Starting phenix.real_space_refine on Sat Jul 20 13:00:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky8_23071/07_2024/7ky8_23071_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky8_23071/07_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_23071/07_2024/7ky8_23071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky8_23071/07_2024/7ky8_23071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky8_23071/07_2024/7ky8_23071_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky8_23071/07_2024/7ky8_23071_neut.cif" } 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 6.46, per 1000 atoms: 0.61 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: 4.03 Conformation dependent library (CDL) restraints added in 1.8 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... Secondary structure from input PDB file: 52 helices and 9 sheets defined 49.9% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 283 through 299 removed outlier: 4.015A pdb=" N VAL A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) 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 589 through 616 removed outlier: 4.306A pdb=" N GLU A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 622 Processing helix chain 'A' and resid 641 through 655 Processing helix chain 'A' and resid 656 through 658 No H-bonds generated for 'chain 'A' and resid 656 through 658' Processing helix chain 'A' and resid 661 through 679 removed outlier: 4.015A pdb=" N GLU A 667 " --> pdb=" O TYR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 682 No H-bonds generated for 'chain 'A' and resid 680 through 682' Processing helix chain 'A' and resid 701 through 706 removed outlier: 3.619A pdb=" N GLN A 705 " --> pdb=" O ASP A 702 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 706 " --> pdb=" O LEU A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 750 Processing helix chain 'A' and resid 754 through 779 Processing helix chain 'A' and resid 793 through 802 removed outlier: 4.129A pdb=" N VAL A 797 " --> pdb=" O SER A 793 " (cutoff:3.500A) 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) removed outlier: 4.153A pdb=" N GLY A 802 " --> pdb=" O GLU A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 822 Processing helix chain 'A' and resid 843 through 857 Processing helix chain 'A' and resid 918 through 925 Processing helix chain 'A' and resid 934 through 949 removed outlier: 3.592A pdb=" N GLU A 949 " --> pdb=" O GLU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 977 Processing helix chain 'A' and resid 982 through 995 removed outlier: 4.420A pdb=" N GLU A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1024 Processing helix chain 'A' and resid 1035 through 1046 Processing helix chain 'A' and resid 1071 through 1088 Processing helix chain 'A' and resid 1095 through 1103 Processing helix chain 'A' and resid 1116 through 1124 Processing helix chain 'A' and resid 1126 through 1137 Processing helix chain 'A' and resid 1149 through 1163 Processing helix chain 'A' and resid 1177 through 1183 Processing helix chain 'A' and resid 1196 through 1201 removed outlier: 3.522A pdb=" N CYS A1201 " --> pdb=" O GLN A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1210 No H-bonds generated for 'chain 'A' and resid 1208 through 1210' Processing helix chain 'A' and resid 1211 through 1216 Processing helix chain 'A' and resid 1218 through 1251 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) Processing helix chain 'A' and resid 1252 through 1255 Processing helix chain 'A' and resid 1274 through 1283 removed outlier: 3.881A pdb=" N ILE A1278 " --> pdb=" O SER A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1295 Processing helix chain 'A' and resid 1296 through 1303 Processing helix chain 'A' and resid 1309 through 1336 removed outlier: 3.533A pdb=" N PHE A1313 " --> pdb=" O ASN A1309 " (cutoff:3.500A) Proline residue: A1331 - end of helix Processing helix chain 'A' and resid 1350 through 1373 Processing helix chain 'A' and resid 1380 through 1401 Processing helix chain 'A' and resid 1402 through 1406 removed outlier: 3.624A pdb=" N ASN A1406 " --> pdb=" O SER A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1416 Processing helix chain 'A' and resid 1418 through 1442 removed outlier: 3.656A pdb=" N TRP A1422 " --> pdb=" O GLN A1418 " (cutoff:3.500A) 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 1449 through 1461 Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 75 through 98 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 194 through 200 removed outlier: 3.564A pdb=" N ILE B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 removed outlier: 3.655A pdb=" N VAL B 208 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.739A pdb=" N MET B 238 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.757A pdb=" N GLU B 290 " --> pdb=" O PRO B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 350 through 354 Processing helix chain 'B' and resid 372 through 399 Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.805A pdb=" N LEU B 409 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 684 through 685 removed outlier: 3.717A pdb=" N ASN A 685 " --> pdb=" O TYR A 690 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 690 " --> pdb=" O ASN A 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1055 through 1057 removed outlier: 6.398A pdb=" N VAL A1030 " --> pdb=" O CYS A1145 " (cutoff:3.500A) Processing sheet with id=AA3, 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=AA4, first strand: chain 'A' and resid 858 through 860 Processing sheet with id=AA5, first strand: chain 'A' and resid 1188 through 1190 removed outlier: 6.548A pdb=" N GLY A1189 " --> pdb=" O ILE A1206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1377 through 1378 Processing sheet with id=AA7, 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=AA8, first strand: chain 'B' and resid 119 through 120 removed outlier: 5.691A pdb=" N ASP B 343 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N GLN B 246 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 227 through 228 removed outlier: 6.342A pdb=" N ILE B 227 " --> pdb=" O ALA B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 490 hydrogen bonds defined for protein. 1362 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: 3.35 Time building geometry restraints manager: 4.40 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: 1263 2.75 - 3.28: 10765 3.28 - 3.82: 17322 3.82 - 4.36: 20255 4.36 - 4.90: 34921 Nonbonded interactions: 84526 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 84521 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: 4.600 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 30.250 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.360 ------------------------------------------------------------------------------- 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= 0.310 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 : 1.053 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: 0.2161 time to fit residues: 46.5491 Evaluate side-chains 110 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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: 3.9990 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1074 GLN ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8202 moved from start: 0.0791 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= 0.184 Angle : 0.584 9.912 14643 Z= 0.293 Chirality : 0.043 0.174 1673 Planarity : 0.003 0.031 1805 Dihedral : 11.205 115.301 1997 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 1.26 % Allowed : 9.35 % Favored : 89.39 % 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 (0.24), residues: 1266 helix: 0.56 (0.22), residues: 579 sheet: -1.53 (0.42), residues: 152 loop : -2.06 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 142 HIS 0.003 0.001 HIS A1336 PHE 0.014 0.001 PHE A1328 TYR 0.018 0.001 TYR A1299 ARG 0.002 0.000 ARG B 162 *********************** 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 137 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 684 TYR cc_start: 0.8435 (t80) cc_final: 0.8232 (t80) REVERT: A 771 MET cc_start: 0.6632 (ttp) cc_final: 0.5961 (ttt) REVERT: A 845 ASP cc_start: 0.7957 (p0) cc_final: 0.7606 (p0) REVERT: A 949 GLU cc_start: 0.7537 (pm20) cc_final: 0.7325 (mt-10) REVERT: A 1410 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7964 (mmtm) REVERT: B 147 ASP cc_start: 0.8583 (t0) cc_final: 0.8341 (t0) outliers start: 14 outliers final: 11 residues processed: 132 average time/residue: 0.2131 time to fit residues: 41.3937 Evaluate side-chains 120 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 1266 THR 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 93 ILE 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: 0.9980 chunk 35 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 114 optimal weight: 0.0010 chunk 39 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- 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: 0.8199 moved from start: 0.1021 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= 0.168 Angle : 0.557 8.310 14643 Z= 0.279 Chirality : 0.042 0.170 1673 Planarity : 0.003 0.034 1805 Dihedral : 10.751 115.745 1997 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.16 % Allowed : 12.23 % Favored : 85.61 % 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: -1.12 (0.25), residues: 1266 helix: 0.62 (0.22), residues: 585 sheet: -1.48 (0.42), residues: 152 loop : -2.09 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 142 HIS 0.003 0.001 HIS A1336 PHE 0.013 0.001 PHE A1408 TYR 0.018 0.001 TYR B 280 ARG 0.003 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 146 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 684 TYR cc_start: 0.8477 (t80) cc_final: 0.8239 (t80) REVERT: A 771 MET cc_start: 0.6634 (ttp) cc_final: 0.5909 (ttt) REVERT: A 845 ASP cc_start: 0.7956 (p0) cc_final: 0.7573 (p0) REVERT: A 1059 LYS cc_start: 0.8192 (ptmm) cc_final: 0.7952 (ptmm) REVERT: A 1410 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7793 (mmtm) REVERT: B 147 ASP cc_start: 0.8601 (t0) cc_final: 0.8366 (t0) outliers start: 24 outliers final: 15 residues processed: 136 average time/residue: 0.2470 time to fit residues: 49.1133 Evaluate side-chains 127 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 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 93 ILE Chi-restraints excluded: chain B residue 94 LEU 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: 4.9990 chunk 86 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 ASN ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8203 moved from start: 0.1193 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= 0.172 Angle : 0.552 8.581 14643 Z= 0.277 Chirality : 0.042 0.162 1673 Planarity : 0.003 0.033 1805 Dihedral : 10.564 117.867 1997 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.61 % Allowed : 14.84 % Favored : 82.55 % 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: -1.00 (0.25), residues: 1266 helix: 0.69 (0.22), residues: 586 sheet: -1.36 (0.42), residues: 148 loop : -2.01 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 142 HIS 0.003 0.001 HIS A1336 PHE 0.013 0.001 PHE A1408 TYR 0.017 0.001 TYR B 280 ARG 0.003 0.000 ARG A1131 *********************** 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 149 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 684 TYR cc_start: 0.8496 (t80) cc_final: 0.8237 (t80) REVERT: A 771 MET cc_start: 0.6860 (ttp) cc_final: 0.6083 (ttt) REVERT: A 845 ASP cc_start: 0.8016 (p0) cc_final: 0.7625 (p0) REVERT: A 871 GLU cc_start: 0.7498 (mp0) cc_final: 0.6118 (mm-30) REVERT: A 891 ARG cc_start: 0.8189 (mtp-110) cc_final: 0.7866 (mtp-110) REVERT: A 949 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7565 (pm20) REVERT: A 1338 ASN cc_start: 0.8511 (p0) cc_final: 0.8211 (p0) REVERT: A 1410 LYS cc_start: 0.8281 (mmtt) cc_final: 0.7688 (tppt) REVERT: B 61 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7114 (mm-40) REVERT: B 147 ASP cc_start: 0.8630 (t0) cc_final: 0.8387 (t0) outliers start: 29 outliers final: 19 residues processed: 134 average time/residue: 0.2157 time to fit residues: 42.5629 Evaluate side-chains 131 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 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 93 ILE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 111 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 1 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.8291 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10770 Z= 0.318 Angle : 0.623 8.284 14643 Z= 0.312 Chirality : 0.045 0.169 1673 Planarity : 0.004 0.044 1805 Dihedral : 10.738 121.833 1997 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 3.15 % Allowed : 15.74 % Favored : 81.12 % 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: -1.21 (0.24), residues: 1266 helix: 0.48 (0.22), residues: 588 sheet: -1.42 (0.43), residues: 152 loop : -2.11 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 142 HIS 0.006 0.001 HIS A1336 PHE 0.017 0.002 PHE A1408 TYR 0.018 0.002 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 149 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 114 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 684 TYR cc_start: 0.8641 (t80) cc_final: 0.8395 (t80) REVERT: A 685 ASN cc_start: 0.8815 (t0) cc_final: 0.8598 (t0) REVERT: A 771 MET cc_start: 0.7053 (ttp) cc_final: 0.6565 (ttt) REVERT: A 845 ASP cc_start: 0.8096 (p0) cc_final: 0.7731 (p0) REVERT: A 871 GLU cc_start: 0.7449 (mp0) cc_final: 0.6087 (mm-30) REVERT: B 61 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7132 (mm-40) REVERT: B 147 ASP cc_start: 0.8627 (t0) cc_final: 0.8373 (t0) REVERT: B 316 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8629 (ptp-170) outliers start: 35 outliers final: 25 residues processed: 135 average time/residue: 0.2066 time to fit residues: 40.7868 Evaluate side-chains 139 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 1206 ILE 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 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 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 194 SER Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 316 ARG 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: 9.9990 chunk 110 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8221 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10770 Z= 0.158 Angle : 0.568 11.481 14643 Z= 0.280 Chirality : 0.042 0.149 1673 Planarity : 0.003 0.043 1805 Dihedral : 10.439 119.743 1997 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 2.34 % Allowed : 17.45 % Favored : 80.22 % 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: -1.01 (0.25), residues: 1266 helix: 0.64 (0.22), residues: 586 sheet: -1.33 (0.43), residues: 148 loop : -1.99 (0.28), residues: 532 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 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 145 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 MET cc_start: 0.7025 (ttp) cc_final: 0.6542 (ttt) REVERT: A 845 ASP cc_start: 0.8030 (p0) cc_final: 0.7666 (p0) REVERT: A 871 GLU cc_start: 0.7489 (mp0) cc_final: 0.6145 (mm-30) REVERT: A 891 ARG cc_start: 0.8225 (mtp-110) cc_final: 0.7942 (mtp-110) REVERT: A 1185 ASP cc_start: 0.8075 (t0) cc_final: 0.7813 (t0) REVERT: A 1410 LYS cc_start: 0.8337 (mmtt) cc_final: 0.7704 (tppt) REVERT: B 61 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7074 (mm-40) REVERT: B 147 ASP cc_start: 0.8619 (t0) cc_final: 0.8380 (t0) REVERT: B 236 ASN cc_start: 0.9388 (t0) cc_final: 0.9036 (t0) outliers start: 26 outliers final: 17 residues processed: 133 average time/residue: 0.2099 time to fit residues: 40.8267 Evaluate side-chains 132 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 1056 LEU 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 1450 ASP 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 220 SER 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: 0.8980 chunk 13 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.8198 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 : 0.002 0.037 10770 Z= 0.150 Angle : 0.550 9.726 14643 Z= 0.272 Chirality : 0.041 0.153 1673 Planarity : 0.003 0.040 1805 Dihedral : 10.163 120.535 1997 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.52 % Allowed : 18.17 % Favored : 79.32 % 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: -0.95 (0.25), residues: 1266 helix: 0.73 (0.22), residues: 587 sheet: -1.31 (0.41), residues: 158 loop : -2.01 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 142 HIS 0.002 0.001 HIS A1336 PHE 0.014 0.001 PHE A1111 TYR 0.018 0.001 TYR B 280 ARG 0.006 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 : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 MET cc_start: 0.7076 (ttp) cc_final: 0.6614 (ttt) REVERT: A 810 LYS cc_start: 0.7310 (tptp) cc_final: 0.5870 (ptpp) REVERT: A 845 ASP cc_start: 0.8017 (p0) cc_final: 0.7637 (p0) REVERT: A 871 GLU cc_start: 0.7473 (mp0) cc_final: 0.6148 (mm-30) REVERT: A 891 ARG cc_start: 0.8227 (mtp-110) cc_final: 0.7904 (mtp-110) REVERT: A 949 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7499 (pm20) REVERT: A 1338 ASN cc_start: 0.8538 (p0) cc_final: 0.8183 (p0) REVERT: B 61 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.6981 (mm-40) REVERT: B 147 ASP cc_start: 0.8631 (t0) cc_final: 0.8401 (t0) REVERT: B 236 ASN cc_start: 0.9384 (t0) cc_final: 0.9027 (t0) REVERT: B 315 MET cc_start: 0.8853 (tpt) cc_final: 0.8650 (tpt) outliers start: 28 outliers final: 19 residues processed: 137 average time/residue: 0.2281 time to fit residues: 45.4254 Evaluate side-chains 137 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 1171 ILE Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1450 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 0.0770 chunk 73 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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: 0.8193 moved from start: 0.1602 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= 0.154 Angle : 0.558 9.272 14643 Z= 0.276 Chirality : 0.041 0.130 1673 Planarity : 0.003 0.041 1805 Dihedral : 9.994 120.197 1997 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.34 % Allowed : 18.79 % Favored : 78.87 % 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: -0.94 (0.25), residues: 1266 helix: 0.71 (0.22), residues: 594 sheet: -1.35 (0.41), residues: 156 loop : -1.98 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 142 HIS 0.002 0.001 HIS A1336 PHE 0.013 0.001 PHE A1328 TYR 0.020 0.001 TYR B 280 ARG 0.003 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 150 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 MET cc_start: 0.7084 (ttp) cc_final: 0.6631 (ttt) REVERT: A 810 LYS cc_start: 0.7311 (tptp) cc_final: 0.5883 (ptpp) REVERT: A 845 ASP cc_start: 0.8039 (p0) cc_final: 0.7682 (p0) REVERT: A 871 GLU cc_start: 0.7471 (mp0) cc_final: 0.6146 (mm-30) REVERT: A 891 ARG cc_start: 0.8232 (mtp-110) cc_final: 0.7909 (mtp-110) REVERT: A 1338 ASN cc_start: 0.8515 (p0) cc_final: 0.8167 (p0) REVERT: B 61 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7163 (mm-40) REVERT: B 147 ASP cc_start: 0.8634 (t0) cc_final: 0.8415 (t0) REVERT: B 236 ASN cc_start: 0.9381 (t0) cc_final: 0.9023 (t0) REVERT: B 238 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8491 (tpt) REVERT: B 348 TRP cc_start: 0.9118 (OUTLIER) cc_final: 0.8711 (t60) outliers start: 26 outliers final: 20 residues processed: 141 average time/residue: 0.2004 time to fit residues: 41.7835 Evaluate side-chains 144 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 1212 VAL Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1410 LYS Chi-restraints excluded: chain A residue 1450 ASP 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 194 SER Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 238 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 0.4980 chunk 117 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 114 optimal weight: 0.0050 chunk 68 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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: 0.8188 moved from start: 0.1678 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= 0.153 Angle : 0.556 8.812 14643 Z= 0.276 Chirality : 0.041 0.161 1673 Planarity : 0.003 0.041 1805 Dihedral : 9.829 119.923 1997 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.25 % Allowed : 19.24 % Favored : 78.51 % 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 (0.25), residues: 1266 helix: 0.74 (0.22), residues: 594 sheet: -1.30 (0.41), residues: 156 loop : -1.98 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1458 HIS 0.002 0.001 HIS A1336 PHE 0.013 0.001 PHE A1328 TYR 0.020 0.001 TYR B 280 ARG 0.008 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 149 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 MET cc_start: 0.7101 (ttp) cc_final: 0.6627 (ttt) REVERT: A 810 LYS cc_start: 0.7293 (tptp) cc_final: 0.5861 (ptpp) REVERT: A 845 ASP cc_start: 0.8070 (p0) cc_final: 0.7676 (p0) REVERT: A 871 GLU cc_start: 0.7475 (mp0) cc_final: 0.6156 (mm-30) REVERT: A 1338 ASN cc_start: 0.8536 (p0) cc_final: 0.8155 (p0) REVERT: B 61 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7418 (mm-40) REVERT: B 147 ASP cc_start: 0.8634 (t0) cc_final: 0.8412 (t0) REVERT: B 236 ASN cc_start: 0.9391 (t0) cc_final: 0.9033 (t0) REVERT: B 238 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8522 (tpt) REVERT: B 315 MET cc_start: 0.8534 (tpt) cc_final: 0.8294 (tpp) REVERT: B 348 TRP cc_start: 0.9113 (OUTLIER) cc_final: 0.8716 (t60) outliers start: 25 outliers final: 21 residues processed: 140 average time/residue: 0.2065 time to fit residues: 42.3975 Evaluate side-chains 142 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 1056 LEU 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 1287 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1410 LYS Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1458 TRP 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 194 SER Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 238 MET 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: 0.3980 chunk 120 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1208 GLN ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8200 moved from start: 0.1699 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= 0.173 Angle : 0.570 9.451 14643 Z= 0.282 Chirality : 0.042 0.140 1673 Planarity : 0.003 0.042 1805 Dihedral : 9.745 120.448 1997 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.16 % Allowed : 19.42 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.25), residues: 1266 helix: 0.74 (0.22), residues: 595 sheet: -1.30 (0.41), residues: 156 loop : -1.99 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 142 HIS 0.003 0.001 HIS A1336 PHE 0.013 0.001 PHE A1408 TYR 0.021 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 145 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 685 ASN cc_start: 0.8481 (t0) cc_final: 0.8206 (p0) REVERT: A 771 MET cc_start: 0.7100 (ttp) cc_final: 0.6632 (ttt) REVERT: A 810 LYS cc_start: 0.7294 (tptp) cc_final: 0.5857 (ptpp) REVERT: A 845 ASP cc_start: 0.8023 (p0) cc_final: 0.7656 (p0) REVERT: A 871 GLU cc_start: 0.7463 (mp0) cc_final: 0.6141 (mm-30) REVERT: A 891 ARG cc_start: 0.8266 (mtp-110) cc_final: 0.8028 (mtp-110) REVERT: A 949 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7573 (pm20) REVERT: A 1338 ASN cc_start: 0.8538 (p0) cc_final: 0.8179 (p0) REVERT: B 147 ASP cc_start: 0.8644 (t0) cc_final: 0.8414 (t0) REVERT: B 236 ASN cc_start: 0.9386 (t0) cc_final: 0.9042 (t0) REVERT: B 238 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8539 (tpt) REVERT: B 348 TRP cc_start: 0.9120 (OUTLIER) cc_final: 0.8724 (t60) outliers start: 24 outliers final: 21 residues processed: 137 average time/residue: 0.2006 time to fit residues: 40.7352 Evaluate side-chains 142 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 1056 LEU 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 1287 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1410 LYS Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1458 TRP Chi-restraints excluded: chain A residue 1473 THR 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 220 SER Chi-restraints excluded: chain B residue 238 MET 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: 2.9990 chunk 107 optimal weight: 0.9990 chunk 30 optimal weight: 0.0870 chunk 92 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.0770 chunk 18 optimal weight: 2.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1208 GLN ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** 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 = 0.3668 r_free = 0.3668 target = 0.156033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.118791 restraints weight = 12976.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.117891 restraints weight = 17739.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.119115 restraints weight = 16231.608| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1777 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= 0.151 Angle : 0.566 9.478 14643 Z= 0.279 Chirality : 0.041 0.146 1673 Planarity : 0.003 0.042 1805 Dihedral : 9.509 119.952 1997 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.34 % Allowed : 19.33 % Favored : 78.33 % 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: -0.78 (0.25), residues: 1266 helix: 0.87 (0.22), residues: 588 sheet: -1.22 (0.41), residues: 156 loop : -1.93 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 142 HIS 0.002 0.001 HIS A1336 PHE 0.012 0.001 PHE A1328 TYR 0.020 0.001 TYR B 280 ARG 0.010 0.000 ARG A1131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2079.29 seconds wall clock time: 38 minutes 45.09 seconds (2325.09 seconds total)