Starting phenix.real_space_refine on Fri Mar 15 03:49:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky8_23071/03_2024/7ky8_23071_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky8_23071/03_2024/7ky8_23071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky8_23071/03_2024/7ky8_23071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky8_23071/03_2024/7ky8_23071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky8_23071/03_2024/7ky8_23071_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky8_23071/03_2024/7ky8_23071_updated.pdb" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 53 5.16 5 C 6798 2.51 5 N 1693 2.21 5 O 1972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 592": "NH1" <-> "NH2" Residue "A PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A TYR 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 740": "OE1" <-> "OE2" Residue "A ARG 746": "NH1" <-> "NH2" Residue "A ARG 748": "NH1" <-> "NH2" Residue "A GLU 754": "OE1" <-> "OE2" Residue "A GLU 756": "OE1" <-> "OE2" Residue "A GLU 760": "OE1" <-> "OE2" Residue "A GLU 763": "OE1" <-> "OE2" Residue "A ASP 767": "OD1" <-> "OD2" Residue "A ARG 768": "NH1" <-> "NH2" Residue "A GLU 769": "OE1" <-> "OE2" Residue "A ASP 773": "OD1" <-> "OD2" Residue "A PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A ASP 799": "OD1" <-> "OD2" Residue "A ASP 832": "OD1" <-> "OD2" Residue "A ASP 833": "OD1" <-> "OD2" Residue "A GLU 871": "OE1" <-> "OE2" Residue "A ARG 891": "NH1" <-> "NH2" Residue "A ARG 893": "NH1" <-> "NH2" Residue "A GLU 937": "OE1" <-> "OE2" Residue "A GLU 949": "OE1" <-> "OE2" Residue "A ARG 959": "NH1" <-> "NH2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A GLU 986": "OE1" <-> "OE2" Residue "A ASP 992": "OD1" <-> "OD2" Residue "A ARG 996": "NH1" <-> "NH2" Residue "A ARG 1009": "NH1" <-> "NH2" Residue "A ASP 1016": "OD1" <-> "OD2" Residue "A GLU 1023": "OE1" <-> "OE2" Residue "A ASP 1052": "OD1" <-> "OD2" Residue "A GLU 1063": "OE1" <-> "OE2" Residue "A ASP 1064": "OD1" <-> "OD2" Residue "A GLU 1067": "OE1" <-> "OE2" Residue "A TYR 1083": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "A GLU 1094": "OE1" <-> "OE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A ARG 1130": "NH1" <-> "NH2" Residue "A ARG 1131": "NH1" <-> "NH2" Residue "A ARG 1147": "NH1" <-> "NH2" Residue "A ARG 1196": "NH1" <-> "NH2" Residue "A ARG 1210": "NH1" <-> "NH2" Residue "A ARG 1214": "NH1" <-> "NH2" Residue "A GLU 1229": "OE1" <-> "OE2" Residue "A PHE 1234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1261": "OE1" <-> "OE2" Residue "A PHE 1267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1300": "NH1" <-> "NH2" Residue "A ARG 1305": "NH1" <-> "NH2" Residue "A ARG 1351": "NH1" <-> "NH2" Residue "A TYR 1369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1376": "NH1" <-> "NH2" Residue "A ASP 1378": "OD1" <-> "OD2" Residue "A TYR 1393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1407": "OE1" <-> "OE2" Residue "A ARG 1414": "NH1" <-> "NH2" Residue "A PHE 1431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1436": "NH1" <-> "NH2" Residue "A PHE 1437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1440": "OD1" <-> "OD2" Residue "A ARG 1443": "NH1" <-> "NH2" Residue "A GLU 1452": "OE1" <-> "OE2" Residue "A ARG 1455": "NH1" <-> "NH2" Residue "A ASP 1474": "OD1" <-> "OD2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B ASP 151": "OD1" <-> "OD2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "B ASP 252": "OD1" <-> "OD2" Residue "B ASP 269": "OD1" <-> "OD2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 401": "NH1" <-> "NH2" 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: 10520 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 7237 Classifications: {'peptide': 910} Link IDs: {'PTRANS': 25, 'TRANS': 884} Chain breaks: 2 Chain: "B" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2950 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 19, 'TRANS': 344} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 156 Unusual residues: {' MG': 1, 'ACP': 1, 'CLR': 4, 'MAN': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.35, per 1000 atoms: 0.60 Number of scatterers: 10520 At special positions: 0 Unit cell: (132.16, 120.596, 131.334, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 53 16.00 P 3 15.00 Mg 1 11.99 O 1972 8.00 N 1693 7.00 C 6798 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-4 " NAG D 2 " - " MAN D 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG B 502 " - " ASN B 113 " " NAG C 1 " - " ASN B 298 " " NAG D 1 " - " ASN B 240 " " NAG E 1 " - " ASN B 256 " " NAG F 1 " - " ASN B 332 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.58 Conformation dependent library (CDL) restraints added in 2.0 seconds 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2382 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 6 sheets defined 42.6% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 284 through 298 removed outlier: 3.893A pdb=" N ILE A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 621 removed outlier: 4.463A pdb=" N GLY A 617 " --> pdb=" O GLY A 613 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 618 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS A 621 " --> pdb=" O GLY A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 657 removed outlier: 5.908A pdb=" N SER A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 678 removed outlier: 4.015A pdb=" N GLU A 667 " --> pdb=" O TYR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'A' and resid 702 through 705 removed outlier: 3.619A pdb=" N GLN A 705 " --> pdb=" O ASP A 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 702 through 705' Processing helix chain 'A' and resid 740 through 749 Processing helix chain 'A' and resid 755 through 778 Processing helix chain 'A' and resid 794 through 801 removed outlier: 3.715A pdb=" N GLU A 798 " --> pdb=" O LYS A 794 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS A 801 " --> pdb=" O VAL A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 821 Processing helix chain 'A' and resid 844 through 856 Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 935 through 948 Processing helix chain 'A' and resid 963 through 976 Processing helix chain 'A' and resid 983 through 994 Processing helix chain 'A' and resid 1014 through 1023 Processing helix chain 'A' and resid 1036 through 1045 Processing helix chain 'A' and resid 1072 through 1087 Processing helix chain 'A' and resid 1096 through 1102 Processing helix chain 'A' and resid 1117 through 1123 Processing helix chain 'A' and resid 1127 through 1138 removed outlier: 3.514A pdb=" N LYS A1138 " --> pdb=" O LEU A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1177 through 1182 removed outlier: 4.000A pdb=" N GLN A1182 " --> pdb=" O ALA A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1200 removed outlier: 3.768A pdb=" N MET A1200 " --> pdb=" O GLN A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1215 removed outlier: 4.388A pdb=" N THR A1213 " --> pdb=" O ARG A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1254 Proline residue: A1232 - end of helix removed outlier: 3.681A pdb=" N ASN A1238 " --> pdb=" O PHE A1234 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE A1241 " --> pdb=" O LYS A1237 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER A1244 " --> pdb=" O ILE A1240 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR A1251 " --> pdb=" O TRP A1247 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN A1252 " --> pdb=" O TYR A1248 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN A1253 " --> pdb=" O GLY A1249 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N PHE A1254 " --> pdb=" O ILE A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1275 through 1282 Processing helix chain 'A' and resid 1289 through 1294 Processing helix chain 'A' and resid 1296 through 1302 Processing helix chain 'A' and resid 1310 through 1335 Proline residue: A1331 - end of helix Processing helix chain 'A' and resid 1351 through 1372 Processing helix chain 'A' and resid 1381 through 1400 Processing helix chain 'A' and resid 1411 through 1415 Processing helix chain 'A' and resid 1419 through 1441 removed outlier: 3.872A pdb=" N VAL A1427 " --> pdb=" O ALA A1423 " (cutoff:3.500A) Proline residue: A1435 - end of helix Processing helix chain 'A' and resid 1450 through 1460 Processing helix chain 'B' and resid 76 through 97 Processing helix chain 'B' and resid 187 through 190 No H-bonds generated for 'chain 'B' and resid 187 through 190' Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 267 through 271 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 373 through 398 Processing helix chain 'B' and resid 406 through 408 No H-bonds generated for 'chain 'B' and resid 406 through 408' Processing sheet with id= A, first strand: chain 'A' and resid 732 through 734 removed outlier: 6.857A pdb=" N ALA A1005 " --> pdb=" O LYS A 725 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N CYS A 727 " --> pdb=" O GLY A1003 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY A1003 " --> pdb=" O CYS A 727 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ILE A 729 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N LEU A1001 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 956 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY A1003 " --> pdb=" O LEU A 954 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 954 " --> pdb=" O GLY A1003 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ALA A1005 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG A 952 " --> pdb=" O ALA A1005 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS A 899 " --> pdb=" O VAL A 881 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 881 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 858 through 860 Processing sheet with id= C, first strand: chain 'A' and resid 1029 through 1031 removed outlier: 6.257A pdb=" N VAL A1143 " --> pdb=" O VAL A1030 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA A1142 " --> pdb=" O PHE A1111 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU A1054 " --> pdb=" O ALA A1112 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ILE A1114 " --> pdb=" O GLU A1054 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU A1056 " --> pdb=" O ILE A1114 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1188 through 1190 removed outlier: 6.131A pdb=" N TYR A1204 " --> pdb=" O GLY A1189 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 127 through 129 removed outlier: 6.179A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU B 179 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N THR B 324 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 141 through 145 408 hydrogen bonds defined for protein. 1152 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: 3.34 Time building geometry restraints manager: 4.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3273 1.34 - 1.46: 2276 1.46 - 1.58: 5137 1.58 - 1.69: 6 1.69 - 1.81: 78 Bond restraints: 10770 Sorted by residual: bond pdb=" O2B ACP A1706 " pdb=" PB ACP A1706 " ideal model delta sigma weight residual 1.507 1.610 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" O3A ACP A1706 " pdb=" PB ACP A1706 " ideal model delta sigma weight residual 1.698 1.610 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C4 ACP A1706 " pdb=" C5 ACP A1706 " ideal model delta sigma weight residual 1.386 1.470 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" O3G ACP A1706 " pdb=" PG ACP A1706 " ideal model delta sigma weight residual 1.532 1.610 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C5 ACP A1706 " pdb=" C6 ACP A1706 " ideal model delta sigma weight residual 1.407 1.482 -0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 10765 not shown) Histogram of bond angle deviations from ideal: 98.84 - 106.28: 242 106.28 - 113.73: 6149 113.73 - 121.18: 5618 121.18 - 128.63: 2557 128.63 - 136.08: 77 Bond angle restraints: 14643 Sorted by residual: angle pdb=" N LEU A1164 " pdb=" CA LEU A1164 " pdb=" C LEU A1164 " ideal model delta sigma weight residual 111.02 104.71 6.31 1.25e+00 6.40e-01 2.54e+01 angle pdb=" C3B ACP A1706 " pdb=" PB ACP A1706 " pdb=" O3A ACP A1706 " ideal model delta sigma weight residual 98.05 109.48 -11.43 3.00e+00 1.11e-01 1.45e+01 angle pdb=" C ARG B 316 " pdb=" CA ARG B 316 " pdb=" CB ARG B 316 " ideal model delta sigma weight residual 110.44 113.63 -3.19 9.00e-01 1.23e+00 1.26e+01 angle pdb=" O1B ACP A1706 " pdb=" PB ACP A1706 " pdb=" O2B ACP A1706 " ideal model delta sigma weight residual 119.60 109.45 10.15 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C PHE A1408 " pdb=" N TYR A1409 " pdb=" CA TYR A1409 " ideal model delta sigma weight residual 121.54 127.60 -6.06 1.91e+00 2.74e-01 1.01e+01 ... (remaining 14638 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.89: 6325 23.89 - 47.78: 391 47.78 - 71.67: 46 71.67 - 95.57: 17 95.57 - 119.46: 6 Dihedral angle restraints: 6785 sinusoidal: 3071 harmonic: 3714 Sorted by residual: dihedral pdb=" CA LYS B 170 " pdb=" C LYS B 170 " pdb=" N ASN B 171 " pdb=" CA ASN B 171 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA GLY A 802 " pdb=" C GLY A 802 " pdb=" N SER A 803 " pdb=" CA SER A 803 " ideal model delta harmonic sigma weight residual 180.00 -157.97 -22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA LEU A1348 " pdb=" C LEU A1348 " pdb=" N ASP A1349 " pdb=" CA ASP A1349 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 6782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1451 0.071 - 0.141: 199 0.141 - 0.212: 8 0.212 - 0.282: 9 0.282 - 0.353: 6 Chirality restraints: 1673 Sorted by residual: chirality pdb=" C14 CLR A1704 " pdb=" C13 CLR A1704 " pdb=" C15 CLR A1704 " pdb=" C8 CLR A1704 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C14 CLR B 501 " pdb=" C13 CLR B 501 " pdb=" C15 CLR B 501 " pdb=" C8 CLR B 501 " both_signs ideal model delta sigma weight residual False -2.32 -2.66 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C14 CLR A1703 " pdb=" C13 CLR A1703 " pdb=" C15 CLR A1703 " pdb=" C8 CLR A1703 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 1670 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A1461 " 0.020 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C GLY A1461 " -0.066 2.00e-02 2.50e+03 pdb=" O GLY A1461 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP A1462 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " 0.016 2.00e-02 2.50e+03 3.05e-02 9.28e+00 pdb=" C PHE B 398 " -0.053 2.00e-02 2.50e+03 pdb=" O PHE B 398 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY B 399 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 142 " 0.021 2.00e-02 2.50e+03 1.92e-02 9.21e+00 pdb=" CG TRP B 142 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP B 142 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 142 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 142 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 142 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 142 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 142 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 142 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 142 " 0.001 2.00e-02 2.50e+03 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1272 2.75 - 3.28: 10822 3.28 - 3.82: 17414 3.82 - 4.36: 20402 4.36 - 4.90: 34944 Nonbonded interactions: 84854 Sorted by model distance: nonbonded pdb=" OG SER A 588 " pdb=" OD1 ASP A 701 " model vdw 2.208 2.440 nonbonded pdb=" OG SER A 588 " pdb=" OD1 ASP A 702 " model vdw 2.218 2.440 nonbonded pdb=" OG1 THR A 929 " pdb=" OE1 GLN A 930 " model vdw 2.222 2.440 nonbonded pdb=" NH1 ARG A1226 " pdb=" O VAL A1282 " model vdw 2.234 2.520 nonbonded pdb=" ND2 ASN A1252 " pdb=" OG SER A1257 " model vdw 2.241 2.520 ... (remaining 84849 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 'C' selection = chain 'E' selection = chain 'F' } 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=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: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 4.960 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 32.720 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 0.103 10770 Z= 0.298 Angle : 0.741 11.425 14643 Z= 0.364 Chirality : 0.053 0.353 1673 Planarity : 0.003 0.038 1805 Dihedral : 15.267 119.457 4397 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: -1.28 (0.25), residues: 1266 helix: 0.39 (0.22), residues: 581 sheet: -1.48 (0.42), residues: 159 loop : -2.05 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 142 HIS 0.003 0.001 HIS B 125 PHE 0.017 0.001 PHE A 791 TYR 0.020 0.001 TYR B 378 ARG 0.007 0.000 ARG A1131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.150 Fit side-chains REVERT: A 771 MET cc_start: 0.6518 (ttp) cc_final: 0.5904 (ttt) REVERT: B 112 THR cc_start: 0.8338 (p) cc_final: 0.8127 (p) REVERT: B 261 ASN cc_start: 0.8935 (p0) cc_final: 0.8677 (p0) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2076 time to fit residues: 44.7895 Evaluate side-chains 110 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 0.0000 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 115 optimal weight: 0.0070 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1074 GLN A1253 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10770 Z= 0.153 Angle : 0.561 9.753 14643 Z= 0.277 Chirality : 0.042 0.162 1673 Planarity : 0.003 0.032 1805 Dihedral : 11.088 115.616 1997 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.08 % Allowed : 9.44 % Favored : 89.48 % 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: -1.11 (0.25), residues: 1266 helix: 0.61 (0.22), residues: 576 sheet: -1.56 (0.42), residues: 153 loop : -1.98 (0.29), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 142 HIS 0.002 0.001 HIS A1350 PHE 0.015 0.001 PHE A1328 TYR 0.020 0.001 TYR A1299 ARG 0.002 0.000 ARG A1147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: A 684 TYR cc_start: 0.8404 (t80) cc_final: 0.8181 (t80) REVERT: A 771 MET cc_start: 0.6537 (ttp) cc_final: 0.5899 (ttt) REVERT: A 845 ASP cc_start: 0.8016 (p0) cc_final: 0.7657 (p0) REVERT: A 1410 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7934 (mmtm) REVERT: B 147 ASP cc_start: 0.8580 (t0) cc_final: 0.8346 (t0) REVERT: B 162 ARG cc_start: 0.7429 (ptp90) cc_final: 0.6769 (ptp90) REVERT: B 236 ASN cc_start: 0.9419 (t0) cc_final: 0.9015 (t0) outliers start: 12 outliers final: 9 residues processed: 135 average time/residue: 0.2068 time to fit residues: 41.1534 Evaluate side-chains 120 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1458 TRP Chi-restraints excluded: chain A residue 1473 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 393 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 ASN A1285 GLN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10770 Z= 0.328 Angle : 0.620 8.187 14643 Z= 0.310 Chirality : 0.045 0.178 1673 Planarity : 0.004 0.033 1805 Dihedral : 11.027 119.284 1997 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 2.52 % Allowed : 12.68 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.24), residues: 1266 helix: 0.35 (0.22), residues: 585 sheet: -1.55 (0.42), residues: 161 loop : -2.16 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 142 HIS 0.007 0.001 HIS A1336 PHE 0.020 0.002 PHE A1408 TYR 0.018 0.002 TYR B 280 ARG 0.005 0.000 ARG A1147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 684 TYR cc_start: 0.8546 (t80) cc_final: 0.8282 (t80) REVERT: A 771 MET cc_start: 0.6678 (ttp) cc_final: 0.5866 (ttt) REVERT: A 845 ASP cc_start: 0.8122 (p0) cc_final: 0.7741 (p0) REVERT: A 871 GLU cc_start: 0.7528 (mp0) cc_final: 0.6086 (mm-30) REVERT: A 949 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7470 (pm20) REVERT: A 1255 ASP cc_start: 0.7474 (t0) cc_final: 0.7222 (t0) REVERT: B 121 ILE cc_start: 0.8564 (mt) cc_final: 0.8199 (mt) REVERT: B 147 ASP cc_start: 0.8581 (t0) cc_final: 0.8330 (t0) outliers start: 28 outliers final: 22 residues processed: 137 average time/residue: 0.2070 time to fit residues: 41.9000 Evaluate side-chains 137 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1458 TRP Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain A residue 1473 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 393 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10770 Z= 0.168 Angle : 0.545 8.556 14643 Z= 0.273 Chirality : 0.042 0.166 1673 Planarity : 0.003 0.031 1805 Dihedral : 10.731 118.848 1997 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.61 % Allowed : 15.65 % Favored : 81.74 % 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: -1.14 (0.25), residues: 1266 helix: 0.64 (0.22), residues: 569 sheet: -1.62 (0.42), residues: 153 loop : -2.03 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 142 HIS 0.003 0.001 HIS A1336 PHE 0.014 0.001 PHE A1328 TYR 0.017 0.001 TYR B 280 ARG 0.004 0.000 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 684 TYR cc_start: 0.8518 (t80) cc_final: 0.8227 (t80) REVERT: A 771 MET cc_start: 0.6813 (ttp) cc_final: 0.6006 (ttt) REVERT: A 845 ASP cc_start: 0.8046 (p0) cc_final: 0.7677 (p0) REVERT: A 871 GLU cc_start: 0.7532 (mp0) cc_final: 0.6119 (mm-30) REVERT: A 878 GLU cc_start: 0.6836 (tm-30) cc_final: 0.6555 (tm-30) REVERT: A 1410 LYS cc_start: 0.8353 (mmtt) cc_final: 0.7843 (mmtm) REVERT: B 121 ILE cc_start: 0.8544 (mt) cc_final: 0.8160 (mt) REVERT: B 147 ASP cc_start: 0.8627 (t0) cc_final: 0.8377 (t0) REVERT: B 236 ASN cc_start: 0.9399 (t0) cc_final: 0.9052 (t0) outliers start: 29 outliers final: 19 residues processed: 131 average time/residue: 0.2191 time to fit residues: 41.9000 Evaluate side-chains 130 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1372 MET Chi-restraints excluded: chain A residue 1458 TRP Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain A residue 1473 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 393 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 0.9990 chunk 69 optimal weight: 0.2980 chunk 1 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 110 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10770 Z= 0.167 Angle : 0.539 8.763 14643 Z= 0.268 Chirality : 0.041 0.161 1673 Planarity : 0.003 0.032 1805 Dihedral : 10.503 119.844 1997 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.34 % Allowed : 16.82 % Favored : 80.85 % 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: -1.12 (0.25), residues: 1266 helix: 0.67 (0.22), residues: 572 sheet: -1.58 (0.42), residues: 153 loop : -2.06 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 142 HIS 0.003 0.001 HIS A1336 PHE 0.013 0.001 PHE A1328 TYR 0.017 0.001 TYR B 280 ARG 0.005 0.000 ARG A1131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 684 TYR cc_start: 0.8572 (t80) cc_final: 0.8319 (t80) REVERT: A 771 MET cc_start: 0.6791 (ttp) cc_final: 0.6027 (ttt) REVERT: A 845 ASP cc_start: 0.8005 (p0) cc_final: 0.7647 (p0) REVERT: A 871 GLU cc_start: 0.7442 (mp0) cc_final: 0.6126 (mm-30) REVERT: A 1410 LYS cc_start: 0.8452 (mmtt) cc_final: 0.7748 (tppt) REVERT: B 61 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7092 (mm-40) REVERT: B 121 ILE cc_start: 0.8553 (mt) cc_final: 0.8181 (mt) REVERT: B 147 ASP cc_start: 0.8627 (t0) cc_final: 0.8384 (t0) outliers start: 26 outliers final: 18 residues processed: 136 average time/residue: 0.2166 time to fit residues: 42.4916 Evaluate side-chains 134 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1372 MET Chi-restraints excluded: chain A residue 1458 TRP Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain A residue 1473 THR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 393 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 0.0970 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1285 GLN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10770 Z= 0.334 Angle : 0.638 11.646 14643 Z= 0.315 Chirality : 0.045 0.164 1673 Planarity : 0.004 0.038 1805 Dihedral : 10.761 122.928 1997 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.24 % Allowed : 17.54 % Favored : 79.23 % 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: -1.35 (0.25), residues: 1266 helix: 0.32 (0.22), residues: 587 sheet: -1.64 (0.43), residues: 153 loop : -2.06 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1458 HIS 0.007 0.001 HIS A1336 PHE 0.018 0.002 PHE A1408 TYR 0.017 0.001 TYR B 280 ARG 0.007 0.000 ARG A1131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 116 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 MET cc_start: 0.6974 (ttp) cc_final: 0.6144 (ttt) REVERT: A 845 ASP cc_start: 0.8063 (p0) cc_final: 0.7713 (p0) REVERT: A 891 ARG cc_start: 0.8303 (mtp-110) cc_final: 0.8052 (mtp-110) REVERT: A 1255 ASP cc_start: 0.7431 (t0) cc_final: 0.7132 (t0) REVERT: B 61 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7389 (mm-40) REVERT: B 121 ILE cc_start: 0.8611 (mt) cc_final: 0.8242 (mt) REVERT: B 147 ASP cc_start: 0.8614 (t0) cc_final: 0.8364 (t0) outliers start: 36 outliers final: 32 residues processed: 139 average time/residue: 0.2070 time to fit residues: 42.6308 Evaluate side-chains 147 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 114 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1339 MET Chi-restraints excluded: chain A residue 1372 MET Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1458 TRP Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain A residue 1473 THR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 393 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 0.9990 chunk 13 optimal weight: 0.0270 chunk 70 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10770 Z= 0.158 Angle : 0.555 10.429 14643 Z= 0.274 Chirality : 0.041 0.131 1673 Planarity : 0.003 0.040 1805 Dihedral : 10.461 120.957 1997 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.52 % Allowed : 19.33 % Favored : 78.15 % 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: -1.08 (0.25), residues: 1266 helix: 0.67 (0.22), residues: 566 sheet: -1.56 (0.43), residues: 149 loop : -1.97 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 142 HIS 0.002 0.001 HIS B 125 PHE 0.014 0.001 PHE A1328 TYR 0.017 0.001 TYR B 280 ARG 0.004 0.000 ARG A1131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 684 TYR cc_start: 0.8245 (t80) cc_final: 0.8044 (t80) REVERT: A 771 MET cc_start: 0.6741 (ttp) cc_final: 0.5980 (ttt) REVERT: A 845 ASP cc_start: 0.8010 (p0) cc_final: 0.7659 (p0) REVERT: A 871 GLU cc_start: 0.7355 (mp0) cc_final: 0.6023 (mm-30) REVERT: A 891 ARG cc_start: 0.8267 (mtp-110) cc_final: 0.7993 (mtp-110) REVERT: A 1410 LYS cc_start: 0.8437 (mmtt) cc_final: 0.7753 (tppt) REVERT: B 61 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7228 (mm-40) REVERT: B 121 ILE cc_start: 0.8630 (mt) cc_final: 0.8300 (mt) REVERT: B 147 ASP cc_start: 0.8617 (t0) cc_final: 0.8379 (t0) REVERT: B 236 ASN cc_start: 0.9408 (t0) cc_final: 0.9068 (t0) REVERT: B 238 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8599 (tpt) REVERT: B 348 TRP cc_start: 0.9129 (OUTLIER) cc_final: 0.8664 (t60) outliers start: 28 outliers final: 18 residues processed: 137 average time/residue: 0.2158 time to fit residues: 43.5055 Evaluate side-chains 137 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1458 TRP Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain A residue 1473 THR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 393 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 73 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10770 Z= 0.194 Angle : 0.570 9.694 14643 Z= 0.282 Chirality : 0.042 0.157 1673 Planarity : 0.003 0.042 1805 Dihedral : 10.351 121.688 1997 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 2.34 % Allowed : 19.87 % Favored : 77.79 % 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: -1.17 (0.25), residues: 1266 helix: 0.60 (0.22), residues: 575 sheet: -1.64 (0.42), residues: 153 loop : -2.06 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 142 HIS 0.003 0.001 HIS A1336 PHE 0.013 0.001 PHE A1328 TYR 0.018 0.001 TYR B 280 ARG 0.006 0.000 ARG A1131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 684 TYR cc_start: 0.8217 (t80) cc_final: 0.7999 (t80) REVERT: A 771 MET cc_start: 0.6789 (ttp) cc_final: 0.6011 (ttt) REVERT: A 845 ASP cc_start: 0.8001 (p0) cc_final: 0.7681 (p0) REVERT: A 871 GLU cc_start: 0.7316 (mp0) cc_final: 0.5823 (mm-30) REVERT: A 891 ARG cc_start: 0.8273 (mtp-110) cc_final: 0.8004 (mtp-110) REVERT: A 1099 GLU cc_start: 0.7291 (mp0) cc_final: 0.7034 (mp0) REVERT: A 1185 ASP cc_start: 0.8013 (t0) cc_final: 0.7778 (t0) REVERT: A 1255 ASP cc_start: 0.7348 (t0) cc_final: 0.7051 (t0) REVERT: A 1410 LYS cc_start: 0.8470 (mmtt) cc_final: 0.7787 (tppt) REVERT: B 61 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7242 (mm-40) REVERT: B 121 ILE cc_start: 0.8648 (mt) cc_final: 0.8315 (mt) REVERT: B 147 ASP cc_start: 0.8598 (t0) cc_final: 0.8369 (t0) REVERT: B 238 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8618 (tpt) REVERT: B 348 TRP cc_start: 0.9138 (OUTLIER) cc_final: 0.8703 (t60) outliers start: 26 outliers final: 22 residues processed: 138 average time/residue: 0.2163 time to fit residues: 44.0363 Evaluate side-chains 143 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1458 TRP Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain A residue 1473 THR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 393 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 114 optimal weight: 0.0020 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 107 optimal weight: 0.0050 chunk 113 optimal weight: 0.6980 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10770 Z= 0.137 Angle : 0.548 9.324 14643 Z= 0.270 Chirality : 0.041 0.138 1673 Planarity : 0.003 0.044 1805 Dihedral : 10.038 120.087 1997 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.43 % Allowed : 19.78 % Favored : 77.79 % 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: -1.03 (0.25), residues: 1266 helix: 0.74 (0.22), residues: 573 sheet: -1.59 (0.42), residues: 147 loop : -2.00 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 142 HIS 0.002 0.001 HIS A 823 PHE 0.013 0.001 PHE A1328 TYR 0.018 0.001 TYR B 280 ARG 0.007 0.000 ARG A1131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 684 TYR cc_start: 0.8149 (t80) cc_final: 0.7939 (t80) REVERT: A 771 MET cc_start: 0.6800 (ttp) cc_final: 0.6081 (ttt) REVERT: A 845 ASP cc_start: 0.7941 (p0) cc_final: 0.7597 (p0) REVERT: A 871 GLU cc_start: 0.7327 (mp0) cc_final: 0.6038 (mm-30) REVERT: A 891 ARG cc_start: 0.8265 (mtp-110) cc_final: 0.7992 (mtp-110) REVERT: A 1059 LYS cc_start: 0.8277 (ptmm) cc_final: 0.8069 (ptmm) REVERT: A 1099 GLU cc_start: 0.7315 (mp0) cc_final: 0.7060 (mp0) REVERT: A 1338 ASN cc_start: 0.8524 (p0) cc_final: 0.8256 (p0) REVERT: A 1410 LYS cc_start: 0.8387 (mmtt) cc_final: 0.8179 (mmtm) REVERT: A 1452 GLU cc_start: 0.7601 (mp0) cc_final: 0.7386 (mp0) REVERT: B 61 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7127 (mm-40) REVERT: B 121 ILE cc_start: 0.8634 (mt) cc_final: 0.8295 (mt) REVERT: B 147 ASP cc_start: 0.8596 (t0) cc_final: 0.8395 (t0) REVERT: B 236 ASN cc_start: 0.9417 (t0) cc_final: 0.9061 (t0) REVERT: B 348 TRP cc_start: 0.9093 (OUTLIER) cc_final: 0.8649 (t60) outliers start: 27 outliers final: 19 residues processed: 146 average time/residue: 0.2083 time to fit residues: 44.8026 Evaluate side-chains 144 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1458 TRP Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain A residue 1473 THR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 393 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10770 Z= 0.160 Angle : 0.564 8.985 14643 Z= 0.280 Chirality : 0.042 0.174 1673 Planarity : 0.003 0.042 1805 Dihedral : 9.910 120.756 1997 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.98 % Allowed : 20.05 % Favored : 77.97 % 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: -1.01 (0.25), residues: 1266 helix: 0.74 (0.22), residues: 573 sheet: -1.55 (0.43), residues: 147 loop : -1.97 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 142 HIS 0.002 0.001 HIS A1336 PHE 0.013 0.001 PHE A1328 TYR 0.018 0.001 TYR B 280 ARG 0.007 0.000 ARG A1131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 684 TYR cc_start: 0.8187 (t80) cc_final: 0.7962 (t80) REVERT: A 771 MET cc_start: 0.6750 (ttp) cc_final: 0.6009 (ttt) REVERT: A 845 ASP cc_start: 0.7940 (p0) cc_final: 0.7627 (p0) REVERT: A 871 GLU cc_start: 0.7364 (mp0) cc_final: 0.5888 (mm-30) REVERT: A 891 ARG cc_start: 0.8299 (mtp-110) cc_final: 0.8012 (mtp-110) REVERT: A 949 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7499 (pm20) REVERT: A 1338 ASN cc_start: 0.8516 (p0) cc_final: 0.8252 (p0) REVERT: A 1410 LYS cc_start: 0.8435 (mmtt) cc_final: 0.8208 (mmtm) REVERT: A 1452 GLU cc_start: 0.7558 (mp0) cc_final: 0.7352 (mp0) REVERT: B 61 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7100 (mm-40) REVERT: B 121 ILE cc_start: 0.8646 (mt) cc_final: 0.8317 (mt) REVERT: B 147 ASP cc_start: 0.8609 (t0) cc_final: 0.8408 (t0) REVERT: B 348 TRP cc_start: 0.9119 (OUTLIER) cc_final: 0.8696 (t60) outliers start: 22 outliers final: 20 residues processed: 139 average time/residue: 0.2098 time to fit residues: 42.8930 Evaluate side-chains 143 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1458 TRP Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain A residue 1473 THR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 393 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 1.9990 chunk 107 optimal weight: 0.0980 chunk 30 optimal weight: 8.9990 chunk 92 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1285 GLN B 60 GLN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.152540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.116248 restraints weight = 13128.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.114152 restraints weight = 20369.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.111393 restraints weight = 19782.832| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 10770 Z= 0.222 Angle : 0.590 8.732 14643 Z= 0.295 Chirality : 0.043 0.165 1673 Planarity : 0.003 0.042 1805 Dihedral : 9.963 122.482 1997 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 2.16 % Allowed : 20.32 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.25), residues: 1266 helix: 0.64 (0.22), residues: 576 sheet: -1.54 (0.42), residues: 153 loop : -2.01 (0.29), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 142 HIS 0.004 0.001 HIS A1336 PHE 0.013 0.001 PHE A1328 TYR 0.018 0.001 TYR B 280 ARG 0.009 0.000 ARG A1131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2138.30 seconds wall clock time: 39 minutes 31.42 seconds (2371.42 seconds total)