Starting phenix.real_space_refine (version: dev) on Sat Feb 25 19:35:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7c_30604/02_2023/7d7c_30604.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7c_30604/02_2023/7d7c_30604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7c_30604/02_2023/7d7c_30604.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7c_30604/02_2023/7d7c_30604.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7c_30604/02_2023/7d7c_30604.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7c_30604/02_2023/7d7c_30604.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 17": "OE1" <-> "OE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B ASP 96": "OD1" <-> "OD2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "C TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 7": "OE1" <-> "OE2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 132": "OD1" <-> "OD2" Residue "C ASP 158": "OD1" <-> "OD2" Residue "C ASP 160": "OD1" <-> "OD2" Residue "C TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 392": "OE1" <-> "OE2" Residue "C ASP 393": "OD1" <-> "OD2" Residue "C PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 423": "OD1" <-> "OD2" Residue "C ASP 434": "OD1" <-> "OD2" Residue "C GLU 441": "OE1" <-> "OE2" Residue "C ASP 483": "OD1" <-> "OD2" Residue "C TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 625": "OE1" <-> "OE2" Residue "C PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 675": "OD1" <-> "OD2" Residue "C ASP 696": "OD1" <-> "OD2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 781": "OD1" <-> "OD2" Residue "C ASP 785": "OD1" <-> "OD2" Residue "C ASP 790": "OD1" <-> "OD2" Residue "C GLU 849": "OE1" <-> "OE2" Residue "C TYR 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 881": "OD1" <-> "OD2" Residue "C GLU 949": "OE1" <-> "OE2" Residue "C GLU 985": "OE1" <-> "OE2" Residue "C ASP 995": "OD1" <-> "OD2" Residue "C GLU 1012": "OE1" <-> "OE2" Residue "C TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1026": "OE1" <-> "OE2" Residue "C GLU 1030": "OE1" <-> "OE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C TYR 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1089": "OE1" <-> "OE2" Residue "C ASP 1095": "OD1" <-> "OD2" Residue "C TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1310": "OD1" <-> "OD2" Residue "C GLU 1316": "OE1" <-> "OE2" Residue "C GLU 1338": "OE1" <-> "OE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D ASP 174": "OD1" <-> "OD2" Residue "D ASP 193": "OD1" <-> "OD2" Residue "D GLU 204": "OE1" <-> "OE2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D GLU 295": "OE1" <-> "OE2" Residue "D ASP 308": "OD1" <-> "OD2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 413": "OD1" <-> "OD2" Residue "D GLU 443": "OE1" <-> "OE2" Residue "D ASP 462": "OD1" <-> "OD2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D GLU 497": "OE1" <-> "OE2" Residue "D ASP 505": "OD1" <-> "OD2" Residue "D TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 558": "OD1" <-> "OD2" Residue "D TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 658": "OE1" <-> "OE2" Residue "D ASP 691": "OD1" <-> "OD2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "D TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 785": "OD1" <-> "OD2" Residue "D ASP 806": "OD1" <-> "OD2" Residue "D ASP 847": "OD1" <-> "OD2" Residue "D ASP 855": "OD1" <-> "OD2" Residue "D GLU 873": "OE1" <-> "OE2" Residue "D ASP 889": "OD1" <-> "OD2" Residue "D ASP 902": "OD1" <-> "OD2" Residue "D GLU 1009": "OE1" <-> "OE2" Residue "D PHE 1034": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1039": "OD1" <-> "OD2" Residue "D ASP 1042": "OD1" <-> "OD2" Residue "D ASP 1073": "OD1" <-> "OD2" Residue "D PHE 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1184": "OD1" <-> "OD2" Residue "D ASP 1239": "OD1" <-> "OD2" Residue "D GLU 1281": "OE1" <-> "OE2" Residue "D GLU 1291": "OE1" <-> "OE2" Residue "D TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 15": "OE1" <-> "OE2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "F TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 135": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 26249 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1686 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1681 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10381 Classifications: {'peptide': 1316} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Chain: "D" Number of atoms: 10384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10384 Classifications: {'peptide': 1335} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1279} Chain breaks: 2 Chain: "T" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 467 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "F" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1128 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 Chain: "N" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 519 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20031 SG CYS D 814 86.451 67.375 129.517 1.00115.32 S ATOM 20596 SG CYS D 888 85.667 67.560 125.979 1.00104.77 S ATOM 20647 SG CYS D 895 84.746 64.207 127.826 1.00105.89 S ATOM 20668 SG CYS D 898 83.177 67.277 128.309 1.00103.24 S Time building chain proxies: 14.97, per 1000 atoms: 0.57 Number of scatterers: 26249 At special positions: 0 Unit cell: (133.314, 160.761, 167.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 110 16.00 P 48 15.00 Mg 1 11.99 O 5128 8.00 N 4625 7.00 C 16335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.90 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " Number of angles added : 6 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5960 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 46 sheets defined 36.4% alpha, 13.7% beta 18 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 7.38 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.635A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.957A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 4.270A pdb=" N LEU B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.710A pdb=" N THR B 157 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 28 through 37 removed outlier: 3.581A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 4.290A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.621A pdb=" N ARG C 245 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 346 through 354 removed outlier: 3.869A pdb=" N THR C 350 " --> pdb=" O TYR C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 391 removed outlier: 3.776A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER C 391 " --> pdb=" O ASN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 478 removed outlier: 3.502A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 481 No H-bonds generated for 'chain 'C' and resid 479 through 481' Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 521 through 527 Processing helix chain 'C' and resid 610 through 614 removed outlier: 3.877A pdb=" N ASN C 613 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 687 Processing helix chain 'C' and resid 705 through 710 removed outlier: 3.693A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.838A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 980 removed outlier: 4.131A pdb=" N LYS C 958 " --> pdb=" O LYS C 954 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASP C 959 " --> pdb=" O GLN C 955 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA C 969 " --> pdb=" O GLN C 965 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE C 972 " --> pdb=" O GLU C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.621A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.689A pdb=" N MET C1085 " --> pdb=" O ILE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.606A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1101 through 1106' Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.859A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.831A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.736A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1177 removed outlier: 3.524A pdb=" N ARG C1171 " --> pdb=" O GLU C1167 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 removed outlier: 3.627A pdb=" N LYS C1242 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.701A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1290 removed outlier: 3.592A pdb=" N GLN C1288 " --> pdb=" O ALA C1284 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1321 through 1331 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 114 through 117 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.884A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.549A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 211 through 230 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 264 through 283 removed outlier: 3.540A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.637A pdb=" N LEU D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 407 through 416 Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.730A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.795A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.757A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 594 removed outlier: 3.641A pdb=" N ASN D 593 " --> pdb=" O TYR D 589 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN D 594 " --> pdb=" O SER D 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 589 through 594' Processing helix chain 'D' and resid 597 through 613 removed outlier: 3.829A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.606A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.560A pdb=" N ALA D 662 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 664 " --> pdb=" O GLU D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.629A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.521A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.597A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 3.911A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 895 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.596A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1069 through 1074 removed outlier: 4.611A pdb=" N ASP D1073 " --> pdb=" O ALA D1069 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU D1074 " --> pdb=" O GLY D1070 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1069 through 1074' Processing helix chain 'D' and resid 1137 through 1147 removed outlier: 3.847A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1225 Processing helix chain 'D' and resid 1225 through 1241 removed outlier: 4.299A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 Processing helix chain 'D' and resid 1282 through 1293 Processing helix chain 'D' and resid 1308 through 1315 removed outlier: 3.995A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1325 removed outlier: 3.910A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.749A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 3.823A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG D1373 " --> pdb=" O ARG D1369 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 28 removed outlier: 3.859A pdb=" N LEU F 17 " --> pdb=" O ASN F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 55 removed outlier: 3.502A pdb=" N GLY F 44 " --> pdb=" O ASN F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 83 removed outlier: 3.709A pdb=" N GLN F 69 " --> pdb=" O GLN F 65 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU F 70 " --> pdb=" O SER F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 125 Processing helix chain 'F' and resid 137 through 142 Processing helix chain 'F' and resid 142 through 150 removed outlier: 3.599A pdb=" N ASP F 150 " --> pdb=" O GLN F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 153 No H-bonds generated for 'chain 'F' and resid 151 through 153' Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 5.073A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 61 removed outlier: 5.448A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.804A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 18 removed outlier: 4.195A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N HIS B 23 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR B 207 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LYS B 25 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N MET B 205 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 101 removed outlier: 6.686A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA8, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.814A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.626A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU C 119 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE C 117 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB6, first strand: chain 'C' and resid 228 through 230 Processing sheet with id=AB7, first strand: chain 'C' and resid 239 through 240 removed outlier: 3.623A pdb=" N ILE C 285 " --> pdb=" O MET C 239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.073A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.747A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.594A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.594A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.757A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 748 through 751 removed outlier: 5.662A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY C 722 " --> pdb=" O VAL C 777 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1065 through 1067 removed outlier: 7.316A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 832 Processing sheet with id=AD1, first strand: chain 'C' and resid 835 through 839 Processing sheet with id=AD2, first strand: chain 'C' and resid 842 through 843 removed outlier: 3.754A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 876 through 877 Processing sheet with id=AD4, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD5, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.305A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD7, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.729A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD9, first strand: chain 'D' and resid 103 through 112 removed outlier: 10.415A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 11.253A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AE2, first strand: chain 'D' and resid 526 through 527 removed outlier: 6.885A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain 'D' and resid 825 through 826 removed outlier: 6.579A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 848 through 849 removed outlier: 6.727A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 949 through 951 removed outlier: 6.852A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN D1019 " --> pdb=" O VAL D1002 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL D1002 " --> pdb=" O ASN D1019 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 958 through 961 removed outlier: 6.564A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1078 through 1079 removed outlier: 3.653A pdb=" N LEU D1078 " --> pdb=" O TYR D1099 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 1162 through 1165 removed outlier: 4.294A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.800A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 973 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 12.25 Time building geometry restraints manager: 11.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7003 1.33 - 1.45: 4364 1.45 - 1.57: 15096 1.57 - 1.69: 92 1.69 - 1.81: 191 Bond restraints: 26746 Sorted by residual: bond pdb=" N TYR C 47 " pdb=" CA TYR C 47 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.44e+00 bond pdb=" N VAL A 74 " pdb=" CA VAL A 74 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.26e-02 6.30e+03 7.51e+00 bond pdb=" C THR C 563 " pdb=" N PRO C 564 " ideal model delta sigma weight residual 1.335 1.312 0.023 8.70e-03 1.32e+04 7.16e+00 bond pdb=" N GLU A 72 " pdb=" CA GLU A 72 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.31e-02 5.83e+03 6.59e+00 bond pdb=" N HIS F 126 " pdb=" CA HIS F 126 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 6.09e+00 ... (remaining 26741 not shown) Histogram of bond angle deviations from ideal: 97.69 - 104.99: 618 104.99 - 112.28: 13900 112.28 - 119.57: 8873 119.57 - 126.86: 12571 126.86 - 134.16: 357 Bond angle restraints: 36319 Sorted by residual: angle pdb=" C SER D 503 " pdb=" N GLN D 504 " pdb=" CA GLN D 504 " ideal model delta sigma weight residual 121.52 111.32 10.20 1.74e+00 3.30e-01 3.44e+01 angle pdb=" N GLY C 162 " pdb=" CA GLY C 162 " pdb=" C GLY C 162 " ideal model delta sigma weight residual 111.67 116.59 -4.92 9.20e-01 1.18e+00 2.86e+01 angle pdb=" N VAL D 839 " pdb=" CA VAL D 839 " pdb=" C VAL D 839 " ideal model delta sigma weight residual 113.20 108.29 4.91 9.60e-01 1.09e+00 2.62e+01 angle pdb=" C VAL D 244 " pdb=" N LEU D 245 " pdb=" CA LEU D 245 " ideal model delta sigma weight residual 120.94 128.01 -7.07 1.90e+00 2.77e-01 1.39e+01 angle pdb=" CA ARG D1345 " pdb=" C ARG D1345 " pdb=" O ARG D1345 " ideal model delta sigma weight residual 122.36 118.17 4.19 1.21e+00 6.83e-01 1.20e+01 ... (remaining 36314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.04: 15753 35.04 - 70.09: 458 70.09 - 105.13: 39 105.13 - 140.17: 0 140.17 - 175.22: 1 Dihedral angle restraints: 16251 sinusoidal: 6984 harmonic: 9267 Sorted by residual: dihedral pdb=" CA GLY D 852 " pdb=" C GLY D 852 " pdb=" N THR D 853 " pdb=" CA THR D 853 " ideal model delta harmonic sigma weight residual -180.00 -151.89 -28.11 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ARG F 132 " pdb=" C ARG F 132 " pdb=" N ASP F 133 " pdb=" CA ASP F 133 " ideal model delta harmonic sigma weight residual 180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA SER B 20 " pdb=" C SER B 20 " pdb=" N SER B 21 " pdb=" CA SER B 21 " ideal model delta harmonic sigma weight residual -180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 16248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2482 0.037 - 0.074: 1174 0.074 - 0.111: 375 0.111 - 0.147: 90 0.147 - 0.184: 16 Chirality restraints: 4137 Sorted by residual: chirality pdb=" CA LEU C 27 " pdb=" N LEU C 27 " pdb=" C LEU C 27 " pdb=" CB LEU C 27 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CB ILE C 176 " pdb=" CA ILE C 176 " pdb=" CG1 ILE C 176 " pdb=" CG2 ILE C 176 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CB ILE C1079 " pdb=" CA ILE C1079 " pdb=" CG1 ILE C1079 " pdb=" CG2 ILE C1079 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.97e-01 ... (remaining 4134 not shown) Planarity restraints: 4580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 42 " -0.094 5.00e-02 4.00e+02 1.44e-01 3.33e+01 pdb=" N PRO C 43 " 0.250 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC N 51 " -0.002 2.00e-02 2.50e+03 1.75e-02 6.88e+00 pdb=" N1 DC N 51 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DC N 51 " -0.042 2.00e-02 2.50e+03 pdb=" O2 DC N 51 " 0.023 2.00e-02 2.50e+03 pdb=" N3 DC N 51 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DC N 51 " -0.015 2.00e-02 2.50e+03 pdb=" N4 DC N 51 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC N 51 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DC N 51 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N 25 " 0.016 2.00e-02 2.50e+03 1.48e-02 6.55e+00 pdb=" N9 DG N 25 " -0.021 2.00e-02 2.50e+03 pdb=" C8 DG N 25 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG N 25 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG N 25 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG N 25 " 0.020 2.00e-02 2.50e+03 pdb=" O6 DG N 25 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG N 25 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG N 25 " 0.030 2.00e-02 2.50e+03 pdb=" N2 DG N 25 " -0.022 2.00e-02 2.50e+03 pdb=" N3 DG N 25 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG N 25 " -0.003 2.00e-02 2.50e+03 ... (remaining 4577 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 337 2.55 - 3.14: 22913 3.14 - 3.73: 39723 3.73 - 4.31: 54469 4.31 - 4.90: 89067 Nonbonded interactions: 206509 Sorted by model distance: nonbonded pdb=" OD2 ASP D 460 " pdb="MG MG D1501 " model vdw 1.967 2.170 nonbonded pdb=" NH1 ARG C 267 " pdb=" O ARG C 268 " model vdw 2.179 2.520 nonbonded pdb=" OG1 THR D 816 " pdb=" OE1 GLU D 818 " model vdw 2.198 2.440 nonbonded pdb=" O ALA D 741 " pdb=" ND2 ASN D 762 " model vdw 2.201 2.520 nonbonded pdb=" OD1 ASP C1214 " pdb=" N GLY C1215 " model vdw 2.202 2.520 ... (remaining 206504 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 232)) selection = (chain 'B' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 48 5.49 5 Mg 1 5.21 5 S 110 5.16 5 C 16335 2.51 5 N 4625 2.21 5 O 5128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 0.010 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 6.120 Check model and map are aligned: 0.400 Process input model: 80.390 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.230 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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 : 0.007 0.126 26746 Z= 0.479 Angle : 0.789 13.191 36319 Z= 0.457 Chirality : 0.047 0.184 4137 Planarity : 0.005 0.144 4580 Dihedral : 16.224 175.217 10291 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.71 % Favored : 88.20 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -4.31 (0.12), residues: 3203 helix: -1.89 (0.13), residues: 1073 sheet: -2.61 (0.21), residues: 437 loop : -3.71 (0.12), residues: 1693 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 315 time to evaluate : 3.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 322 average time/residue: 0.4612 time to fit residues: 222.6410 Evaluate side-chains 231 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 225 time to evaluate : 2.872 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2518 time to fit residues: 6.7001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 293 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 117 HIS A 147 GLN B 23 HIS B 117 HIS ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN C 343 HIS C 618 GLN C 856 ASN ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 GLN C1038 GLN C1134 GLN C1136 GLN D 45 ASN D 320 ASN D 340 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN ** D 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 929 GLN D 962 ASN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.129 26746 Z= 0.403 Angle : 0.690 8.408 36319 Z= 0.364 Chirality : 0.045 0.169 4137 Planarity : 0.005 0.074 4580 Dihedral : 12.868 168.801 3996 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.43 % Favored : 90.54 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.04 (0.13), residues: 3203 helix: -0.50 (0.15), residues: 1100 sheet: -2.18 (0.22), residues: 425 loop : -3.14 (0.13), residues: 1678 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 244 time to evaluate : 3.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 43 residues processed: 288 average time/residue: 0.3895 time to fit residues: 180.7437 Evaluate side-chains 255 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 212 time to evaluate : 2.923 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2535 time to fit residues: 24.4287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 163 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 244 optimal weight: 9.9990 chunk 199 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 293 optimal weight: 5.9990 chunk 317 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 291 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 665 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.091 26746 Z= 0.252 Angle : 0.606 10.877 36319 Z= 0.319 Chirality : 0.042 0.156 4137 Planarity : 0.004 0.052 4580 Dihedral : 12.647 172.013 3996 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.68 % Favored : 92.29 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.27 (0.14), residues: 3203 helix: 0.30 (0.16), residues: 1094 sheet: -1.86 (0.24), residues: 392 loop : -2.76 (0.13), residues: 1717 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 249 time to evaluate : 2.986 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: 52 outliers final: 30 residues processed: 289 average time/residue: 0.3699 time to fit residues: 174.9942 Evaluate side-chains 251 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 221 time to evaluate : 3.412 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2483 time to fit residues: 18.1619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 290 optimal weight: 0.9990 chunk 220 optimal weight: 7.9990 chunk 152 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 294 optimal weight: 3.9990 chunk 312 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 279 optimal weight: 0.0270 chunk 84 optimal weight: 0.0970 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 GLN D 419 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN F 84 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 26746 Z= 0.171 Angle : 0.567 9.704 36319 Z= 0.298 Chirality : 0.041 0.156 4137 Planarity : 0.004 0.052 4580 Dihedral : 12.449 173.532 3996 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.82 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.75 (0.14), residues: 3203 helix: 0.72 (0.16), residues: 1102 sheet: -1.41 (0.25), residues: 385 loop : -2.49 (0.14), residues: 1716 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 267 time to evaluate : 3.276 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 outliers start: 43 outliers final: 23 residues processed: 292 average time/residue: 0.3902 time to fit residues: 185.8917 Evaluate side-chains 259 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 236 time to evaluate : 3.255 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2786 time to fit residues: 16.5828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 260 optimal weight: 0.7980 chunk 177 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 232 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 280 optimal weight: 0.4980 chunk 78 optimal weight: 10.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 684 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 26746 Z= 0.225 Angle : 0.583 9.190 36319 Z= 0.305 Chirality : 0.042 0.152 4137 Planarity : 0.004 0.048 4580 Dihedral : 12.400 174.575 3996 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.74 % Favored : 93.23 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.53 (0.14), residues: 3203 helix: 0.87 (0.16), residues: 1098 sheet: -1.23 (0.25), residues: 392 loop : -2.35 (0.14), residues: 1713 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 248 time to evaluate : 3.325 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 outliers start: 51 outliers final: 27 residues processed: 283 average time/residue: 0.3624 time to fit residues: 169.0322 Evaluate side-chains 257 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 230 time to evaluate : 3.094 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2455 time to fit residues: 16.9700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 105 optimal weight: 8.9990 chunk 281 optimal weight: 40.0000 chunk 61 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 312 optimal weight: 8.9990 chunk 259 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 164 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 26746 Z= 0.233 Angle : 0.587 12.294 36319 Z= 0.307 Chirality : 0.042 0.166 4137 Planarity : 0.004 0.057 4580 Dihedral : 12.380 174.831 3996 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.77 % Favored : 93.19 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.15), residues: 3203 helix: 0.95 (0.16), residues: 1101 sheet: -1.05 (0.26), residues: 387 loop : -2.25 (0.14), residues: 1715 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 239 time to evaluate : 3.008 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 outliers start: 46 outliers final: 28 residues processed: 271 average time/residue: 0.3761 time to fit residues: 168.6197 Evaluate side-chains 253 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 225 time to evaluate : 3.107 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3332 time to fit residues: 20.4854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 301 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 228 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 263 optimal weight: 0.6980 chunk 174 optimal weight: 7.9990 chunk 311 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 760 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.107 26746 Z= 0.246 Angle : 0.598 13.988 36319 Z= 0.311 Chirality : 0.042 0.162 4137 Planarity : 0.004 0.055 4580 Dihedral : 12.364 175.120 3996 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.12 % Favored : 92.85 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.29 (0.15), residues: 3203 helix: 1.01 (0.16), residues: 1099 sheet: -1.00 (0.26), residues: 386 loop : -2.18 (0.14), residues: 1718 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 239 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 20 residues processed: 263 average time/residue: 0.3593 time to fit residues: 157.8999 Evaluate side-chains 247 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 227 time to evaluate : 3.393 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2484 time to fit residues: 13.2982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 192 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 197 optimal weight: 9.9990 chunk 212 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 26746 Z= 0.204 Angle : 0.596 12.309 36319 Z= 0.307 Chirality : 0.042 0.180 4137 Planarity : 0.004 0.054 4580 Dihedral : 12.301 175.409 3996 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.18 % Favored : 93.79 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.13 (0.15), residues: 3203 helix: 1.08 (0.16), residues: 1101 sheet: -0.90 (0.26), residues: 387 loop : -2.05 (0.14), residues: 1715 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 246 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 261 average time/residue: 0.3829 time to fit residues: 165.3673 Evaluate side-chains 243 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 234 time to evaluate : 3.177 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2663 time to fit residues: 9.0684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 283 optimal weight: 4.9990 chunk 298 optimal weight: 8.9990 chunk 272 optimal weight: 2.9990 chunk 290 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 126 optimal weight: 0.2980 chunk 227 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 262 optimal weight: 10.0000 chunk 274 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.090 26746 Z= 0.285 Angle : 0.633 12.156 36319 Z= 0.326 Chirality : 0.043 0.184 4137 Planarity : 0.004 0.054 4580 Dihedral : 12.341 175.818 3996 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.90 % Favored : 92.07 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.15 (0.15), residues: 3203 helix: 1.06 (0.16), residues: 1099 sheet: -0.95 (0.26), residues: 409 loop : -2.05 (0.14), residues: 1695 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 236 time to evaluate : 2.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 251 average time/residue: 0.3587 time to fit residues: 149.4637 Evaluate side-chains 240 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 229 time to evaluate : 3.197 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2420 time to fit residues: 9.3709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 190 optimal weight: 7.9990 chunk 306 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 213 optimal weight: 0.7980 chunk 321 optimal weight: 10.0000 chunk 296 optimal weight: 8.9990 chunk 256 optimal weight: 0.0070 chunk 26 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 26746 Z= 0.206 Angle : 0.614 12.381 36319 Z= 0.314 Chirality : 0.042 0.210 4137 Planarity : 0.004 0.055 4580 Dihedral : 12.273 175.581 3996 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.82 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.15), residues: 3203 helix: 1.16 (0.16), residues: 1097 sheet: -0.86 (0.26), residues: 394 loop : -1.96 (0.14), residues: 1712 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 246 time to evaluate : 3.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 252 average time/residue: 0.3765 time to fit residues: 157.2941 Evaluate side-chains 241 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 238 time to evaluate : 3.161 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2659 time to fit residues: 6.2112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 203 optimal weight: 6.9990 chunk 272 optimal weight: 0.3980 chunk 78 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 chunk 37 optimal weight: 0.4980 chunk 71 optimal weight: 6.9990 chunk 256 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.088281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.064302 restraints weight = 80012.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.066394 restraints weight = 39811.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.067810 restraints weight = 25292.514| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 26746 Z= 0.196 Angle : 0.608 12.062 36319 Z= 0.311 Chirality : 0.042 0.244 4137 Planarity : 0.004 0.054 4580 Dihedral : 12.206 176.170 3996 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.40 % Favored : 93.57 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.93 (0.15), residues: 3203 helix: 1.22 (0.16), residues: 1094 sheet: -0.82 (0.26), residues: 396 loop : -1.88 (0.14), residues: 1713 =============================================================================== Job complete usr+sys time: 4705.60 seconds wall clock time: 87 minutes 41.94 seconds (5261.94 seconds total)