Starting phenix.real_space_refine (version: 1.21rc1) on Fri May 5 21:56:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/05_2023/7s6c_24868_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/05_2023/7s6c_24868.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/05_2023/7s6c_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_24868/05_2023/7s6c_24868_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/05_2023/7s6c_24868_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/05_2023/7s6c_24868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/05_2023/7s6c_24868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/05_2023/7s6c_24868_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6c_24868/05_2023/7s6c_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 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-1.21rc1-4953/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: 15.61, 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: 35.07 Conformation dependent library (CDL) restraints added in 3.2 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: 2.61 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: 17.86 Time building geometry restraints manager: 36.58 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: 17270 17.79 - 35.58: 1525 35.58 - 53.37: 208 53.37 - 71.16: 53 71.16 - 88.95: 36 Dihedral angle restraints: 19092 sinusoidal: 8749 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 19089 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: 0.000 Normalize map: mean=0, sd=1: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.310 Construct map_model_manager: 0.570 Extract box with map and model: 12.450 Check model and map are aligned: 0.560 Set scattering table: 0.320 Process input model: 124.240 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.150 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.460 ------------------------------------------------------------------------------- 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 % 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 : 3.014 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: 0.7760 time to fit residues: 337.8177 Evaluate side-chains 229 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 3.008 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5898 ------------------------------------------------------------------------------- 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: A 127 GLN F 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 24478 Z= 0.214 Angle : 0.544 19.528 33398 Z= 0.256 Chirality : 0.039 0.153 3813 Planarity : 0.004 0.063 4375 Dihedral : 5.761 72.079 3483 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.30 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 : -0.50 (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 238 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 233 time to evaluate : 3.049 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: 234 average time/residue: 0.7732 time to fit residues: 274.4611 Evaluate side-chains 224 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 219 time to evaluate : 3.013 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4367 time to fit residues: 7.7712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.0182 > 50: distance: 131 - 140: 32.552 distance: 140 - 141: 4.635 distance: 140 - 147: 66.381 distance: 141 - 144: 39.656 distance: 141 - 148: 48.969 distance: 142 - 143: 70.424 distance: 142 - 156: 55.466 distance: 144 - 145: 20.098 distance: 144 - 146: 40.108 distance: 144 - 149: 39.490 distance: 145 - 150: 56.368 distance: 145 - 151: 39.385 distance: 145 - 152: 45.736 distance: 146 - 153: 55.658 distance: 146 - 154: 62.688 distance: 146 - 155: 40.716 distance: 156 - 167: 52.873 distance: 157 - 158: 70.687 distance: 157 - 160: 69.325 distance: 157 - 168: 55.845 distance: 158 - 159: 37.601 distance: 158 - 176: 68.856 distance: 160 - 161: 41.356 distance: 160 - 169: 55.945 distance: 160 - 170: 39.932 distance: 161 - 162: 26.002 distance: 161 - 163: 16.338 distance: 162 - 164: 15.518 distance: 162 - 171: 22.711 distance: 163 - 165: 23.283 distance: 163 - 172: 13.584 distance: 164 - 166: 18.900 distance: 164 - 173: 13.271 distance: 165 - 166: 20.789 distance: 165 - 174: 19.533 distance: 166 - 175: 16.954 distance: 176 - 177: 57.306 distance: 176 - 184: 39.897 distance: 177 - 178: 56.219 distance: 177 - 180: 57.465 distance: 177 - 185: 57.122 distance: 178 - 179: 68.677 distance: 178 - 195: 69.205 distance: 180 - 181: 57.938 distance: 180 - 182: 54.271 distance: 180 - 186: 56.004 distance: 181 - 183: 17.096 distance: 181 - 188: 7.817 distance: 182 - 189: 3.592 distance: 182 - 190: 42.823 distance: 182 - 191: 8.928 distance: 183 - 192: 48.559 distance: 183 - 193: 38.976 distance: 183 - 194: 43.386 distance: 195 - 196: 56.081 distance: 195 - 206: 41.625 distance: 196 - 197: 56.416 distance: 196 - 199: 56.588 distance: 196 - 207: 57.386 distance: 197 - 198: 39.703 distance: 197 - 215: 38.691 distance: 199 - 200: 27.507 distance: 199 - 209: 5.135 distance: 200 - 201: 14.183 distance: 201 - 203: 32.093 distance: 201 - 210: 12.519 distance: 202 - 204: 21.334 distance: 202 - 211: 31.360 distance: 203 - 205: 21.090 distance: 203 - 212: 21.153 distance: 204 - 205: 31.460 distance: 204 - 213: 36.875 distance: 205 - 214: 4.930 distance: 215 - 216: 39.646 distance: 215 - 221: 56.139 distance: 216 - 217: 69.099 distance: 216 - 222: 39.495 distance: 217 - 218: 57.534 distance: 219 - 220: 40.106 distance: 219 - 223: 56.821 distance: 219 - 224: 53.716 distance: 220 - 221: 54.057 distance: 220 - 225: 47.130 distance: 220 - 226: 37.605 distance: 221 - 227: 57.210 distance: 221 - 228: 56.373 distance: 229 - 235: 44.955 distance: 230 - 231: 68.545 distance: 230 - 233: 40.389 distance: 230 - 236: 57.486 distance: 231 - 232: 39.680 distance: 231 - 243: 20.157 distance: 233 - 237: 54.027 distance: 233 - 238: 39.134 distance: 234 - 235: 43.118 distance: 234 - 239: 41.947 distance: 234 - 240: 39.497 distance: 235 - 241: 43.664 distance: 235 - 242: 44.329 distance: 243 - 244: 44.584 distance: 243 - 249: 43.405 distance: 244 - 245: 6.236 distance: 244 - 247: 10.339 distance: 244 - 250: 39.354 distance: 245 - 246: 41.435 distance: 245 - 254: 40.360 distance: 247 - 248: 42.256 distance: 247 - 251: 56.317 distance: 247 - 252: 40.609 distance: 254 - 255: 47.497 distance: 254 - 262: 59.512 distance: 255 - 256: 58.699 distance: 255 - 258: 47.300 distance: 255 - 263: 49.200 distance: 256 - 257: 40.995 distance: 256 - 266: 39.358 distance: 257 - 317: 31.973 distance: 258 - 259: 67.979 distance: 258 - 264: 61.648 distance: 258 - 265: 58.243 distance: 259 - 260: 54.117 distance: 259 - 261: 22.695 distance: 266 - 267: 56.292 distance: 266 - 275: 39.977 distance: 267 - 268: 55.438 distance: 267 - 270: 63.792 distance: 267 - 276: 56.914 distance: 268 - 269: 57.304 distance: 268 - 281: 55.329 distance: 269 - 339: 32.458 distance: 270 - 271: 36.226 distance: 270 - 277: 49.117 distance: 270 - 278: 50.178 distance: 271 - 272: 33.107 distance: 271 - 279: 38.587 distance: 271 - 280: 50.842 distance: 272 - 273: 51.440 distance: 272 - 274: 19.202 distance: 281 - 282: 69.995 distance: 281 - 290: 40.342 distance: 282 - 283: 55.677 distance: 282 - 285: 55.621 distance: 282 - 291: 56.956 distance: 283 - 284: 40.244 distance: 283 - 298: 33.503 distance: 285 - 286: 70.684 distance: 285 - 292: 60.796 distance: 285 - 293: 57.616 distance: 286 - 287: 5.935 distance: 286 - 295: 29.467 distance: 287 - 288: 21.866 distance: 287 - 289: 6.247 distance: 289 - 296: 41.494 distance: 289 - 297: 29.953