Starting phenix.real_space_refine (version: dev) on Tue Apr 5 13:12:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/04_2022/7s6c_24868_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/04_2022/7s6c_24868.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/04_2022/7s6c_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_24868/04_2022/7s6c_24868_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/04_2022/7s6c_24868_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/04_2022/7s6c_24868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/04_2022/7s6c_24868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/04_2022/7s6c_24868_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/04_2022/7s6c_24868_trim_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 1.126 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {'PTRANS': 10, 'TRANS': 195, 'PCIS': 1} 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: {'PTRANS': 12, 'TRANS': 201, 'PCIS': 2} 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: {'PTRANS': 12, 'TRANS': 199, 'PCIS': 2} 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: {'PTRANS': 10, 'TRANS': 193, 'PCIS': 1} 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 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: 16.00, per 1000 atoms: 0.34 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: 29.06 Conformation dependent library (CDL) restraints added in 3.0 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: 2.58 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: 15.46 Time building geometry restraints manager: 30.61 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 1.241 1.553 -0.312 2.00e-02 2.50e+03 2.43e+02 bond pdb=" O3B ATR C1701 " pdb=" PB ATR C1701 " ideal model delta sigma weight residual 1.521 1.756 -0.235 2.00e-02 2.50e+03 1.39e+02 bond pdb=" O2' ATR C1701 " pdb=" P2' ATR C1701 " ideal model delta sigma weight residual 1.648 1.826 -0.178 2.00e-02 2.50e+03 7.95e+01 bond pdb=" C2' ATR C1701 " pdb=" O2' ATR C1701 " ideal model delta sigma weight residual 1.483 1.328 0.155 2.00e-02 2.50e+03 5.99e+01 bond pdb=" O3A ATR C1701 " pdb=" PB ATR C1701 " ideal model delta sigma weight residual 1.700 1.584 0.116 2.00e-02 2.50e+03 3.35e+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 95.72 127.94 -32.22 3.00e+00 1.11e-01 1.15e+02 angle pdb=" C1' ATR C1701 " pdb=" N9 ATR C1701 " pdb=" C4 ATR C1701 " ideal model delta sigma weight residual 146.37 125.18 21.19 3.00e+00 1.11e-01 4.99e+01 angle pdb=" PA ATR C1701 " pdb=" O3A ATR C1701 " pdb=" PB ATR C1701 " ideal model delta sigma weight residual 123.59 107.68 15.91 3.00e+00 1.11e-01 2.81e+01 angle pdb=" O1B ATR C1701 " pdb=" PB ATR C1701 " pdb=" O2B ATR C1701 " ideal model delta sigma weight residual 109.35 123.59 -14.24 3.00e+00 1.11e-01 2.25e+01 angle pdb=" C5' ATR C1701 " pdb=" O5' ATR C1701 " pdb=" PA ATR C1701 " ideal model delta sigma weight residual 118.48 104.30 14.18 3.00e+00 1.11e-01 2.24e+01 ... (remaining 86456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 17265 17.79 - 35.58: 1514 35.58 - 53.37: 199 53.37 - 71.16: 46 71.16 - 88.95: 35 Dihedral angle restraints: 19059 sinusoidal: 8716 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 19056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3318 0.061 - 0.121: 444 0.121 - 0.182: 54 0.182 - 0.242: 1 0.242 - 0.303: 1 Chirality restraints: 3818 Sorted by residual: chirality pdb=" C3' ATR C1701 " pdb=" C2' ATR C1701 " pdb=" C4' ATR C1701 " pdb=" O3' ATR C1701 " both_signs ideal model delta sigma weight residual False -2.43 -2.73 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C2' ATR C1701 " pdb=" C1' ATR C1701 " pdb=" C3' ATR C1701 " pdb=" O2' ATR C1701 " both_signs ideal model delta sigma weight residual False -2.35 -2.57 0.23 2.00e-01 2.50e+01 1.29e+00 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 ... (remaining 3815 not shown) Planarity restraints: 7349 Sorted by residual: 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 delta sigma weight rms_deltas residual plane pdb=" C GLY A 387 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO A 388 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " -0.032 5.00e-02 4.00e+02 ... (remaining 7346 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 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. 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: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.370 Construct map_model_manager: 0.610 Extract box with map and model: 11.970 Check model and map are aligned: 0.510 Convert atoms to be neutral: 0.330 Process input model: 109.740 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 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 0.312 24478 Z= 0.295 Angle : 0.739 32.224 33398 Z= 0.343 Chirality : 0.043 0.303 3818 Planarity : 0.005 0.064 4374 Dihedral : 13.965 88.951 8699 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 % 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 *********************** 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 : 2.737 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 outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.7246 time to fit residues: 317.7914 Evaluate side-chains 228 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.816 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4631 ------------------------------------------------------------------------------- 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: 2.9990 chunk 239 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 161 optimal weight: 0.0010 chunk 127 optimal weight: 1.9990 chunk 247 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 286 optimal weight: 8.9990 overall best weight: 1.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.087 24478 Z= 0.218 Angle : 0.489 6.939 33398 Z= 0.244 Chirality : 0.039 0.154 3818 Planarity : 0.004 0.092 4374 Dihedral : 4.101 46.309 3450 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 0.20 % 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: -0.22 (0.15), residues: 3144 helix: 1.18 (0.17), residues: 989 sheet: -1.07 (0.19), residues: 694 loop : -0.49 (0.17), residues: 1461 *********************** 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 236 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 231 time to evaluate : 3.028 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 outliers start: 5 outliers final: 5 residues processed: 232 average time/residue: 0.7127 time to fit residues: 253.0205 Evaluate side-chains 221 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 216 time to evaluate : 2.769 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4227 time to fit residues: 7.4942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0980 chunk 238 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 287 optimal weight: 0.9990 chunk 310 optimal weight: 0.9990 chunk 256 optimal weight: 0.5980 chunk 285 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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: 0.7639 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 24478 Z= 0.148 Angle : 0.459 4.918 33398 Z= 0.226 Chirality : 0.039 0.152 3818 Planarity : 0.004 0.062 4374 Dihedral : 3.868 42.909 3450 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.16 % 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: -0.05 (0.15), residues: 3144 helix: 1.34 (0.17), residues: 980 sheet: -0.94 (0.19), residues: 702 loop : -0.40 (0.17), residues: 1462 *********************** 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 228 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 224 time to evaluate : 2.828 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 outliers start: 4 outliers final: 2 residues processed: 227 average time/residue: 0.6947 time to fit residues: 241.3996 Evaluate side-chains 215 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 213 time to evaluate : 2.727 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4944 time to fit residues: 5.0903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 284 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 149 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 288 optimal weight: 9.9990 chunk 305 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 273 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN B 404 HIS D1552 HIS ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1150 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= 0.259 Angle : 0.485 6.025 33398 Z= 0.243 Chirality : 0.039 0.147 3818 Planarity : 0.004 0.059 4374 Dihedral : 3.928 49.131 3450 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 0.32 % 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: -0.17 (0.15), residues: 3144 helix: 1.13 (0.17), residues: 996 sheet: -0.95 (0.19), residues: 691 loop : -0.45 (0.17), residues: 1457 *********************** 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 224 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 216 time to evaluate : 2.818 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 outliers start: 8 outliers final: 4 residues processed: 219 average time/residue: 0.7233 time to fit residues: 246.7920 Evaluate side-chains 215 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 211 time to evaluate : 2.740 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.4061 time to fit residues: 6.4644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 4 optimal weight: 0.0470 chunk 227 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 260 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 274 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 906 GLN B 184 ASN ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 24478 Z= 0.273 Angle : 0.494 5.002 33398 Z= 0.247 Chirality : 0.040 0.149 3818 Planarity : 0.004 0.057 4374 Dihedral : 3.993 53.058 3450 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.36 % 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: -0.24 (0.15), residues: 3144 helix: 1.01 (0.17), residues: 991 sheet: -0.92 (0.19), residues: 683 loop : -0.49 (0.17), residues: 1470 *********************** 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 227 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 218 time to evaluate : 3.216 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 outliers start: 9 outliers final: 8 residues processed: 220 average time/residue: 0.7072 time to fit residues: 240.9129 Evaluate side-chains 216 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 208 time to evaluate : 2.817 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 0.4268 time to fit residues: 9.6743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 102 optimal weight: 0.6980 chunk 275 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 305 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 24478 Z= 0.260 Angle : 0.492 6.902 33398 Z= 0.246 Chirality : 0.040 0.148 3818 Planarity : 0.004 0.055 4374 Dihedral : 4.000 54.750 3450 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 0.32 % 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: -0.24 (0.15), residues: 3144 helix: 1.01 (0.17), residues: 992 sheet: -0.93 (0.20), residues: 685 loop : -0.47 (0.17), residues: 1467 *********************** 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 229 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 221 time to evaluate : 3.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 225 average time/residue: 0.7104 time to fit residues: 247.2041 Evaluate side-chains 215 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 209 time to evaluate : 2.781 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 6 average time/residue: 0.5376 time to fit residues: 8.8211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 257 optimal weight: 0.9980 chunk 170 optimal weight: 0.6980 chunk 304 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.7670 moved from start: 0.1532 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 : 0.479 5.332 33398 Z= 0.238 Chirality : 0.039 0.150 3818 Planarity : 0.004 0.053 4374 Dihedral : 3.950 55.407 3450 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 0.36 % 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: -0.16 (0.15), residues: 3144 helix: 1.09 (0.17), residues: 992 sheet: -0.91 (0.19), residues: 691 loop : -0.43 (0.17), residues: 1461 *********************** 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 223 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 214 time to evaluate : 2.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 219 average time/residue: 0.7079 time to fit residues: 241.1774 Evaluate side-chains 215 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 209 time to evaluate : 3.454 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 6 average time/residue: 0.4911 time to fit residues: 8.7379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 188 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 193 optimal weight: 1.9990 chunk 207 optimal weight: 0.0980 chunk 150 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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: 0.7666 moved from start: 0.1564 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= 0.198 Angle : 0.477 5.586 33398 Z= 0.236 Chirality : 0.039 0.149 3818 Planarity : 0.004 0.053 4374 Dihedral : 3.923 56.271 3450 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer Outliers : 0.24 % 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: -0.10 (0.15), residues: 3144 helix: 1.14 (0.17), residues: 994 sheet: -0.88 (0.20), residues: 691 loop : -0.38 (0.17), residues: 1459 *********************** 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 220 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 214 time to evaluate : 2.929 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 outliers start: 6 outliers final: 5 residues processed: 216 average time/residue: 0.7142 time to fit residues: 239.3020 Evaluate side-chains 216 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 211 time to evaluate : 2.795 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.4352 time to fit residues: 7.4619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 291 optimal weight: 4.9990 chunk 266 optimal weight: 1.9990 chunk 283 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 222 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 282 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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: 0.7666 moved from start: 0.1604 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= 0.200 Angle : 0.477 5.668 33398 Z= 0.237 Chirality : 0.039 0.149 3818 Planarity : 0.004 0.052 4374 Dihedral : 3.906 57.630 3450 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.12 % 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: 1.17 (0.17), residues: 994 sheet: -0.85 (0.20), residues: 691 loop : -0.37 (0.17), residues: 1459 *********************** 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 217 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 214 time to evaluate : 2.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 215 average time/residue: 0.6980 time to fit residues: 232.4124 Evaluate side-chains 215 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 212 time to evaluate : 2.738 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.4514 time to fit residues: 5.8088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 300 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 142 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 314 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 chunk 250 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 193 optimal weight: 0.2980 chunk 153 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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: 0.7653 moved from start: 0.1584 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= 0.161 Angle : 0.467 5.640 33398 Z= 0.230 Chirality : 0.039 0.149 3818 Planarity : 0.004 0.069 4374 Dihedral : 3.842 58.116 3450 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 0.08 % 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: 0.04 (0.16), residues: 3144 helix: 1.26 (0.17), residues: 999 sheet: -0.82 (0.20), residues: 696 loop : -0.29 (0.17), residues: 1449 ********************** 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 218 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 216 time to evaluate : 2.802 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 outliers start: 2 outliers final: 2 residues processed: 217 average time/residue: 0.7316 time to fit residues: 244.8165 Evaluate side-chains 211 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 209 time to evaluate : 2.769 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.4623 time to fit residues: 5.0435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 231 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 251 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.090268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.067025 restraints weight = 180302.321| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.36 r_work: 0.3046 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work: 0.3017 rms_B_bonded: 3.11 restraints_weight: 0.1250 r_work: 0.3002 rms_B_bonded: 3.21 restraints_weight: 0.0625 r_work: 0.2986 rms_B_bonded: 3.35 restraints_weight: 0.0312 r_work: 0.2969 rms_B_bonded: 3.54 restraints_weight: 0.0156 r_work: 0.2951 rms_B_bonded: 3.77 restraints_weight: 0.0078 r_work: 0.2932 rms_B_bonded: 4.06 restraints_weight: 0.0039 r_work: 0.2911 rms_B_bonded: 4.39 restraints_weight: 0.0020 r_work: 0.2889 rms_B_bonded: 4.79 restraints_weight: 0.0010 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1683 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= 0.236 Angle : 0.484 5.579 33398 Z= 0.241 Chirality : 0.039 0.147 3818 Planarity : 0.004 0.099 4374 Dihedral : 3.922 59.952 3450 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.16 % 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: -0.00 (0.15), residues: 3144 helix: 1.17 (0.17), residues: 999 sheet: -0.74 (0.20), residues: 682 loop : -0.35 (0.17), residues: 1463 =============================================================================== Job complete usr+sys time: 6944.17 seconds wall clock time: 121 minutes 51.87 seconds (7311.87 seconds total)