Starting phenix.real_space_refine on Tue Mar 12 17:26:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/03_2024/7s6c_24868_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/03_2024/7s6c_24868.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/03_2024/7s6c_24868_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/03_2024/7s6c_24868_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/03_2024/7s6c_24868_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/03_2024/7s6c_24868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/03_2024/7s6c_24868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/03_2024/7s6c_24868_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/03_2024/7s6c_24868_trim_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 1.126 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16919 atoms to isotropic. 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 4 5.49 5 S 70 5.16 5 C 14983 2.51 5 N 4278 2.21 5 O 4614 1.98 5 H 23420 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 61": "OE1" <-> "OE2" Residue "A ASP 551": "OD1" <-> "OD2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "A GLU 913": "OE1" <-> "OE2" Residue "B ASP 207": "OD1" <-> "OD2" Residue "B ASP 318": "OD1" <-> "OD2" Residue "B ASP 884": "OD1" <-> "OD2" Residue "C ASP 1151": "OD1" <-> "OD2" Residue "C GLU 1321": "OE1" <-> "OE2" Residue "C PHE 1334": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 1424": "OD1" <-> "OD2" Residue "D ASP 1521": "OD1" <-> "OD2" Residue "D ASP 1525": "OD1" <-> "OD2" Residue "E TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 47369 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 13235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 13235 Classifications: {'peptide': 895} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 56, 'TRANS': 838} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 13199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 13199 Classifications: {'peptide': 891} Link IDs: {'PTRANS': 54, 'TRANS': 836} Chain breaks: 2 Chain: "C" Number of atoms: 6988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 6988 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 29, 'TRANS': 450} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1257 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain breaks: 1 Chain: "E" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3081 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 195} Chain breaks: 2 Chain: "F" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3255 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 3249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3249 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 199} Chain breaks: 1 Chain: "H" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 3053 Classifications: {'peptide': 205} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 193} Chain breaks: 2 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N GLN F 66 " occ=0.90 ... (15 atoms not shown) pdb="HE22 GLN F 66 " occ=0.90 residue: pdb=" N GLN G 66 " occ=0.90 ... (15 atoms not shown) pdb="HE22 GLN G 66 " occ=0.90 Time building chain proxies: 15.46, per 1000 atoms: 0.33 Number of scatterers: 47369 At special positions: 0 Unit cell: (119.945, 156.45, 198.17, 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 70 16.00 P 4 15.00 O 4614 8.00 N 4278 7.00 C 14983 6.00 H 23420 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 100 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.04 Simple disulfide: pdb=" SG CYS F 39 " - pdb=" SG CYS F 109 " distance=2.03 Simple disulfide: pdb=" SG CYS G 39 " - pdb=" SG CYS G 109 " distance=2.04 Simple disulfide: pdb=" SG CYS H 24 " - pdb=" SG CYS H 100 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " 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 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 30.48 Conformation dependent library (CDL) restraints added in 3.7 seconds 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5788 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 29 sheets defined 30.4% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.89 Creating SS restraints... Processing helix chain 'A' and resid 10 through 36 removed outlier: 3.558A pdb=" N GLU A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 126 through 142 removed outlier: 3.624A pdb=" N GLU A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 149 Processing helix chain 'A' and resid 186 through 197 removed outlier: 3.983A pdb=" N SER A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 225 removed outlier: 3.780A pdb=" N SER A 212 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N SER A 213 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 214 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 removed outlier: 3.638A pdb=" N PHE A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 318 through 331 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 350 through 363 Proline residue: A 354 - end of helix Processing helix chain 'A' and resid 380 through 383 No H-bonds generated for 'chain 'A' and resid 380 through 383' Processing helix chain 'A' and resid 390 through 404 removed outlier: 3.740A pdb=" N ILE A 396 " --> pdb=" O VAL A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 503 Processing helix chain 'A' and resid 510 through 519 Processing helix chain 'A' and resid 538 through 547 Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.649A pdb=" N HIS A 585 " --> pdb=" O ARG A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 604 removed outlier: 4.576A pdb=" N ASP A 603 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'A' and resid 625 through 645 removed outlier: 3.522A pdb=" N GLN A 629 " --> pdb=" O VAL A 625 " (cutoff:3.500A) Proline residue: A 630 - end of helix Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 672 through 689 Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 702 through 708 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 733 through 746 Processing helix chain 'A' and resid 762 through 774 removed outlier: 5.562A pdb=" N ASP A 769 " --> pdb=" O SER A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 800 No H-bonds generated for 'chain 'A' and resid 798 through 800' Processing helix chain 'A' and resid 803 through 811 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 841 through 851 Processing helix chain 'A' and resid 868 through 880 Processing helix chain 'A' and resid 887 through 891 Processing helix chain 'B' and resid 10 through 34 removed outlier: 3.723A pdb=" N ALA B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR B 17 " --> pdb=" O LYS B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 126 through 141 Processing helix chain 'B' and resid 146 through 149 removed outlier: 3.546A pdb=" N GLN B 149 " --> pdb=" O PRO B 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 149' Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 186 through 196 removed outlier: 3.977A pdb=" N SER B 190 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ARG B 192 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 193 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 196 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 225 removed outlier: 5.241A pdb=" N SER B 213 " --> pdb=" O CYS B 210 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 214 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 215 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 247 No H-bonds generated for 'chain 'B' and resid 244 through 247' Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 318 through 332 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 350 through 363 Proline residue: B 354 - end of helix Processing helix chain 'B' and resid 380 through 383 No H-bonds generated for 'chain 'B' and resid 380 through 383' Processing helix chain 'B' and resid 387 through 404 removed outlier: 4.252A pdb=" N GLY B 391 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 392 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 395 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE B 396 " --> pdb=" O ALA B 393 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET B 402 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS B 404 " --> pdb=" O ALA B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 488 through 503 Processing helix chain 'B' and resid 510 through 519 Processing helix chain 'B' and resid 537 through 547 Processing helix chain 'B' and resid 588 through 600 Processing helix chain 'B' and resid 609 through 614 Processing helix chain 'B' and resid 625 through 645 Proline residue: B 630 - end of helix Processing helix chain 'B' and resid 659 through 666 Processing helix chain 'B' and resid 672 through 685 Processing helix chain 'B' and resid 687 through 689 No H-bonds generated for 'chain 'B' and resid 687 through 689' Processing helix chain 'B' and resid 702 through 708 Processing helix chain 'B' and resid 710 through 715 removed outlier: 7.934A pdb=" N GLN B 714 " --> pdb=" O PRO B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 745 removed outlier: 3.705A pdb=" N THR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 765 No H-bonds generated for 'chain 'B' and resid 763 through 765' Processing helix chain 'B' and resid 773 through 775 No H-bonds generated for 'chain 'B' and resid 773 through 775' Processing helix chain 'B' and resid 798 through 800 No H-bonds generated for 'chain 'B' and resid 798 through 800' Processing helix chain 'B' and resid 803 through 811 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 841 through 851 Processing helix chain 'B' and resid 868 through 880 Processing helix chain 'B' and resid 887 through 891 Processing helix chain 'C' and resid 967 through 979 removed outlier: 4.087A pdb=" N LEU C 979 " --> pdb=" O ALA C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1023 Processing helix chain 'C' and resid 1041 through 1052 Processing helix chain 'C' and resid 1065 through 1067 No H-bonds generated for 'chain 'C' and resid 1065 through 1067' Processing helix chain 'C' and resid 1080 through 1095 Processing helix chain 'C' and resid 1120 through 1133 Processing helix chain 'C' and resid 1152 through 1162 Processing helix chain 'C' and resid 1211 through 1221 Processing helix chain 'C' and resid 1235 through 1237 No H-bonds generated for 'chain 'C' and resid 1235 through 1237' Processing helix chain 'C' and resid 1241 through 1251 removed outlier: 3.839A pdb=" N LEU C1251 " --> pdb=" O GLU C1247 " (cutoff:3.500A) Processing helix chain 'C' and resid 1265 through 1274 removed outlier: 3.623A pdb=" N SER C1273 " --> pdb=" O GLN C1269 " (cutoff:3.500A) Processing helix chain 'C' and resid 1302 through 1312 removed outlier: 3.953A pdb=" N VAL C1311 " --> pdb=" O GLN C1307 " (cutoff:3.500A) Processing helix chain 'C' and resid 1314 through 1322 Processing helix chain 'C' and resid 1337 through 1340 No H-bonds generated for 'chain 'C' and resid 1337 through 1340' Processing helix chain 'C' and resid 1347 through 1366 Proline residue: C1351 - end of helix removed outlier: 3.677A pdb=" N GLU C1357 " --> pdb=" O ASN C1353 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C1358 " --> pdb=" O ALA C1354 " (cutoff:3.500A) Processing helix chain 'C' and resid 1402 through 1414 removed outlier: 3.868A pdb=" N GLU C1414 " --> pdb=" O GLU C1410 " (cutoff:3.500A) Processing helix chain 'C' and resid 1430 through 1437 Processing helix chain 'C' and resid 1447 through 1455 Processing helix chain 'D' and resid 1484 through 1500 Processing helix chain 'D' and resid 1526 through 1540 Processing helix chain 'D' and resid 1555 through 1564 Processing helix chain 'E' and resid 66 through 68 No H-bonds generated for 'chain 'E' and resid 66 through 68' Processing helix chain 'F' and resid 144 through 148 Processing helix chain 'F' and resid 205 through 208 No H-bonds generated for 'chain 'F' and resid 205 through 208' Processing helix chain 'G' and resid 101 through 103 No H-bonds generated for 'chain 'G' and resid 101 through 103' Processing helix chain 'G' and resid 144 through 149 Processing helix chain 'G' and resid 205 through 208 No H-bonds generated for 'chain 'G' and resid 205 through 208' Processing helix chain 'H' and resid 66 through 68 No H-bonds generated for 'chain 'H' and resid 66 through 68' Processing helix chain 'H' and resid 92 through 94 No H-bonds generated for 'chain 'H' and resid 92 through 94' Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing sheet with id= A, first strand: chain 'A' and resid 203 through 206 removed outlier: 8.408A pdb=" N VAL A 204 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL A 156 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE A 206 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 158 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR A 231 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N PHE A 157 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU A 233 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY A 159 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY A 235 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLU A 283 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ILE A 42 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 297 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE A 460 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR A 302 " --> pdb=" O HIS A 458 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N HIS A 458 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE A 304 " --> pdb=" O ASN A 456 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN A 456 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 374 through 376 Processing sheet with id= C, first strand: chain 'A' and resid 481 through 485 Processing sheet with id= D, first strand: chain 'A' and resid 652 through 655 removed outlier: 7.161A pdb=" N VAL A 566 " --> pdb=" O ARG A 829 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE A 831 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL A 568 " --> pdb=" O PHE A 831 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU A 833 " --> pdb=" O VAL A 568 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG A 856 " --> pdb=" O PHE A 831 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLU A 833 " --> pdb=" O ARG A 856 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR A 858 " --> pdb=" O GLU A 833 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 750 through 752 removed outlier: 5.940A pdb=" N SER A 730 " --> pdb=" O ILE A 718 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE A 718 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N THR A 732 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU A 716 " --> pdb=" O THR A 732 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 235 through 238 removed outlier: 6.785A pdb=" N GLU B 283 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ILE B 42 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B 297 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE B 460 " --> pdb=" O ARG B 300 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR B 302 " --> pdb=" O HIS B 458 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N HIS B 458 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE B 304 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN B 456 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA B 341 " --> pdb=" O GLY B 446 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N SER B 448 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLU B 343 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N PHE B 450 " --> pdb=" O GLU B 343 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 156 through 158 Processing sheet with id= H, first strand: chain 'B' and resid 374 through 376 Processing sheet with id= I, first strand: chain 'B' and resid 481 through 485 Processing sheet with id= J, first strand: chain 'B' and resid 652 through 654 removed outlier: 6.812A pdb=" N VAL B 566 " --> pdb=" O ARG B 829 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE B 831 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL B 568 " --> pdb=" O PHE B 831 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU B 833 " --> pdb=" O VAL B 568 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG B 856 " --> pdb=" O PHE B 831 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLU B 833 " --> pdb=" O ARG B 856 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR B 858 " --> pdb=" O GLU B 833 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 750 through 753 removed outlier: 4.553A pdb=" N MET B 695 " --> pdb=" O ILE B 753 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N SER B 730 " --> pdb=" O ILE B 718 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ILE B 718 " --> pdb=" O SER B 730 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 982 through 988 removed outlier: 4.380A pdb=" N VAL C1178 " --> pdb=" O THR C 988 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLN C1170 " --> pdb=" O ARG C1181 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL C1171 " --> pdb=" O ALA C1141 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU C1143 " --> pdb=" O VAL C1171 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU C1173 " --> pdb=" O LEU C1143 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP C1145 " --> pdb=" O LEU C1173 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU C1101 " --> pdb=" O ALA C1141 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU C1143 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N CYS C1103 " --> pdb=" O LEU C1143 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ASP C1145 " --> pdb=" O CYS C1103 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N THR C1105 " --> pdb=" O ASP C1145 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA C1060 " --> pdb=" O THR C 999 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ARG C1027 " --> pdb=" O TRP C1000 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL C1002 " --> pdb=" O ARG C1027 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N VAL C1029 " --> pdb=" O VAL C1002 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C1004 " --> pdb=" O VAL C1029 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU C1031 " --> pdb=" O VAL C1004 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 1227 through 1231 removed outlier: 7.280A pdb=" N LEU C1204 " --> pdb=" O THR C1283 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL C1285 " --> pdb=" O LEU C1204 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR C1206 " --> pdb=" O VAL C1285 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS C1287 " --> pdb=" O THR C1206 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ALA C1330 " --> pdb=" O VAL C1285 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N HIS C1287 " --> pdb=" O ALA C1330 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL C1332 " --> pdb=" O HIS C1287 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 5 through 9 Processing sheet with id= O, first strand: chain 'E' and resid 99 through 102 removed outlier: 5.613A pdb=" N ARG E 40 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TRP E 49 " --> pdb=" O ARG E 40 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 96 through 98 Processing sheet with id= Q, first strand: chain 'E' and resid 127 through 131 removed outlier: 3.691A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA E 143 " --> pdb=" O VAL E 191 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 158 through 161 Processing sheet with id= S, first strand: chain 'F' and resid 21 through 23 Processing sheet with id= T, first strand: chain 'F' and resid 106 through 111 removed outlier: 6.111A pdb=" N LEU F 58 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LEU F 67 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 167 through 171 Processing sheet with id= V, first strand: chain 'G' and resid 21 through 23 Processing sheet with id= W, first strand: chain 'G' and resid 105 through 111 removed outlier: 5.576A pdb=" N LEU G 58 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU G 67 " --> pdb=" O LEU G 58 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 167 through 171 Processing sheet with id= Y, first strand: chain 'G' and resid 181 through 185 removed outlier: 7.202A pdb=" N LEU G 197 " --> pdb=" O ASN G 159 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASN G 159 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N SER G 199 " --> pdb=" O LEU G 157 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU G 157 " --> pdb=" O SER G 199 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU G 201 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N VAL G 155 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU G 203 " --> pdb=" O SER G 153 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N SER G 153 " --> pdb=" O LEU G 203 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 5 through 9 Processing sheet with id= AA, first strand: chain 'H' and resid 12 through 14 removed outlier: 5.981A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA H 42 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU H 47 " --> pdb=" O ALA H 42 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 129 through 131 removed outlier: 3.885A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 157 through 161 removed outlier: 4.114A pdb=" N TYR H 201 " --> pdb=" O VAL H 218 " (cutoff:3.500A) 841 hydrogen bonds defined for protein. 2229 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: 17.66 Time building geometry restraints manager: 32.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 23398 1.03 - 1.23: 595 1.23 - 1.43: 9654 1.43 - 1.63: 14141 1.63 - 1.83: 110 Bond restraints: 47898 Sorted by residual: bond pdb=" C2' ATR C1701 " pdb=" C3' ATR C1701 " ideal model delta sigma weight residual 1.245 1.553 -0.308 2.00e-02 2.50e+03 2.37e+02 bond pdb=" O3B ATR C1701 " pdb=" PB ATR C1701 " ideal model delta sigma weight residual 1.508 1.756 -0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C2' ATR C1701 " pdb=" O2' ATR C1701 " ideal model delta sigma weight residual 1.514 1.328 0.186 2.00e-02 2.50e+03 8.63e+01 bond pdb=" O2' ATR C1701 " pdb=" P2' ATR C1701 " ideal model delta sigma weight residual 1.671 1.826 -0.155 2.00e-02 2.50e+03 6.04e+01 bond pdb=" C1' ATR C1701 " pdb=" N9 ATR C1701 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.78e+01 ... (remaining 47893 not shown) Histogram of bond angle deviations from ideal: 96.53 - 104.03: 434 104.03 - 111.53: 53561 111.53 - 119.03: 12227 119.03 - 126.53: 19739 126.53 - 134.03: 500 Bond angle restraints: 86461 Sorted by residual: angle pdb=" C1' ATR C1701 " pdb=" N9 ATR C1701 " pdb=" C8 ATR C1701 " ideal model delta sigma weight residual 102.81 127.94 -25.13 3.00e+00 1.11e-01 7.02e+01 angle pdb=" C1' ATR C1701 " pdb=" N9 ATR C1701 " pdb=" C4 ATR C1701 " ideal model delta sigma weight residual 149.16 125.18 23.98 3.00e+00 1.11e-01 6.39e+01 angle pdb=" C5 ATR C1701 " pdb=" C6 ATR C1701 " pdb=" N6 ATR C1701 " ideal model delta sigma weight residual 138.99 120.18 18.81 3.00e+00 1.11e-01 3.93e+01 angle pdb=" N1 ATR C1701 " pdb=" C6 ATR C1701 " pdb=" N6 ATR C1701 " ideal model delta sigma weight residual 100.02 118.24 -18.22 3.00e+00 1.11e-01 3.69e+01 angle pdb=" PA ATR C1701 " pdb=" O3A ATR C1701 " pdb=" PB ATR C1701 " ideal model delta sigma weight residual 123.61 107.68 15.93 3.00e+00 1.11e-01 2.82e+01 ... (remaining 86456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 20141 17.79 - 35.58: 1895 35.58 - 53.37: 523 53.37 - 71.16: 145 71.16 - 88.95: 36 Dihedral angle restraints: 22740 sinusoidal: 12397 harmonic: 10343 Sorted by residual: dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 203 " pdb=" CB CYS E 203 " ideal model delta sinusoidal sigma weight residual 93.00 155.82 -62.82 1 1.00e+01 1.00e-02 5.21e+01 dihedral pdb=" CB CYS H 147 " pdb=" SG CYS H 147 " pdb=" SG CYS H 203 " pdb=" CB CYS H 203 " ideal model delta sinusoidal sigma weight residual 93.00 134.82 -41.82 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CA THR B 95 " pdb=" C THR B 95 " pdb=" N TYR B 96 " pdb=" CA TYR B 96 " ideal model delta harmonic sigma weight residual 180.00 156.45 23.55 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 22737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2557 0.035 - 0.070: 850 0.070 - 0.105: 257 0.105 - 0.140: 137 0.140 - 0.175: 12 Chirality restraints: 3813 Sorted by residual: chirality pdb=" CB ILE B 648 " pdb=" CA ILE B 648 " pdb=" CG1 ILE B 648 " pdb=" CG2 ILE B 648 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.63e-01 chirality pdb=" CA ILE A 785 " pdb=" N ILE A 785 " pdb=" C ILE A 785 " pdb=" CB ILE A 785 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA ILE B 785 " pdb=" N ILE B 785 " pdb=" C ILE B 785 " pdb=" CB ILE B 785 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.78e-01 ... (remaining 3810 not shown) Planarity restraints: 7350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATR C1701 " -0.380 2.00e-02 2.50e+03 3.56e-01 2.85e+03 pdb=" C2' ATR C1701 " 0.499 2.00e-02 2.50e+03 pdb=" C3' ATR C1701 " 0.376 2.00e-02 2.50e+03 pdb=" C4' ATR C1701 " -0.343 2.00e-02 2.50e+03 pdb=" C5' ATR C1701 " 0.416 2.00e-02 2.50e+03 pdb=" N9 ATR C1701 " 0.176 2.00e-02 2.50e+03 pdb=" O2' ATR C1701 " 0.005 2.00e-02 2.50e+03 pdb=" O3' ATR C1701 " -0.422 2.00e-02 2.50e+03 pdb=" O4' ATR C1701 " -0.327 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 145 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO A 146 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 387 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO B 388 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 388 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 388 " 0.034 5.00e-02 4.00e+02 ... (remaining 7347 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 6744 2.26 - 2.84: 106866 2.84 - 3.43: 127047 3.43 - 4.01: 174922 4.01 - 4.60: 268002 Nonbonded interactions: 683581 Sorted by model distance: nonbonded pdb=" O LYS B 380 " pdb=" H GLY B 384 " model vdw 1.674 1.850 nonbonded pdb=" H GLU B 343 " pdb=" O GLY B 446 " model vdw 1.685 1.850 nonbonded pdb=" OE1 GLU C1414 " pdb=" H GLU C1414 " model vdw 1.690 1.850 nonbonded pdb=" H GLU C1006 " pdb=" O VAL C1033 " model vdw 1.706 1.850 nonbonded pdb=" H HIS A 345 " pdb=" OE2 GLU A 356 " model vdw 1.708 1.850 ... (remaining 683576 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 166 or (resid 178 and (name N or name CA or name \ C or name O or name HA2 or name HA3)) or resid 179 through 467 or (resid 473 an \ d (name N or name CA or name C or name O or name CB or name HA or name HB1 or na \ me HB2 or name HB3)) or resid 474 through 914)) selection = (chain 'B' and (resid 8 through 87 or (resid 91 and (name N or name CA or name C \ or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or resid \ 92 through 423 or (resid 426 and (name N or name CA or name C or name O or name \ CB or name HA or name HB1 or name HB2 or name HB3)) or resid 427 through 436 or \ (resid 440 and (name N or name CA or name C or name O )) or resid 441 through 50 \ 6 or (resid 507 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 508 through 768 or (resid 769 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 770 through 914)) } ncs_group { reference = (chain 'E' and (resid 3 through 133 or resid 142 through 193 or (resid 200 and ( \ name N or name CA or name C or name O or name CB or name OG1 or name CG2 or name \ HA or name HB or name HG1 or name HG21 or name HG22 or name HG23)) or resid 201 \ through 220)) selection = (chain 'H' and (resid 3 through 193 or resid 200 through 220)) } ncs_group { reference = (chain 'F' and ((resid 18 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 19 through 172 or resid 1 \ 76 through 234)) selection = (chain 'G' and (resid 18 through 211 or (resid 212 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or (resid 214 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name \ CE1 or name CE2 or name CZ or name OH or name HA or name HB2 or name HB3 or name \ HD1 or name HD2 or name HE1 or name HE2 or name HH )) or resid 215 through 234) \ ) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.90 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.280 Construct map_model_manager: 0.540 Extract box with map and model: 11.110 Check model and map are aligned: 0.530 Set scattering table: 0.330 Process input model: 120.420 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.140 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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 0.308 24478 Z= 0.296 Angle : 0.745 25.134 33398 Z= 0.345 Chirality : 0.043 0.175 3813 Planarity : 0.007 0.356 4375 Dihedral : 14.162 88.951 8732 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3144 helix: 1.20 (0.17), residues: 961 sheet: -1.09 (0.19), residues: 689 loop : -0.59 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 712 HIS 0.006 0.001 HIS B 345 PHE 0.018 0.001 PHE A 604 TYR 0.017 0.001 TYR H 183 ARG 0.009 0.000 ARG G 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 493 is missing expected H atoms. Skipping. Residue ALA 493 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue LYS 1437 is missing expected H atoms. Skipping. Residue SER 1526 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Evaluate side-chains 291 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.8111 (mtp) cc_final: 0.7608 (mtp) REVERT: A 366 HIS cc_start: 0.7481 (t70) cc_final: 0.7178 (t-90) REVERT: B 54 ASP cc_start: 0.7753 (m-30) cc_final: 0.7369 (t0) REVERT: B 80 ASP cc_start: 0.7955 (t70) cc_final: 0.7627 (t70) REVERT: B 757 TYR cc_start: 0.7946 (p90) cc_final: 0.7696 (p90) REVERT: D 1514 GLU cc_start: 0.8538 (pm20) cc_final: 0.7829 (pm20) REVERT: E 33 ASP cc_start: 0.8897 (m-30) cc_final: 0.8567 (m-30) REVERT: E 171 HIS cc_start: 0.8654 (m-70) cc_final: 0.8403 (m90) REVERT: F 40 ARG cc_start: 0.7999 (mmm160) cc_final: 0.7738 (mmm160) REVERT: F 95 LYS cc_start: 0.8850 (tmtt) cc_final: 0.8642 (tmtt) REVERT: F 160 ASN cc_start: 0.9154 (m-40) cc_final: 0.8947 (m110) REVERT: G 103 ASP cc_start: 0.7159 (m-30) cc_final: 0.6253 (m-30) REVERT: H 87 MET cc_start: 0.8357 (mpp) cc_final: 0.8018 (mpp) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.7853 time to fit residues: 346.4942 Evaluate side-chains 234 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 0.8980 chunk 239 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 161 optimal weight: 0.3980 chunk 127 optimal weight: 1.9990 chunk 247 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 286 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 114 GLN G 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24478 Z= 0.201 Angle : 0.537 19.107 33398 Z= 0.252 Chirality : 0.039 0.153 3813 Planarity : 0.004 0.062 4375 Dihedral : 5.747 71.469 3483 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.24 % Allowed : 4.56 % Favored : 95.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 3144 helix: 1.26 (0.17), residues: 980 sheet: -1.07 (0.19), residues: 695 loop : -0.48 (0.17), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 60 HIS 0.004 0.001 HIS B 665 PHE 0.011 0.001 PHE A 604 TYR 0.010 0.001 TYR A 807 ARG 0.004 0.000 ARG D1520 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 493 is missing expected H atoms. Skipping. Residue ALA 493 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue LYS 1437 is missing expected H atoms. Skipping. Residue SER 1526 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Evaluate side-chains 244 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 238 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LYS cc_start: 0.9026 (tttt) cc_final: 0.8710 (tttp) REVERT: A 240 MET cc_start: 0.7514 (mtt) cc_final: 0.7022 (mtt) REVERT: A 398 MET cc_start: 0.8279 (mmp) cc_final: 0.7993 (mmp) REVERT: B 54 ASP cc_start: 0.7796 (m-30) cc_final: 0.7399 (t0) REVERT: B 80 ASP cc_start: 0.7924 (t70) cc_final: 0.7598 (t70) REVERT: B 207 ASP cc_start: 0.8440 (t0) cc_final: 0.8027 (t0) REVERT: C 1195 ARG cc_start: 0.7678 (ttp80) cc_final: 0.7455 (ttp80) REVERT: D 1514 GLU cc_start: 0.8578 (pm20) cc_final: 0.8224 (pm20) REVERT: E 63 GLU cc_start: 0.7956 (mp0) cc_final: 0.7390 (mp0) REVERT: E 171 HIS cc_start: 0.8708 (m-70) cc_final: 0.8325 (m90) REVERT: F 40 ARG cc_start: 0.8026 (mmm160) cc_final: 0.7725 (mmm160) REVERT: F 160 ASN cc_start: 0.9194 (m-40) cc_final: 0.8986 (m110) REVERT: G 103 ASP cc_start: 0.6786 (m-30) cc_final: 0.6569 (m-30) REVERT: G 159 ASN cc_start: 0.8323 (t0) cc_final: 0.7814 (t0) REVERT: G 160 ASN cc_start: 0.8987 (m-40) cc_final: 0.8756 (m-40) outliers start: 6 outliers final: 5 residues processed: 240 average time/residue: 0.8046 time to fit residues: 296.7224 Evaluate side-chains 230 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 225 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain H residue 151 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 159 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 238 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 287 optimal weight: 5.9990 chunk 310 optimal weight: 0.9990 chunk 256 optimal weight: 0.9990 chunk 285 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN B 184 ASN B 404 HIS D1552 HIS ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 24478 Z= 0.305 Angle : 0.559 17.329 33398 Z= 0.268 Chirality : 0.040 0.149 3813 Planarity : 0.004 0.061 4375 Dihedral : 5.830 78.920 3483 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.44 % Allowed : 6.51 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.15), residues: 3144 helix: 0.93 (0.16), residues: 1002 sheet: -1.03 (0.19), residues: 691 loop : -0.53 (0.17), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 985 HIS 0.006 0.001 HIS C1287 PHE 0.011 0.001 PHE C1341 TYR 0.015 0.001 TYR A 807 ARG 0.004 0.000 ARG B 368 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 493 is missing expected H atoms. Skipping. Residue ALA 493 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue LYS 1437 is missing expected H atoms. Skipping. Residue SER 1526 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 221 time to evaluate : 2.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.7855 (tpt) cc_final: 0.7357 (tpt) REVERT: A 185 MET cc_start: 0.8004 (mtp) cc_final: 0.7537 (mtp) REVERT: A 240 MET cc_start: 0.7793 (mtt) cc_final: 0.7430 (mtt) REVERT: A 398 MET cc_start: 0.8349 (mmp) cc_final: 0.8110 (mmp) REVERT: A 695 MET cc_start: 0.8366 (mtt) cc_final: 0.8157 (mtm) REVERT: B 54 ASP cc_start: 0.7809 (m-30) cc_final: 0.7380 (t0) REVERT: B 80 ASP cc_start: 0.7955 (t70) cc_final: 0.7615 (t70) REVERT: B 687 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8862 (mm) REVERT: D 1514 GLU cc_start: 0.8564 (pm20) cc_final: 0.8202 (pm20) REVERT: E 36 MET cc_start: 0.8952 (mmm) cc_final: 0.8286 (mmm) REVERT: E 63 GLU cc_start: 0.7967 (mp0) cc_final: 0.7358 (mp0) REVERT: E 171 HIS cc_start: 0.8687 (m-70) cc_final: 0.8374 (m-70) REVERT: F 40 ARG cc_start: 0.8089 (mmm160) cc_final: 0.7798 (mmm160) REVERT: F 160 ASN cc_start: 0.9253 (m-40) cc_final: 0.9040 (m-40) REVERT: G 103 ASP cc_start: 0.7032 (m-30) cc_final: 0.6796 (m-30) outliers start: 11 outliers final: 7 residues processed: 225 average time/residue: 0.7426 time to fit residues: 256.1288 Evaluate side-chains 223 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 215 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 740 HIS Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 151 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 284 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 149 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 193 optimal weight: 0.6980 chunk 288 optimal weight: 10.0000 chunk 305 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 273 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24478 Z= 0.174 Angle : 0.514 17.145 33398 Z= 0.240 Chirality : 0.039 0.151 3813 Planarity : 0.004 0.055 4375 Dihedral : 5.566 74.412 3483 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.52 % Allowed : 7.11 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3144 helix: 1.15 (0.17), residues: 994 sheet: -0.93 (0.19), residues: 688 loop : -0.42 (0.17), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 60 HIS 0.004 0.000 HIS B 345 PHE 0.011 0.001 PHE C1430 TYR 0.009 0.001 TYR A 807 ARG 0.004 0.000 ARG D1520 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 493 is missing expected H atoms. Skipping. Residue ALA 493 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue LYS 1437 is missing expected H atoms. Skipping. Residue SER 1526 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 226 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.7690 (mtt) cc_final: 0.7327 (mtt) REVERT: A 398 MET cc_start: 0.8354 (mmp) cc_final: 0.8114 (mmp) REVERT: B 54 ASP cc_start: 0.7799 (m-30) cc_final: 0.7396 (t0) REVERT: B 80 ASP cc_start: 0.7956 (t70) cc_final: 0.7630 (t70) REVERT: B 207 ASP cc_start: 0.8507 (t0) cc_final: 0.8243 (t0) REVERT: D 1514 GLU cc_start: 0.8544 (pm20) cc_final: 0.8173 (pm20) REVERT: E 171 HIS cc_start: 0.8699 (m-70) cc_final: 0.8322 (m90) REVERT: F 40 ARG cc_start: 0.8027 (mmm160) cc_final: 0.7757 (mmm160) REVERT: F 160 ASN cc_start: 0.9256 (m-40) cc_final: 0.9043 (m-40) REVERT: G 103 ASP cc_start: 0.7017 (m-30) cc_final: 0.6814 (m-30) outliers start: 13 outliers final: 9 residues processed: 231 average time/residue: 0.7468 time to fit residues: 264.8702 Evaluate side-chains 224 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 215 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 740 HIS Chi-restraints excluded: chain C residue 1361 GLU Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain H residue 151 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 254 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 4 optimal weight: 0.0670 chunk 227 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 260 optimal weight: 4.9990 chunk 211 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 274 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24478 Z= 0.206 Angle : 0.520 17.327 33398 Z= 0.244 Chirality : 0.039 0.148 3813 Planarity : 0.004 0.055 4375 Dihedral : 5.474 77.238 3483 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.52 % Allowed : 8.27 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3144 helix: 1.16 (0.17), residues: 995 sheet: -0.91 (0.19), residues: 693 loop : -0.40 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 712 HIS 0.004 0.001 HIS B 345 PHE 0.010 0.001 PHE C1430 TYR 0.011 0.001 TYR A 807 ARG 0.009 0.000 ARG D1520 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 493 is missing expected H atoms. Skipping. Residue ALA 493 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue LYS 1437 is missing expected H atoms. Skipping. Residue SER 1526 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 227 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.7705 (mtt) cc_final: 0.7352 (mtt) REVERT: A 398 MET cc_start: 0.8357 (mmp) cc_final: 0.8087 (mmp) REVERT: B 54 ASP cc_start: 0.7800 (m-30) cc_final: 0.7404 (t0) REVERT: B 80 ASP cc_start: 0.7950 (t70) cc_final: 0.7641 (t70) REVERT: B 207 ASP cc_start: 0.8519 (t0) cc_final: 0.8227 (t0) REVERT: C 1195 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7599 (ttp80) REVERT: D 1514 GLU cc_start: 0.8520 (pm20) cc_final: 0.8130 (pm20) REVERT: E 171 HIS cc_start: 0.8699 (m-70) cc_final: 0.8391 (m-70) REVERT: F 40 ARG cc_start: 0.8047 (mmm160) cc_final: 0.7783 (mmm160) REVERT: F 160 ASN cc_start: 0.9252 (m-40) cc_final: 0.9007 (m110) REVERT: G 159 ASN cc_start: 0.8355 (t0) cc_final: 0.8046 (t0) outliers start: 13 outliers final: 11 residues processed: 233 average time/residue: 0.7393 time to fit residues: 264.5145 Evaluate side-chains 227 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 216 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 740 HIS Chi-restraints excluded: chain C residue 1361 GLU Chi-restraints excluded: chain C residue 1400 LEU Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain H residue 151 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 102 optimal weight: 2.9990 chunk 275 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 305 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 906 GLN ** C1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 24478 Z= 0.320 Angle : 0.558 17.451 33398 Z= 0.268 Chirality : 0.040 0.146 3813 Planarity : 0.004 0.056 4375 Dihedral : 5.606 80.527 3483 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.84 % Allowed : 8.63 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3144 helix: 0.91 (0.17), residues: 989 sheet: -0.93 (0.19), residues: 691 loop : -0.49 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 712 HIS 0.005 0.001 HIS B 665 PHE 0.010 0.001 PHE C1341 TYR 0.014 0.001 TYR A 807 ARG 0.010 0.000 ARG D1520 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 493 is missing expected H atoms. Skipping. Residue ALA 493 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue LYS 1437 is missing expected H atoms. Skipping. Residue SER 1526 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 218 time to evaluate : 2.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7291 (mt-10) REVERT: A 240 MET cc_start: 0.7790 (mtt) cc_final: 0.7470 (mtt) REVERT: A 398 MET cc_start: 0.8308 (mmp) cc_final: 0.7990 (mmp) REVERT: B 54 ASP cc_start: 0.7787 (m-30) cc_final: 0.7401 (t0) REVERT: B 80 ASP cc_start: 0.7945 (t70) cc_final: 0.7638 (t70) REVERT: D 1514 GLU cc_start: 0.8575 (pm20) cc_final: 0.8176 (pm20) REVERT: E 171 HIS cc_start: 0.8674 (m-70) cc_final: 0.8380 (m-70) REVERT: F 40 ARG cc_start: 0.8100 (mmm160) cc_final: 0.7823 (mmm160) REVERT: F 160 ASN cc_start: 0.9256 (m-40) cc_final: 0.9032 (m-40) REVERT: G 159 ASN cc_start: 0.8349 (t0) cc_final: 0.8125 (t0) outliers start: 21 outliers final: 20 residues processed: 227 average time/residue: 0.7542 time to fit residues: 263.7896 Evaluate side-chains 233 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 213 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 740 HIS Chi-restraints excluded: chain C residue 1361 GLU Chi-restraints excluded: chain C residue 1400 LEU Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 151 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 257 optimal weight: 0.0000 chunk 170 optimal weight: 0.2980 chunk 304 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24478 Z= 0.214 Angle : 0.529 17.308 33398 Z= 0.249 Chirality : 0.039 0.151 3813 Planarity : 0.004 0.052 4375 Dihedral : 5.487 78.520 3483 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.68 % Allowed : 9.19 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3144 helix: 1.06 (0.17), residues: 991 sheet: -0.84 (0.20), residues: 676 loop : -0.41 (0.17), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 60 HIS 0.004 0.001 HIS B 345 PHE 0.008 0.001 PHE C1430 TYR 0.011 0.001 TYR A 807 ARG 0.011 0.000 ARG A 682 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 493 is missing expected H atoms. Skipping. Residue ALA 493 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue LYS 1437 is missing expected H atoms. Skipping. Residue SER 1526 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 221 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7277 (mt-10) REVERT: A 240 MET cc_start: 0.7832 (mtt) cc_final: 0.7513 (mtt) REVERT: B 54 ASP cc_start: 0.7748 (m-30) cc_final: 0.7410 (t0) REVERT: B 80 ASP cc_start: 0.7936 (t70) cc_final: 0.7633 (t70) REVERT: D 1514 GLU cc_start: 0.8581 (pm20) cc_final: 0.8302 (pm20) REVERT: E 171 HIS cc_start: 0.8638 (m-70) cc_final: 0.8346 (m-70) REVERT: F 40 ARG cc_start: 0.8061 (mmm160) cc_final: 0.7805 (mmm160) REVERT: F 160 ASN cc_start: 0.9243 (m-40) cc_final: 0.9008 (m-40) REVERT: G 159 ASN cc_start: 0.8273 (t0) cc_final: 0.8072 (t0) outliers start: 17 outliers final: 14 residues processed: 231 average time/residue: 0.7245 time to fit residues: 258.8089 Evaluate side-chains 229 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 215 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 740 HIS Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain C residue 1361 GLU Chi-restraints excluded: chain C residue 1400 LEU Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 151 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 188 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 193 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 chunk 277 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24478 Z= 0.229 Angle : 0.532 17.367 33398 Z= 0.251 Chirality : 0.040 0.149 3813 Planarity : 0.004 0.063 4375 Dihedral : 5.460 79.892 3483 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.68 % Allowed : 9.47 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3144 helix: 1.04 (0.17), residues: 994 sheet: -0.83 (0.20), residues: 679 loop : -0.39 (0.17), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 712 HIS 0.003 0.001 HIS B 665 PHE 0.009 0.001 PHE C1430 TYR 0.012 0.001 TYR A 807 ARG 0.010 0.000 ARG D1520 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 493 is missing expected H atoms. Skipping. Residue ALA 493 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue LYS 1437 is missing expected H atoms. Skipping. Residue SER 1526 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Evaluate side-chains 236 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 219 time to evaluate : 2.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7284 (mt-10) REVERT: A 240 MET cc_start: 0.7855 (mtt) cc_final: 0.7544 (mtt) REVERT: B 54 ASP cc_start: 0.7727 (m-30) cc_final: 0.7448 (t0) REVERT: B 80 ASP cc_start: 0.7944 (t70) cc_final: 0.7638 (t70) REVERT: C 1195 ARG cc_start: 0.7758 (ttp80) cc_final: 0.7521 (ttp80) REVERT: D 1514 GLU cc_start: 0.8571 (pm20) cc_final: 0.8281 (pm20) REVERT: E 171 HIS cc_start: 0.8614 (m-70) cc_final: 0.8336 (m-70) REVERT: F 40 ARG cc_start: 0.8071 (mmm160) cc_final: 0.7820 (mmm160) REVERT: F 160 ASN cc_start: 0.9253 (m-40) cc_final: 0.8987 (m110) outliers start: 17 outliers final: 17 residues processed: 228 average time/residue: 0.7359 time to fit residues: 259.1091 Evaluate side-chains 232 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 215 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 740 HIS Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain C residue 1361 GLU Chi-restraints excluded: chain C residue 1400 LEU Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 151 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 291 optimal weight: 8.9990 chunk 266 optimal weight: 2.9990 chunk 283 optimal weight: 7.9990 chunk 170 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 256 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24478 Z= 0.275 Angle : 0.547 17.445 33398 Z= 0.261 Chirality : 0.040 0.148 3813 Planarity : 0.004 0.053 4375 Dihedral : 5.518 81.678 3483 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.72 % Allowed : 9.55 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3144 helix: 0.95 (0.17), residues: 990 sheet: -0.76 (0.20), residues: 680 loop : -0.45 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 712 HIS 0.004 0.001 HIS B 665 PHE 0.009 0.001 PHE C1430 TYR 0.013 0.001 TYR A 807 ARG 0.012 0.000 ARG D1520 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 493 is missing expected H atoms. Skipping. Residue ALA 493 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue LYS 1437 is missing expected H atoms. Skipping. Residue SER 1526 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 215 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7296 (mt-10) REVERT: A 240 MET cc_start: 0.7824 (mtt) cc_final: 0.7542 (mtt) REVERT: B 54 ASP cc_start: 0.7725 (m-30) cc_final: 0.7457 (t0) REVERT: B 80 ASP cc_start: 0.7953 (t70) cc_final: 0.7647 (t70) REVERT: C 1195 ARG cc_start: 0.7784 (ttp80) cc_final: 0.7540 (ttp80) REVERT: E 171 HIS cc_start: 0.8628 (m-70) cc_final: 0.8290 (m-70) REVERT: F 40 ARG cc_start: 0.8096 (mmm160) cc_final: 0.7847 (mmm160) REVERT: F 160 ASN cc_start: 0.9262 (m-40) cc_final: 0.9007 (m-40) outliers start: 18 outliers final: 18 residues processed: 224 average time/residue: 0.7513 time to fit residues: 259.3255 Evaluate side-chains 230 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 212 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 740 HIS Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain C residue 1361 GLU Chi-restraints excluded: chain C residue 1400 LEU Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 151 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 300 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 142 optimal weight: 0.2980 chunk 208 optimal weight: 0.6980 chunk 314 optimal weight: 7.9990 chunk 289 optimal weight: 0.9990 chunk 250 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24478 Z= 0.151 Angle : 0.519 17.192 33398 Z= 0.242 Chirality : 0.039 0.152 3813 Planarity : 0.004 0.054 4375 Dihedral : 5.366 79.011 3483 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.64 % Allowed : 9.67 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3144 helix: 1.18 (0.17), residues: 998 sheet: -0.72 (0.20), residues: 679 loop : -0.26 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.004 0.000 HIS B 345 PHE 0.009 0.001 PHE C1430 TYR 0.009 0.001 TYR A 807 ARG 0.010 0.000 ARG D1520 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 493 is missing expected H atoms. Skipping. Residue ALA 493 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue LYS 1437 is missing expected H atoms. Skipping. Residue SER 1526 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 225 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.7774 (mtt) cc_final: 0.7500 (mtt) REVERT: B 54 ASP cc_start: 0.7708 (m-30) cc_final: 0.7462 (t0) REVERT: B 80 ASP cc_start: 0.7922 (t70) cc_final: 0.7614 (t70) REVERT: C 1195 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7550 (ttp80) REVERT: C 1424 ASP cc_start: 0.7850 (t0) cc_final: 0.7638 (t0) REVERT: D 1514 GLU cc_start: 0.8540 (pm20) cc_final: 0.8326 (pm20) REVERT: E 171 HIS cc_start: 0.8642 (m-70) cc_final: 0.8231 (m90) REVERT: F 40 ARG cc_start: 0.8065 (mmm160) cc_final: 0.7817 (mmm160) REVERT: F 160 ASN cc_start: 0.9270 (m-40) cc_final: 0.9014 (m110) outliers start: 16 outliers final: 15 residues processed: 233 average time/residue: 0.7621 time to fit residues: 270.0180 Evaluate side-chains 236 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 221 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 740 HIS Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain C residue 1361 GLU Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 151 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 267 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 231 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 251 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.0000 chunk 220 optimal weight: 5.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.090025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.066914 restraints weight = 179944.429| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.34 r_work: 0.2941 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24478 Z= 0.188 Angle : 0.522 17.336 33398 Z= 0.244 Chirality : 0.039 0.148 3813 Planarity : 0.004 0.052 4375 Dihedral : 5.355 81.362 3483 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.60 % Allowed : 9.87 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 3144 helix: 1.18 (0.17), residues: 998 sheet: -0.68 (0.20), residues: 679 loop : -0.25 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 60 HIS 0.003 0.001 HIS B 345 PHE 0.008 0.001 PHE C1430 TYR 0.011 0.001 TYR A 807 ARG 0.010 0.000 ARG D1520 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7841.18 seconds wall clock time: 137 minutes 5.45 seconds (8225.45 seconds total)