 0.134 4877 Planarity : 0.003 0.058 4953 Dihedral : 17.717 178.583 4833 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 43.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3620 helix: 1.67 (0.15), residues: 1380 sheet: -1.58 (0.30), residues: 296 loop : -2.20 (0.14), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 309 is missing expected H atoms. Skipping. Residue ALA 1011 is missing expected H atoms. Skipping. Residue SER 1012 is missing expected H atoms. Skipping. Residue LEU 1014 is missing expected H atoms. Skipping. Evaluate side-chains 314 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 303 time to evaluate : 3.378 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 312 average time/residue: 0.4265 time to fit residues: 218.8358 Evaluate side-chains 303 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 293 time to evaluate : 3.684 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 10 average time/residue: 0.4608 time to fit residues: 11.6350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 3.9990 chunk 353 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 370 optimal weight: 7.9990 chunk 341 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 30666 Z= 0.352 Angle : 0.563 9.442 41848 Z= 0.296 Chirality : 0.039 0.138 4877 Planarity : 0.003 0.058 4953 Dihedral : 17.821 179.334 4833 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 46.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.14), residues: 3620 helix: 1.47 (0.15), residues: 1382 sheet: -1.74 (0.30), residues: 292 loop : -2.34 (0.14), residues: 1946 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 309 is missing expected H atoms. Skipping. Residue ALA 1011 is missing expected H atoms. Skipping. Residue SER 1012 is missing expected H atoms. Skipping. Residue LEU 1014 is missing expected H atoms. Skipping. Evaluate side-chains 311 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 292 time to evaluate : 3.501 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 304 average time/residue: 0.4277 time to fit residues: 214.5779 Evaluate side-chains 299 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 284 time to evaluate : 3.354 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 6 residues processed: 15 average time/residue: 0.3727 time to fit residues: 14.0425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 7.9990 chunk 314 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 272 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 295 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 303 optimal weight: 0.0030 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.105450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.074442 restraints weight = 104247.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.075785 restraints weight = 57895.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.076752 restraints weight = 36905.014| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 30666 Z= 0.126 Angle : 0.435 8.515 41848 Z= 0.233 Chirality : 0.037 0.136 4877 Planarity : 0.003 0.054 4953 Dihedral : 17.700 176.778 4833 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 42.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.15), residues: 3620 helix: 1.80 (0.15), residues: 1395 sheet: -1.44 (0.30), residues: 293 loop : -2.13 (0.14), residues: 1932 =============================================================================== Job complete usr+sys time: 5639.46 seconds wall clock time: 104 minutes 8.25 seconds (6248.25 seconds total)