Starting phenix.real_space_refine on Sat Mar 16 11:31:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8p_21108/03_2024/6v8p_21108_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8p_21108/03_2024/6v8p_21108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8p_21108/03_2024/6v8p_21108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8p_21108/03_2024/6v8p_21108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8p_21108/03_2024/6v8p_21108_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8p_21108/03_2024/6v8p_21108_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 36 5.16 5 C 9428 2.51 5 N 2446 2.21 5 O 2634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 236": "OD1" <-> "OD2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 598": not complete - not flipped Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 685": "OD1" <-> "OD2" Residue "A PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 750": "OE1" <-> "OE2" Residue "A TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1057": "NH1" <-> "NH2" Residue "A PHE 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1267": "OD1" <-> "OD2" Residue "A ASP 1356": "OD1" <-> "OD2" Residue "D TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 56": "OD1" <-> "OD2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 33": "OD1" <-> "OD2" Residue "E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 137": "OD1" <-> "OD2" Residue "E PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 120": "OD1" <-> "OD2" Residue "F ASP 138": "OD1" <-> "OD2" Residue "F PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14548 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8324 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1190, 8319 Classifications: {'peptide': 1190} Incomplete info: {'truncation_to_alanine': 288} Link IDs: {'PTRANS': 58, 'TRANS': 1131} Chain breaks: 13 Unresolved non-hydrogen bonds: 1436 Unresolved non-hydrogen angles: 1787 Unresolved non-hydrogen dihedrals: 1137 Unresolved non-hydrogen chiralities: 124 Planarities with less than four sites: {'GLN:plan1': 29, 'HIS:plan': 3, 'TYR:plan': 9, 'ASN:plan1': 15, 'ASP:plan': 38, 'PHE:plan': 6, 'GLU:plan': 64, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 736 Conformer: "B" Number of residues, atoms: 1190, 8319 Classifications: {'peptide': 1190} Incomplete info: {'truncation_to_alanine': 288} Link IDs: {'PTRANS': 58, 'TRANS': 1131} Chain breaks: 13 Unresolved non-hydrogen bonds: 1436 Unresolved non-hydrogen angles: 1787 Unresolved non-hydrogen dihedrals: 1137 Unresolved non-hydrogen chiralities: 124 Planarities with less than four sites: {'GLN:plan1': 29, 'HIS:plan': 3, 'TYR:plan': 9, 'ASN:plan1': 15, 'ASP:plan': 38, 'PHE:plan': 6, 'GLU:plan': 64, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 736 bond proxies already assigned to first conformer: 8519 Chain: "D" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1095 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 2 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 290 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 115 Chain: "E" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1445 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 15, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 117 Chain: "F" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 2917 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PTRANS': 26, 'TRANS': 433} Chain breaks: 4 Unresolved non-hydrogen bonds: 796 Unresolved non-hydrogen angles: 991 Unresolved non-hydrogen dihedrals: 661 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 1, 'TYR:plan': 9, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 26, 'PHE:plan': 8, 'GLU:plan': 24, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 464 Chain: "G" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 759 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain breaks: 1 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 72 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8218 SG CYS A1473 32.544 59.992 83.144 1.00138.14 S ATOM 8044 SG CYS A1449 37.379 55.609 83.762 1.00132.78 S ATOM 8181 SG CYS A1468 31.202 54.299 85.357 1.00132.62 S ATOM 8024 SG CYS A1446 32.667 55.000 79.017 1.00136.80 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN A1259 " occ=0.50 ... (8 atoms not shown) pdb=" CB BGLN A1259 " occ=0.50 Time building chain proxies: 12.50, per 1000 atoms: 0.86 Number of scatterers: 14548 At special positions: 0 Unit cell: (80.301, 146.302, 171.602, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 36 16.00 O 2634 8.00 N 2446 7.00 C 9428 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: 5.72 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1601 " pdb="FE3 SF4 A1601 " - pdb=" SG CYS A1468 " pdb="FE1 SF4 A1601 " - pdb=" SG CYS A1473 " pdb="FE2 SF4 A1601 " - pdb=" SG CYS A1449 " pdb="FE4 SF4 A1601 " - pdb=" SG CYS A1446 " Number of angles added : 12 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4074 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 16 sheets defined 33.9% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'A' and resid 96 through 115 Processing helix chain 'A' and resid 166 through 178 removed outlier: 3.809A pdb=" N SER A 170 " --> pdb=" O PRO A 166 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 229 through 232 No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 236 through 245 Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 386 through 389 No H-bonds generated for 'chain 'A' and resid 386 through 389' Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 613 through 621 Processing helix chain 'A' and resid 726 through 734 Processing helix chain 'A' and resid 745 through 759 Processing helix chain 'A' and resid 773 through 783 Processing helix chain 'A' and resid 790 through 793 No H-bonds generated for 'chain 'A' and resid 790 through 793' Processing helix chain 'A' and resid 826 through 833 Processing helix chain 'A' and resid 841 through 848 Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 871 through 895 removed outlier: 3.667A pdb=" N ASN A 888 " --> pdb=" O ARG A 884 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 889 " --> pdb=" O ALA A 885 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 892 " --> pdb=" O ASN A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 917 removed outlier: 3.859A pdb=" N TYR A 917 " --> pdb=" O SER A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 933 removed outlier: 3.662A pdb=" N ARG A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 948 Processing helix chain 'A' and resid 979 through 987 Processing helix chain 'A' and resid 1020 through 1023 No H-bonds generated for 'chain 'A' and resid 1020 through 1023' Processing helix chain 'A' and resid 1045 through 1065 Processing helix chain 'A' and resid 1072 through 1094 removed outlier: 4.698A pdb=" N TYR A1093 " --> pdb=" O ALA A1089 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY A1094 " --> pdb=" O ASN A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1129 Processing helix chain 'A' and resid 1155 through 1172 removed outlier: 3.602A pdb=" N PHE A1159 " --> pdb=" O ALA A1155 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER A1160 " --> pdb=" O ILE A1156 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN A1172 " --> pdb=" O ARG A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1240 Processing helix chain 'A' and resid 1244 through 1260 Processing helix chain 'A' and resid 1330 through 1334 Processing helix chain 'A' and resid 1345 through 1360 Proline residue: A1353 - end of helix Processing helix chain 'A' and resid 1367 through 1373 removed outlier: 3.505A pdb=" N GLU A1372 " --> pdb=" O ASN A1368 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE A1373 " --> pdb=" O TRP A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1454 removed outlier: 4.289A pdb=" N ARG A1452 " --> pdb=" O THR A1448 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TYR A1453 " --> pdb=" O CYS A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1467 removed outlier: 4.263A pdb=" N LYS A1467 " --> pdb=" O HIS A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1474 through 1486 Processing helix chain 'D' and resid 4 through 22 Processing helix chain 'D' and resid 52 through 68 removed outlier: 3.723A pdb=" N LYS D 68 " --> pdb=" O ASP D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 128 removed outlier: 3.527A pdb=" N PHE D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 23 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 52 through 70 removed outlier: 4.774A pdb=" N THR E 70 " --> pdb=" O LEU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 130 removed outlier: 3.797A pdb=" N LYS E 130 " --> pdb=" O MET E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 174 Processing helix chain 'F' and resid 1 through 8 Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 52 through 75 Processing helix chain 'F' and resid 93 through 95 No H-bonds generated for 'chain 'F' and resid 93 through 95' Processing helix chain 'F' and resid 116 through 125 removed outlier: 4.397A pdb=" N ASP F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 228 through 240 Processing helix chain 'F' and resid 248 through 253 removed outlier: 5.063A pdb=" N LEU F 253 " --> pdb=" O ASP F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 291 removed outlier: 3.750A pdb=" N PHE F 286 " --> pdb=" O GLU F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 326 removed outlier: 4.367A pdb=" N SER F 326 " --> pdb=" O SER F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 349 No H-bonds generated for 'chain 'F' and resid 347 through 349' Processing helix chain 'F' and resid 358 through 363 Processing helix chain 'F' and resid 392 through 404 Processing helix chain 'F' and resid 412 through 415 No H-bonds generated for 'chain 'F' and resid 412 through 415' Processing helix chain 'G' and resid 4 through 14 Processing helix chain 'G' and resid 22 through 29 Processing helix chain 'G' and resid 33 through 44 Processing sheet with id= A, first strand: chain 'A' and resid 23 through 26 removed outlier: 3.585A pdb=" N ILE A 25 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 29 through 35 Processing sheet with id= C, first strand: chain 'A' and resid 739 through 742 removed outlier: 8.511A pdb=" N MET A 740 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE A 714 " --> pdb=" O MET A 740 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N TYR A 742 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 716 " --> pdb=" O TYR A 742 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N SER A 692 " --> pdb=" O VAL A 717 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N HIS A 675 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE A 694 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU A 673 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TRP A 696 " --> pdb=" O THR A 671 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR A 671 " --> pdb=" O TRP A 696 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 971 through 975 Processing sheet with id= E, first strand: chain 'A' and resid 1006 through 1008 Processing sheet with id= F, first strand: chain 'A' and resid 1210 through 1214 removed outlier: 7.565A pdb=" N VAL A1197 " --> pdb=" O LEU A1190 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU A1190 " --> pdb=" O VAL A1197 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N PHE A1199 " --> pdb=" O SER A1188 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER A1188 " --> pdb=" O PHE A1199 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1270 through 1274 removed outlier: 3.943A pdb=" N ILE A1310 " --> pdb=" O VAL A1274 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 137 through 145 removed outlier: 7.024A pdb=" N SER A 162 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL A 140 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LYS A 160 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL A 142 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE A 158 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A 144 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN A 156 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 994 through 997 removed outlier: 6.486A pdb=" N VAL A1035 " --> pdb=" O ILE A 995 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 139 through 145 removed outlier: 3.771A pdb=" N GLU D 89 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN D 81 " --> pdb=" O CYS D 87 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS D 87 " --> pdb=" O ASN D 81 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS D 90 " --> pdb=" O GLU D 217 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU D 217 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE D 215 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 32 through 35 Processing sheet with id= L, first strand: chain 'E' and resid 139 through 147 removed outlier: 6.869A pdb=" N ASN E 81 " --> pdb=" O CYS E 87 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS E 87 " --> pdb=" O ASN E 81 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 107 through 109 Processing sheet with id= N, first strand: chain 'F' and resid 480 through 483 removed outlier: 7.545A pdb=" N ALA F 215 " --> pdb=" O GLY F 255 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU F 257 " --> pdb=" O ALA F 215 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL F 217 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE F 259 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER F 295 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE F 259 " --> pdb=" O SER F 295 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP F 297 " --> pdb=" O ILE F 259 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 343 through 347 removed outlier: 6.444A pdb=" N VAL F 435 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N VAL F 355 " --> pdb=" O VAL F 435 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE F 437 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS F 457 " --> pdb=" O TYR F 436 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL F 438 " --> pdb=" O LYS F 457 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE F 459 " --> pdb=" O VAL F 438 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY F 445 " --> pdb=" O SER F 460 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 64 through 67 removed outlier: 4.004A pdb=" N THR G 64 " --> pdb=" O TYR G 60 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS G 66 " --> pdb=" O CYS G 58 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS G 58 " --> pdb=" O LYS G 66 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE G 57 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ILE G 85 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N CYS G 59 " --> pdb=" O CYS G 83 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N CYS G 83 " --> pdb=" O CYS G 59 " (cutoff:3.500A) 562 hydrogen bonds defined for protein. 1624 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.69 Time building geometry restraints manager: 6.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.41: 6192 1.41 - 1.59: 8650 1.59 - 1.78: 0 1.78 - 1.96: 36 1.96 - 2.14: 12 Bond restraints: 14890 Sorted by residual: bond pdb=" S1 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 2.280 2.106 0.174 3.00e-02 1.11e+03 3.36e+01 bond pdb=" S3 SF4 A1601 " pdb="FE2 SF4 A1601 " ideal model delta sigma weight residual 2.280 2.125 0.155 3.00e-02 1.11e+03 2.67e+01 bond pdb=" S1 SF4 A1601 " pdb="FE3 SF4 A1601 " ideal model delta sigma weight residual 2.280 2.125 0.155 3.00e-02 1.11e+03 2.66e+01 bond pdb=" S3 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 2.280 2.125 0.155 3.00e-02 1.11e+03 2.65e+01 bond pdb=" S2 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 2.280 2.126 0.154 3.00e-02 1.11e+03 2.65e+01 ... (remaining 14885 not shown) Histogram of bond angle deviations from ideal: 88.84 - 97.89: 24 97.89 - 106.93: 458 106.93 - 115.98: 9284 115.98 - 125.02: 10423 125.02 - 134.06: 263 Bond angle restraints: 20452 Sorted by residual: angle pdb="FE3 SF4 A1601 " pdb=" S1 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 73.70 91.18 -17.48 1.50e+00 4.44e-01 1.36e+02 angle pdb="FE1 SF4 A1601 " pdb=" S4 SF4 A1601 " pdb="FE3 SF4 A1601 " ideal model delta sigma weight residual 73.70 90.62 -16.92 1.50e+00 4.44e-01 1.27e+02 angle pdb="FE2 SF4 A1601 " pdb=" S1 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 73.70 90.59 -16.89 1.50e+00 4.44e-01 1.27e+02 angle pdb="FE1 SF4 A1601 " pdb=" S3 SF4 A1601 " pdb="FE2 SF4 A1601 " ideal model delta sigma weight residual 73.70 90.57 -16.87 1.50e+00 4.44e-01 1.27e+02 angle pdb="FE1 SF4 A1601 " pdb=" S4 SF4 A1601 " pdb="FE2 SF4 A1601 " ideal model delta sigma weight residual 73.70 90.55 -16.85 1.50e+00 4.44e-01 1.26e+02 ... (remaining 20447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.89: 7962 14.89 - 29.78: 569 29.78 - 44.67: 142 44.67 - 59.56: 14 59.56 - 74.45: 2 Dihedral angle restraints: 8689 sinusoidal: 2445 harmonic: 6244 Sorted by residual: dihedral pdb=" CA PHE A1181 " pdb=" C PHE A1181 " pdb=" N GLU A1182 " pdb=" CA GLU A1182 " ideal model delta harmonic sigma weight residual 180.00 158.19 21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" C ASP D 94 " pdb=" N ASP D 94 " pdb=" CA ASP D 94 " pdb=" CB ASP D 94 " ideal model delta harmonic sigma weight residual -122.60 -132.34 9.74 0 2.50e+00 1.60e-01 1.52e+01 dihedral pdb=" CA PHE A 772 " pdb=" C PHE A 772 " pdb=" N SER A 773 " pdb=" CA SER A 773 " ideal model delta harmonic sigma weight residual -180.00 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 8686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.048: 2453 4.048 - 8.096: 0 8.096 - 12.144: 0 12.144 - 16.192: 0 16.192 - 20.240: 4 Chirality restraints: 2457 Sorted by residual: chirality pdb="FE3 SF4 A1601 " pdb=" S1 SF4 A1601 " pdb=" S2 SF4 A1601 " pdb=" S4 SF4 A1601 " both_signs ideal model delta sigma weight residual False -10.55 9.68 -20.24 2.00e-01 2.50e+01 1.02e+04 chirality pdb="FE1 SF4 A1601 " pdb=" S2 SF4 A1601 " pdb=" S3 SF4 A1601 " pdb=" S4 SF4 A1601 " both_signs ideal model delta sigma weight residual False -10.55 9.61 -20.16 2.00e-01 2.50e+01 1.02e+04 chirality pdb="FE2 SF4 A1601 " pdb=" S1 SF4 A1601 " pdb=" S3 SF4 A1601 " pdb=" S4 SF4 A1601 " both_signs ideal model delta sigma weight residual False 10.55 -9.60 20.16 2.00e-01 2.50e+01 1.02e+04 ... (remaining 2454 not shown) Planarity restraints: 2636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 285 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C LYS F 285 " -0.052 2.00e-02 2.50e+03 pdb=" O LYS F 285 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE F 286 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 91 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C TYR D 91 " 0.038 2.00e-02 2.50e+03 pdb=" O TYR D 91 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL D 92 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 561 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 562 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 562 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 562 " 0.026 5.00e-02 4.00e+02 ... (remaining 2633 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1589 2.75 - 3.29: 14570 3.29 - 3.82: 22759 3.82 - 4.36: 24297 4.36 - 4.90: 43410 Nonbonded interactions: 106625 Sorted by model distance: nonbonded pdb=" O SER A 170 " pdb=" OG SER A 173 " model vdw 2.210 2.440 nonbonded pdb=" O ILE A 78 " pdb=" OH TYR A 195 " model vdw 2.252 2.440 nonbonded pdb=" O ASP A1456 " pdb=" ND2 ASN A1461 " model vdw 2.271 2.520 nonbonded pdb=" O TYR A1093 " pdb=" OG1 THR A1096 " model vdw 2.272 2.440 nonbonded pdb=" O THR F 411 " pdb=" OG1 THR F 415 " model vdw 2.287 2.440 ... (remaining 106620 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.100 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 49.910 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 : 0.005 0.174 14890 Z= 0.336 Angle : 0.756 17.478 20452 Z= 0.468 Chirality : 0.815 20.240 2457 Planarity : 0.003 0.047 2636 Dihedral : 11.303 74.451 4615 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.74 % Favored : 93.21 % Rotamer: Outliers : 0.29 % Allowed : 2.42 % Favored : 97.29 % 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: -2.58 (0.17), residues: 2066 helix: -0.14 (0.18), residues: 764 sheet: -2.09 (0.28), residues: 263 loop : -2.94 (0.16), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 881 HIS 0.004 0.000 HIS A 287 PHE 0.007 0.001 PHE A1181 TYR 0.011 0.001 TYR A 880 ARG 0.004 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 207 time to evaluate : 1.746 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1232 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 1368 ASN cc_start: 0.9310 (m-40) cc_final: 0.9027 (m110) REVERT: D 40 PHE cc_start: 0.8509 (m-80) cc_final: 0.7989 (m-80) REVERT: D 214 GLN cc_start: 0.8883 (tt0) cc_final: 0.8676 (tm-30) REVERT: E 23 TYR cc_start: 0.8717 (m-80) cc_final: 0.8443 (m-80) REVERT: E 32 PHE cc_start: 0.9154 (m-80) cc_final: 0.8579 (m-10) REVERT: E 37 TYR cc_start: 0.8426 (t80) cc_final: 0.8197 (t80) REVERT: E 163 ASP cc_start: 0.8677 (m-30) cc_final: 0.8224 (p0) REVERT: G 103 GLN cc_start: 0.8289 (mt0) cc_final: 0.8019 (mp10) outliers start: 3 outliers final: 1 residues processed: 209 average time/residue: 0.1926 time to fit residues: 66.6032 Evaluate side-chains 140 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.5980 chunk 159 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 0.0040 chunk 164 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 100 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 overall best weight: 3.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN A1065 ASN A1080 ASN A1090 ASN A1115 GLN A1206 GLN ** A1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 HIS E 122 ASN F 55 HIS F 198 GLN F 434 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.260 14890 Z= 0.515 Angle : 1.378 50.308 20452 Z= 0.890 Chirality : 0.261 6.499 2457 Planarity : 0.004 0.047 2636 Dihedral : 3.612 21.677 2203 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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: -1.50 (0.18), residues: 2066 helix: 0.95 (0.19), residues: 773 sheet: -1.78 (0.28), residues: 261 loop : -2.42 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 210 HIS 0.005 0.001 HIS A 770 PHE 0.029 0.001 PHE A 927 TYR 0.015 0.001 TYR A 387 ARG 0.007 0.001 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.583 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1232 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 975 ASP cc_start: 0.8550 (t0) cc_final: 0.8280 (t0) REVERT: E 25 ASN cc_start: 0.9276 (t0) cc_final: 0.8860 (t0) REVERT: E 32 PHE cc_start: 0.9303 (m-80) cc_final: 0.8854 (m-10) REVERT: E 37 TYR cc_start: 0.8257 (t80) cc_final: 0.7814 (t80) REVERT: E 163 ASP cc_start: 0.8562 (m-30) cc_final: 0.8040 (p0) REVERT: F 272 ASN cc_start: 0.8948 (t0) cc_final: 0.8507 (t0) REVERT: F 347 TYR cc_start: 0.9304 (m-10) cc_final: 0.9047 (m-10) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1852 time to fit residues: 48.8044 Evaluate side-chains 122 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 158 optimal weight: 0.0270 chunk 129 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 191 optimal weight: 0.0010 chunk 206 optimal weight: 0.0020 chunk 170 optimal weight: 40.0000 chunk 189 optimal weight: 0.0070 chunk 65 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 overall best weight: 1.4072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 HIS A1173 ASN ** A1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 14890 Z= 0.475 Angle : 1.368 50.522 20452 Z= 0.886 Chirality : 0.259 6.375 2457 Planarity : 0.004 0.053 2636 Dihedral : 3.540 23.017 2203 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % 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: -0.93 (0.19), residues: 2066 helix: 1.48 (0.20), residues: 771 sheet: -1.43 (0.29), residues: 252 loop : -2.13 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 210 HIS 0.003 0.000 HIS A 287 PHE 0.028 0.001 PHE G 94 TYR 0.014 0.001 TYR A 613 ARG 0.002 0.000 ARG A 884 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.785 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1232 " (corrupted residue). Skipping it. REVERT: A 878 LEU cc_start: 0.9281 (mp) cc_final: 0.9058 (tt) REVERT: D 214 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8506 (tm-30) REVERT: E 25 ASN cc_start: 0.9257 (t0) cc_final: 0.8967 (t0) REVERT: E 32 PHE cc_start: 0.9113 (m-80) cc_final: 0.8384 (m-10) REVERT: E 37 TYR cc_start: 0.8169 (t80) cc_final: 0.7721 (t80) REVERT: E 49 ASN cc_start: 0.8919 (t0) cc_final: 0.8684 (m-40) REVERT: E 122 ASN cc_start: 0.9512 (m-40) cc_final: 0.9199 (m110) REVERT: E 163 ASP cc_start: 0.8703 (m-30) cc_final: 0.8055 (p0) REVERT: F 156 LEU cc_start: 0.9389 (mt) cc_final: 0.8972 (tt) REVERT: F 272 ASN cc_start: 0.8848 (t0) cc_final: 0.8444 (t0) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1777 time to fit residues: 46.9562 Evaluate side-chains 128 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 202 optimal weight: 30.0000 chunk 100 optimal weight: 30.0000 chunk 181 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 165 ASN ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A 785 HIS A1006 ASN A1172 ASN ** A1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 GLN F 332 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.234 14890 Z= 0.602 Angle : 1.461 50.808 20452 Z= 0.932 Chirality : 0.261 6.384 2457 Planarity : 0.005 0.054 2636 Dihedral : 4.687 25.777 2203 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.93 % 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: -1.19 (0.18), residues: 2066 helix: 0.91 (0.19), residues: 762 sheet: -1.26 (0.30), residues: 236 loop : -2.03 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 210 HIS 0.011 0.002 HIS F 55 PHE 0.030 0.002 PHE E 45 TYR 0.019 0.002 TYR E 57 ARG 0.010 0.001 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 1.570 Fit side-chains revert: symmetry clash REVERT: A 600 MET cc_start: 0.8962 (mpp) cc_final: 0.8707 (mmm) REVERT: A 878 LEU cc_start: 0.9387 (mp) cc_final: 0.9159 (tt) REVERT: E 25 ASN cc_start: 0.9363 (t0) cc_final: 0.9132 (t0) REVERT: E 37 TYR cc_start: 0.8278 (t80) cc_final: 0.7849 (t80) REVERT: F 146 ILE cc_start: 0.9509 (mm) cc_final: 0.9274 (tp) REVERT: F 156 LEU cc_start: 0.9457 (mt) cc_final: 0.9070 (tt) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.1814 time to fit residues: 39.2452 Evaluate side-chains 103 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 173 optimal weight: 20.0000 chunk 140 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.245 14890 Z= 0.526 Angle : 1.410 50.684 20452 Z= 0.907 Chirality : 0.259 6.366 2457 Planarity : 0.005 0.052 2636 Dihedral : 4.533 27.210 2203 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.58 % Favored : 91.37 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: -0.91 (0.19), residues: 2066 helix: 1.19 (0.19), residues: 769 sheet: -1.01 (0.32), residues: 222 loop : -1.95 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 210 HIS 0.005 0.001 HIS F 55 PHE 0.019 0.001 PHE E 45 TYR 0.014 0.002 TYR E 34 ARG 0.006 0.000 ARG A1057 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.892 Fit side-chains revert: symmetry clash REVERT: A 600 MET cc_start: 0.9017 (mpp) cc_final: 0.8807 (mmm) REVERT: E 25 ASN cc_start: 0.9316 (t0) cc_final: 0.9055 (t0) REVERT: E 32 PHE cc_start: 0.8992 (m-80) cc_final: 0.8741 (m-80) REVERT: E 37 TYR cc_start: 0.8203 (t80) cc_final: 0.7864 (t80) REVERT: E 44 GLN cc_start: 0.8860 (tt0) cc_final: 0.8523 (mt0) REVERT: F 156 LEU cc_start: 0.9462 (mt) cc_final: 0.9099 (tt) REVERT: F 272 ASN cc_start: 0.9292 (t0) cc_final: 0.8785 (t0) REVERT: F 274 ASP cc_start: 0.8915 (m-30) cc_final: 0.8225 (m-30) REVERT: F 427 PHE cc_start: 0.9260 (m-80) cc_final: 0.8767 (m-80) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1839 time to fit residues: 42.9721 Evaluate side-chains 104 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 50 optimal weight: 0.4980 chunk 203 optimal weight: 20.0000 chunk 168 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 14890 Z= 0.477 Angle : 1.379 50.506 20452 Z= 0.891 Chirality : 0.258 6.357 2457 Planarity : 0.004 0.053 2636 Dihedral : 4.106 24.549 2203 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: -0.45 (0.19), residues: 2066 helix: 1.71 (0.20), residues: 758 sheet: -0.79 (0.32), residues: 237 loop : -1.77 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 774 HIS 0.004 0.001 HIS A 287 PHE 0.013 0.001 PHE A 927 TYR 0.011 0.001 TYR A 880 ARG 0.007 0.000 ARG A1057 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 HIS cc_start: 0.8455 (m-70) cc_final: 0.7795 (m90) REVERT: E 25 ASN cc_start: 0.9254 (t0) cc_final: 0.9006 (t0) REVERT: E 32 PHE cc_start: 0.8935 (m-80) cc_final: 0.8698 (m-10) REVERT: E 37 TYR cc_start: 0.8108 (t80) cc_final: 0.7798 (t80) REVERT: E 44 GLN cc_start: 0.8909 (tt0) cc_final: 0.8609 (mt0) REVERT: F 66 GLU cc_start: 0.9410 (tm-30) cc_final: 0.9075 (tm-30) REVERT: F 156 LEU cc_start: 0.9429 (mt) cc_final: 0.9054 (tt) REVERT: F 272 ASN cc_start: 0.9197 (t0) cc_final: 0.8658 (t0) REVERT: F 274 ASP cc_start: 0.8873 (m-30) cc_final: 0.8122 (m-30) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1809 time to fit residues: 44.5629 Evaluate side-chains 110 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 202 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 123 optimal weight: 0.1980 chunk 93 optimal weight: 10.0000 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A1206 GLN ** A1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 ASN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.236 14890 Z= 0.515 Angle : 1.407 50.651 20452 Z= 0.905 Chirality : 0.259 6.340 2457 Planarity : 0.005 0.068 2636 Dihedral : 4.423 27.610 2203 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: -0.51 (0.19), residues: 2066 helix: 1.50 (0.19), residues: 769 sheet: -0.52 (0.32), residues: 234 loop : -1.77 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 210 HIS 0.007 0.001 HIS F 55 PHE 0.015 0.001 PHE A1147 TYR 0.021 0.002 TYR G 86 ARG 0.003 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.738 Fit side-chains revert: symmetry clash REVERT: A 34 MET cc_start: 0.8544 (mmm) cc_final: 0.8343 (mmm) REVERT: A 822 HIS cc_start: 0.8522 (m-70) cc_final: 0.7977 (m90) REVERT: A 823 MET cc_start: 0.8064 (ptm) cc_final: 0.7561 (ptp) REVERT: E 25 ASN cc_start: 0.9316 (t0) cc_final: 0.9105 (t0) REVERT: E 32 PHE cc_start: 0.9044 (m-80) cc_final: 0.8810 (m-10) REVERT: E 37 TYR cc_start: 0.8257 (t80) cc_final: 0.7999 (t80) REVERT: E 44 GLN cc_start: 0.8940 (tt0) cc_final: 0.8680 (mt0) REVERT: F 66 GLU cc_start: 0.9411 (tm-30) cc_final: 0.9082 (tm-30) REVERT: F 156 LEU cc_start: 0.9440 (mt) cc_final: 0.9049 (tt) REVERT: F 272 ASN cc_start: 0.9296 (t0) cc_final: 0.8814 (t0) REVERT: F 274 ASP cc_start: 0.8954 (m-30) cc_final: 0.8346 (m-30) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1798 time to fit residues: 39.8190 Evaluate side-chains 105 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 128 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.238 14890 Z= 0.482 Angle : 1.383 50.492 20452 Z= 0.893 Chirality : 0.258 6.326 2457 Planarity : 0.004 0.057 2636 Dihedral : 4.193 26.910 2203 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -0.33 (0.19), residues: 2066 helix: 1.74 (0.20), residues: 765 sheet: -0.60 (0.32), residues: 244 loop : -1.69 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 199 HIS 0.004 0.001 HIS A 287 PHE 0.011 0.001 PHE A1147 TYR 0.015 0.001 TYR G 86 ARG 0.007 0.000 ARG A1057 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 MET cc_start: 0.9107 (mmm) cc_final: 0.8765 (mmp) REVERT: A 822 HIS cc_start: 0.8501 (m-70) cc_final: 0.8004 (m90) REVERT: A 823 MET cc_start: 0.8104 (ptm) cc_final: 0.7611 (ptp) REVERT: E 25 ASN cc_start: 0.9310 (t0) cc_final: 0.9085 (t0) REVERT: E 32 PHE cc_start: 0.8925 (m-80) cc_final: 0.8692 (m-10) REVERT: E 37 TYR cc_start: 0.8164 (t80) cc_final: 0.7933 (t80) REVERT: E 44 GLN cc_start: 0.8933 (tt0) cc_final: 0.8679 (mt0) REVERT: F 66 GLU cc_start: 0.9404 (tm-30) cc_final: 0.9077 (tm-30) REVERT: F 156 LEU cc_start: 0.9447 (mt) cc_final: 0.9073 (tt) REVERT: F 272 ASN cc_start: 0.9220 (t0) cc_final: 0.8655 (t0) REVERT: F 274 ASP cc_start: 0.8866 (m-30) cc_final: 0.8289 (m-30) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1834 time to fit residues: 42.2209 Evaluate side-chains 110 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 170 optimal weight: 30.0000 chunk 178 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 165 ASN ** A1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.236 14890 Z= 0.516 Angle : 1.409 50.713 20452 Z= 0.906 Chirality : 0.259 6.348 2457 Planarity : 0.005 0.068 2636 Dihedral : 4.499 29.479 2203 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -0.53 (0.19), residues: 2066 helix: 1.46 (0.19), residues: 780 sheet: -0.55 (0.32), residues: 234 loop : -1.80 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 210 HIS 0.007 0.001 HIS F 55 PHE 0.015 0.001 PHE A 927 TYR 0.017 0.002 TYR A 620 ARG 0.006 0.000 ARG A1057 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 MET cc_start: 0.9087 (mmm) cc_final: 0.8764 (mmp) REVERT: A 822 HIS cc_start: 0.8485 (m-70) cc_final: 0.8044 (m90) REVERT: A 823 MET cc_start: 0.8264 (ptm) cc_final: 0.7775 (ptp) REVERT: E 34 TYR cc_start: 0.8430 (m-80) cc_final: 0.8181 (m-80) REVERT: F 66 GLU cc_start: 0.9419 (tm-30) cc_final: 0.9094 (tm-30) REVERT: F 156 LEU cc_start: 0.9453 (mt) cc_final: 0.9059 (tt) REVERT: F 272 ASN cc_start: 0.9310 (t0) cc_final: 0.8794 (t0) REVERT: F 274 ASP cc_start: 0.8953 (m-30) cc_final: 0.8504 (m-30) REVERT: F 427 PHE cc_start: 0.9243 (m-80) cc_final: 0.8787 (m-80) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1773 time to fit residues: 38.0627 Evaluate side-chains 102 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 209 optimal weight: 20.0000 chunk 192 optimal weight: 0.0970 chunk 166 optimal weight: 3.9990 chunk 17 optimal weight: 0.0370 chunk 128 optimal weight: 20.0000 chunk 102 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 overall best weight: 1.3860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.250 14890 Z= 0.477 Angle : 1.378 50.572 20452 Z= 0.890 Chirality : 0.260 6.414 2457 Planarity : 0.004 0.056 2636 Dihedral : 4.169 28.480 2203 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: -0.20 (0.19), residues: 2066 helix: 1.75 (0.20), residues: 777 sheet: -0.27 (0.34), residues: 223 loop : -1.62 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 774 HIS 0.003 0.001 HIS A 287 PHE 0.041 0.001 PHE E 32 TYR 0.013 0.001 TYR A 387 ARG 0.007 0.000 ARG A1057 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ILE cc_start: 0.9389 (pt) cc_final: 0.9153 (mm) REVERT: A 600 MET cc_start: 0.9061 (mmm) cc_final: 0.8770 (mmp) REVERT: A 822 HIS cc_start: 0.8509 (m-70) cc_final: 0.8079 (m90) REVERT: A 823 MET cc_start: 0.8206 (ptm) cc_final: 0.7630 (ptp) REVERT: E 34 TYR cc_start: 0.8362 (m-80) cc_final: 0.8135 (m-80) REVERT: E 44 GLN cc_start: 0.8547 (mt0) cc_final: 0.8248 (mm-40) REVERT: E 122 ASN cc_start: 0.9389 (m-40) cc_final: 0.8999 (m110) REVERT: F 66 GLU cc_start: 0.9397 (tm-30) cc_final: 0.9067 (tm-30) REVERT: F 156 LEU cc_start: 0.9448 (mt) cc_final: 0.9070 (tt) REVERT: F 272 ASN cc_start: 0.9158 (t0) cc_final: 0.8824 (t0) REVERT: F 427 PHE cc_start: 0.9212 (m-80) cc_final: 0.8769 (m-80) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1762 time to fit residues: 42.7557 Evaluate side-chains 116 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 20.0000 chunk 51 optimal weight: 0.0000 chunk 153 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 21 optimal weight: 0.0470 chunk 30 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 overall best weight: 1.8088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** 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 = 0.2989 r_free = 0.2989 target = 0.051674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.042552 restraints weight = 92062.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.043809 restraints weight = 53668.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.044714 restraints weight = 36955.492| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 14890 Z= 0.477 Angle : 1.375 50.575 20452 Z= 0.889 Chirality : 0.259 6.408 2457 Planarity : 0.004 0.054 2636 Dihedral : 4.046 26.239 2203 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -0.11 (0.19), residues: 2066 helix: 1.82 (0.20), residues: 782 sheet: -0.38 (0.31), residues: 264 loop : -1.58 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 199 HIS 0.004 0.001 HIS A 287 PHE 0.017 0.001 PHE A 772 TYR 0.016 0.001 TYR A 620 ARG 0.006 0.000 ARG A1057 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2457.84 seconds wall clock time: 45 minutes 8.28 seconds (2708.28 seconds total)