Starting phenix.real_space_refine on Sat Nov 18 14:27:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3a_25652/11_2023/7t3a_25652_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3a_25652/11_2023/7t3a_25652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3a_25652/11_2023/7t3a_25652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3a_25652/11_2023/7t3a_25652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3a_25652/11_2023/7t3a_25652_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3a_25652/11_2023/7t3a_25652_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 131 5.16 5 C 14912 2.51 5 N 3942 2.21 5 O 4322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A PHE 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 979": "OE1" <-> "OE2" Residue "A TYR 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1400": "OE1" <-> "OE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 89": "OD1" <-> "OD2" Residue "C PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 224": "OD1" <-> "OD2" Residue "K GLU 253": "OE1" <-> "OE2" Residue "K PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 181": "OD1" <-> "OD2" Residue "L PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 290": "OD1" <-> "OD2" Residue "L PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 117": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 23310 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 8120 Classifications: {'peptide': 990} Link IDs: {'PTRANS': 41, 'TRANS': 948} Chain breaks: 7 Chain: "B" Number of atoms: 2926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2926 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Chain: "C" Number of atoms: 3242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3242 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 385} Chain breaks: 5 Chain: "K" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2416 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 5, 'TRANS': 288} Chain: "L" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2420 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 7, 'TRANS': 291} Chain: "M" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 892 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "N" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 940 Classifications: {'peptide': 125} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 122} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 918 Classifications: {'peptide': 118} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 111} Chain: "P" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 738 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "Q" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 666 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GNP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.81, per 1000 atoms: 0.51 Number of scatterers: 23310 At special positions: 0 Unit cell: (123.795, 159.165, 233.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 131 16.00 P 3 15.00 O 4322 8.00 N 3942 7.00 C 14912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS K 124 " - pdb=" SG CYS K 159 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.18 Conformation dependent library (CDL) restraints added in 4.5 seconds 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5548 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 27 sheets defined 33.7% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.10 Creating SS restraints... Processing helix chain 'A' and resid 71 through 77 Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 111 through 121 Processing helix chain 'A' and resid 191 through 197 Processing helix chain 'A' and resid 200 through 209 Processing helix chain 'A' and resid 267 through 280 removed outlier: 3.545A pdb=" N LEU A 270 " --> pdb=" O TRP A 267 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 272 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 307 through 317 Processing helix chain 'A' and resid 347 through 359 removed outlier: 3.926A pdb=" N ASP A 359 " --> pdb=" O GLN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 748 No H-bonds generated for 'chain 'A' and resid 745 through 748' Processing helix chain 'A' and resid 763 through 768 Processing helix chain 'A' and resid 779 through 782 removed outlier: 4.132A pdb=" N ASP A 782 " --> pdb=" O PRO A 779 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 779 through 782' Processing helix chain 'A' and resid 795 through 808 removed outlier: 4.307A pdb=" N PHE A 799 " --> pdb=" O ALA A 795 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU A 800 " --> pdb=" O GLN A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 927 Processing helix chain 'A' and resid 937 through 939 No H-bonds generated for 'chain 'A' and resid 937 through 939' Processing helix chain 'A' and resid 953 through 961 removed outlier: 3.853A pdb=" N ARG A 958 " --> pdb=" O THR A 954 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 959 " --> pdb=" O ALA A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 993 removed outlier: 5.107A pdb=" N GLN A 981 " --> pdb=" O GLU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1185 Processing helix chain 'A' and resid 1207 through 1217 Processing helix chain 'A' and resid 1224 through 1236 Processing helix chain 'A' and resid 1287 through 1290 No H-bonds generated for 'chain 'A' and resid 1287 through 1290' Processing helix chain 'A' and resid 1310 through 1312 No H-bonds generated for 'chain 'A' and resid 1310 through 1312' Processing helix chain 'A' and resid 1395 through 1412 removed outlier: 3.586A pdb=" N CYS A1412 " --> pdb=" O LYS A1408 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1448 No H-bonds generated for 'chain 'A' and resid 1446 through 1448' Processing helix chain 'A' and resid 1462 through 1479 removed outlier: 4.242A pdb=" N TYR A1465 " --> pdb=" O PRO A1462 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TRP A1466 " --> pdb=" O GLU A1463 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP A1467 " --> pdb=" O THR A1464 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1580 removed outlier: 4.271A pdb=" N ALA A1569 " --> pdb=" O GLU A1566 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP A1570 " --> pdb=" O LYS A1567 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1598 removed outlier: 6.062A pdb=" N LEU A1587 " --> pdb=" O ASP A1584 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A1588 " --> pdb=" O ASN A1585 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A1592 " --> pdb=" O THR A1589 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET A1598 " --> pdb=" O LEU A1595 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 44 No H-bonds generated for 'chain 'B' and resid 41 through 44' Processing helix chain 'B' and resid 98 through 116 removed outlier: 3.675A pdb=" N GLU B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 139 Proline residue: B 130 - end of helix 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 191 through 199 Proline residue: B 198 - end of helix Processing helix chain 'B' and resid 207 through 210 No H-bonds generated for 'chain 'B' and resid 207 through 210' Processing helix chain 'B' and resid 217 through 228 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 259 through 267 Processing helix chain 'B' and resid 278 through 286 Processing helix chain 'B' and resid 294 through 300 Processing helix chain 'B' and resid 310 through 319 removed outlier: 4.047A pdb=" N ILE B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 358 Processing helix chain 'B' and resid 362 through 369 removed outlier: 5.004A pdb=" N GLU B 367 " --> pdb=" O HIS B 363 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 136 through 159 Processing helix chain 'C' and resid 162 through 173 Processing helix chain 'C' and resid 200 through 211 Processing helix chain 'C' and resid 267 through 273 Processing helix chain 'C' and resid 280 through 287 Processing helix chain 'C' and resid 295 through 301 Processing helix chain 'C' and resid 306 through 319 Processing helix chain 'C' and resid 348 through 355 removed outlier: 4.018A pdb=" N PHE C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 367 Processing helix chain 'C' and resid 384 through 399 Processing helix chain 'C' and resid 481 through 488 Processing helix chain 'C' and resid 492 through 499 Processing helix chain 'C' and resid 507 through 515 Processing helix chain 'C' and resid 517 through 519 No H-bonds generated for 'chain 'C' and resid 517 through 519' Processing helix chain 'C' and resid 526 through 533 Processing helix chain 'C' and resid 537 through 546 Processing helix chain 'C' and resid 559 through 563 Processing helix chain 'K' and resid 20 through 27 removed outlier: 4.208A pdb=" N ARG K 24 " --> pdb=" O LYS K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 38 Processing helix chain 'K' and resid 67 through 75 Processing helix chain 'K' and resid 78 through 82 removed outlier: 3.538A pdb=" N PHE K 82 " --> pdb=" O ARG K 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 78 through 82' Processing helix chain 'K' and resid 99 through 116 Processing helix chain 'K' and resid 129 through 131 No H-bonds generated for 'chain 'K' and resid 129 through 131' Processing helix chain 'K' and resid 134 through 151 Processing helix chain 'K' and resid 168 through 180 Processing helix chain 'K' and resid 184 through 198 Processing helix chain 'K' and resid 228 through 245 removed outlier: 4.219A pdb=" N LYS K 244 " --> pdb=" O LEU K 240 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU K 245 " --> pdb=" O SER K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 296 Processing helix chain 'L' and resid 74 through 85 Processing helix chain 'L' and resid 102 through 110 Processing helix chain 'L' and resid 126 through 129 No H-bonds generated for 'chain 'L' and resid 126 through 129' Processing helix chain 'L' and resid 150 through 160 removed outlier: 4.612A pdb=" N HIS L 158 " --> pdb=" O LEU L 154 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE L 159 " --> pdb=" O THR L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 167 Processing helix chain 'L' and resid 185 through 203 removed outlier: 3.585A pdb=" N ASN L 200 " --> pdb=" O HIS L 196 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ASP L 201 " --> pdb=" O GLN L 197 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ASP L 202 " --> pdb=" O ARG L 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 234 Processing helix chain 'L' and resid 240 through 250 Processing helix chain 'L' and resid 281 through 299 removed outlier: 3.543A pdb=" N VAL L 295 " --> pdb=" O VAL L 291 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR L 299 " --> pdb=" O VAL L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 357 removed outlier: 3.775A pdb=" N TYR L 354 " --> pdb=" O LEU L 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 63 Processing helix chain 'M' and resid 79 through 94 removed outlier: 3.709A pdb=" N ASP M 83 " --> pdb=" O HIS M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 119 Processing helix chain 'M' and resid 126 through 143 Processing helix chain 'N' and resid 4 through 12 Processing helix chain 'N' and resid 44 through 55 removed outlier: 4.129A pdb=" N ALA N 47 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE N 48 " --> pdb=" O THR N 45 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA N 49 " --> pdb=" O ALA N 46 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TRP N 53 " --> pdb=" O SER N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 115 Processing helix chain 'N' and resid 118 through 123 Processing helix chain 'O' and resid 4 through 11 Processing helix chain 'O' and resid 13 through 15 No H-bonds generated for 'chain 'O' and resid 13 through 15' Processing helix chain 'O' and resid 42 through 44 No H-bonds generated for 'chain 'O' and resid 42 through 44' Processing helix chain 'O' and resid 47 through 59 removed outlier: 3.577A pdb=" N PHE O 53 " --> pdb=" O PHE O 49 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA O 54 " --> pdb=" O LEU O 50 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU O 55 " --> pdb=" O SER O 51 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA O 56 " --> pdb=" O THR O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 113 Proline residue: O 112 - end of helix Processing helix chain 'O' and resid 115 through 119 removed outlier: 4.271A pdb=" N GLN O 119 " --> pdb=" O GLU O 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 115 through 119' Processing helix chain 'P' and resid 37 through 52 removed outlier: 5.421A pdb=" N GLY P 52 " --> pdb=" O SER P 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 14 removed outlier: 3.558A pdb=" N GLU Q 10 " --> pdb=" O GLN Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 54 removed outlier: 4.717A pdb=" N VAL Q 44 " --> pdb=" O GLU Q 40 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA Q 53 " --> pdb=" O ALA Q 49 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS Q 54 " --> pdb=" O GLN Q 50 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 8 through 12 removed outlier: 3.900A pdb=" N ILE A 67 " --> pdb=" O LYS A 8 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 51 through 54 Processing sheet with id= C, first strand: chain 'A' and resid 99 through 104 removed outlier: 6.545A pdb=" N ARG A 161 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N LEU A 102 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL A 163 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N PHE A 104 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG A 165 " --> pdb=" O PHE A 104 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 131 through 134 Processing sheet with id= E, first strand: chain 'A' and resid 902 through 908 removed outlier: 3.582A pdb=" N MET A 332 " --> pdb=" O MET A 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 380 through 382 removed outlier: 4.286A pdb=" N ASP A 396 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 770 through 777 Processing sheet with id= H, first strand: chain 'A' and resid 1414 through 1419 removed outlier: 3.913A pdb=" N VAL A1419 " --> pdb=" O ARG A 945 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG A 945 " --> pdb=" O VAL A1419 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLU A1385 " --> pdb=" O HIS A1375 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1204 through 1206 Processing sheet with id= J, first strand: chain 'A' and resid 1439 through 1442 removed outlier: 5.212A pdb=" N VAL A1509 " --> pdb=" O HIS A1504 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN A1501 " --> pdb=" O ASP A1485 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 62 through 65 removed outlier: 7.726A pdb=" N ASP B 90 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ILE B 7 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU B 14 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ILE B 23 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 145 through 148 Processing sheet with id= M, first strand: chain 'B' and resid 174 through 177 Processing sheet with id= N, first strand: chain 'B' and resid 245 through 247 Processing sheet with id= O, first strand: chain 'C' and resid 84 through 87 removed outlier: 6.989A pdb=" N SER C 15 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N PHE C 124 " --> pdb=" O VAL C 13 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL C 13 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL C 126 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE C 11 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N PHE C 128 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N SER C 9 " --> pdb=" O PHE C 128 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER C 14 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU C 22 " --> pdb=" O SER C 14 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 259 through 263 Processing sheet with id= Q, first strand: chain 'C' and resid 334 through 336 Processing sheet with id= R, first strand: chain 'C' and resid 406 through 412 Processing sheet with id= S, first strand: chain 'K' and resid 158 through 161 removed outlier: 3.511A pdb=" N LYS K 8 " --> pdb=" O VAL K 57 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN K 59 " --> pdb=" O LYS K 8 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS K 63 " --> pdb=" O LEU K 12 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'K' and resid 251 through 256 removed outlier: 6.913A pdb=" N GLU K 207 " --> pdb=" O VAL K 213 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL K 213 " --> pdb=" O GLU K 207 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 140 through 144 Processing sheet with id= V, first strand: chain 'L' and resid 258 through 262 Processing sheet with id= W, first strand: chain 'N' and resid 80 through 86 removed outlier: 3.542A pdb=" N SER N 35 " --> pdb=" O THR N 22 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'O' and resid 70 through 74 removed outlier: 3.593A pdb=" N VAL O 80 " --> pdb=" O CYS O 73 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N SER O 95 " --> pdb=" O LEU O 19 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU O 19 " --> pdb=" O SER O 95 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP O 26 " --> pdb=" O PRO O 31 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'P' and resid 66 through 69 removed outlier: 6.368A pdb=" N GLN P 90 " --> pdb=" O GLN P 15 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLN P 15 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'P' and resid 19 through 22 removed outlier: 6.391A pdb=" N SER P 22 " --> pdb=" O VAL P 26 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL P 26 " --> pdb=" O SER P 22 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Q' and resid 65 through 68 removed outlier: 3.565A pdb=" N VAL Q 86 " --> pdb=" O MET Q 75 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN Q 77 " --> pdb=" O VAL Q 84 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA Q 85 " --> pdb=" O LEU Q 22 " (cutoff:3.500A) 838 hydrogen bonds defined for protein. 2226 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: 8.04 Time building geometry restraints manager: 9.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7565 1.35 - 1.48: 5839 1.48 - 1.61: 10202 1.61 - 1.74: 4 1.74 - 1.87: 197 Bond restraints: 23807 Sorted by residual: bond pdb=" C VAL A 733 " pdb=" N PRO A 734 " ideal model delta sigma weight residual 1.337 1.414 -0.077 9.80e-03 1.04e+04 6.22e+01 bond pdb=" C GLU N 117 " pdb=" N PRO N 118 " ideal model delta sigma weight residual 1.336 1.399 -0.064 1.23e-02 6.61e+03 2.67e+01 bond pdb=" C ASP L 125 " pdb=" N PRO L 126 " ideal model delta sigma weight residual 1.336 1.398 -0.062 1.23e-02 6.61e+03 2.54e+01 bond pdb=" N3B GNP K 500 " pdb=" PG GNP K 500 " ideal model delta sigma weight residual 1.801 1.703 0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" O5' GNP K 500 " pdb=" PA GNP K 500 " ideal model delta sigma weight residual 1.660 1.570 0.090 2.00e-02 2.50e+03 2.01e+01 ... (remaining 23802 not shown) Histogram of bond angle deviations from ideal: 97.50 - 104.84: 402 104.84 - 112.17: 11157 112.17 - 119.51: 9035 119.51 - 126.84: 11322 126.84 - 134.18: 332 Bond angle restraints: 32248 Sorted by residual: angle pdb=" C PHE K 52 " pdb=" N LEU K 53 " pdb=" CA LEU K 53 " ideal model delta sigma weight residual 122.46 130.46 -8.00 1.41e+00 5.03e-01 3.22e+01 angle pdb=" N VAL A 733 " pdb=" CA VAL A 733 " pdb=" C VAL A 733 " ideal model delta sigma weight residual 108.88 120.92 -12.04 2.16e+00 2.14e-01 3.11e+01 angle pdb=" C GLU C 226 " pdb=" N VAL C 227 " pdb=" CA VAL C 227 " ideal model delta sigma weight residual 120.62 129.73 -9.11 1.64e+00 3.72e-01 3.08e+01 angle pdb=" C GLU A 288 " pdb=" N GLN A 289 " pdb=" CA GLN A 289 " ideal model delta sigma weight residual 122.61 131.03 -8.42 1.56e+00 4.11e-01 2.91e+01 angle pdb=" CB MET K 252 " pdb=" CG MET K 252 " pdb=" SD MET K 252 " ideal model delta sigma weight residual 112.70 128.59 -15.89 3.00e+00 1.11e-01 2.81e+01 ... (remaining 32243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 12473 17.39 - 34.78: 1539 34.78 - 52.18: 251 52.18 - 69.57: 45 69.57 - 86.96: 23 Dihedral angle restraints: 14331 sinusoidal: 5802 harmonic: 8529 Sorted by residual: dihedral pdb=" CA VAL A 258 " pdb=" C VAL A 258 " pdb=" N VAL A 259 " pdb=" CA VAL A 259 " ideal model delta harmonic sigma weight residual -180.00 -123.04 -56.96 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA VAL N 86 " pdb=" C VAL N 86 " pdb=" N ALA N 87 " pdb=" CA ALA N 87 " ideal model delta harmonic sigma weight residual -180.00 -131.18 -48.82 0 5.00e+00 4.00e-02 9.53e+01 dihedral pdb=" CA VAL L 264 " pdb=" C VAL L 264 " pdb=" N VAL L 265 " pdb=" CA VAL L 265 " ideal model delta harmonic sigma weight residual -180.00 -140.70 -39.30 0 5.00e+00 4.00e-02 6.18e+01 ... (remaining 14328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3269 0.103 - 0.207: 348 0.207 - 0.310: 25 0.310 - 0.414: 3 0.414 - 0.517: 2 Chirality restraints: 3647 Sorted by residual: chirality pdb=" CB ILE L 237 " pdb=" CA ILE L 237 " pdb=" CG1 ILE L 237 " pdb=" CG2 ILE L 237 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CB ILE C 324 " pdb=" CA ILE C 324 " pdb=" CG1 ILE C 324 " pdb=" CG2 ILE C 324 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" CB ILE K 181 " pdb=" CA ILE K 181 " pdb=" CG1 ILE K 181 " pdb=" CG2 ILE K 181 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 3644 not shown) Planarity restraints: 4109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 106 " 0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" CG ASP A 106 " -0.068 2.00e-02 2.50e+03 pdb=" OD1 ASP A 106 " 0.026 2.00e-02 2.50e+03 pdb=" OD2 ASP A 106 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 282 " -0.019 2.00e-02 2.50e+03 2.62e-02 1.21e+01 pdb=" CG PHE B 282 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE B 282 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE B 282 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE B 282 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 282 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 282 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 305 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C ASN A 305 " -0.060 2.00e-02 2.50e+03 pdb=" O ASN A 305 " 0.022 2.00e-02 2.50e+03 pdb=" N TYR A 306 " 0.020 2.00e-02 2.50e+03 ... (remaining 4106 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4096 2.77 - 3.30: 21472 3.30 - 3.83: 39706 3.83 - 4.37: 43415 4.37 - 4.90: 73024 Nonbonded interactions: 181713 Sorted by model distance: nonbonded pdb=" OG1 THR A 864 " pdb=" OG1 THR A 871 " model vdw 2.234 2.440 nonbonded pdb=" O THR A 217 " pdb=" OG1 THR A 217 " model vdw 2.253 2.440 nonbonded pdb=" OG SER B 187 " pdb=" OE1 GLN B 188 " model vdw 2.263 2.440 nonbonded pdb=" OG1 THR P 74 " pdb=" OD1 ASN P 91 " model vdw 2.283 2.440 nonbonded pdb=" OH TYR B 241 " pdb=" OE2 GLU B 310 " model vdw 2.287 2.440 ... (remaining 181708 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 18.900 Check model and map are aligned: 0.390 Set scattering table: 0.210 Process input model: 62.490 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 : 0.006 0.098 23807 Z= 0.401 Angle : 1.197 16.722 32248 Z= 0.614 Chirality : 0.065 0.517 3647 Planarity : 0.007 0.069 4109 Dihedral : 15.374 86.959 8780 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.26 % Favored : 90.71 % Rotamer: Outliers : 0.04 % Allowed : 1.16 % Favored : 98.80 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.22 (0.14), residues: 2851 helix: -2.24 (0.13), residues: 1004 sheet: -1.38 (0.22), residues: 534 loop : -2.29 (0.16), residues: 1313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 317 time to evaluate : 3.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 318 average time/residue: 0.3396 time to fit residues: 171.0863 Evaluate side-chains 222 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 2.755 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2035 time to fit residues: 4.2000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 5.9990 chunk 216 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 145 optimal weight: 20.0000 chunk 115 optimal weight: 0.8980 chunk 223 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 166 optimal weight: 20.0000 chunk 258 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN ** A 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1216 ASN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS C 355 GLN K 186 GLN L 212 HIS ** L 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 23807 Z= 0.384 Angle : 0.767 10.319 32248 Z= 0.402 Chirality : 0.047 0.246 3647 Planarity : 0.005 0.061 4109 Dihedral : 6.827 58.880 3132 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.94 % Favored : 90.99 % Rotamer: Outliers : 1.24 % Allowed : 11.27 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.29 (0.15), residues: 2851 helix: -0.89 (0.15), residues: 1003 sheet: -1.31 (0.23), residues: 519 loop : -2.06 (0.16), residues: 1329 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 228 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 23 residues processed: 243 average time/residue: 0.3403 time to fit residues: 134.4587 Evaluate side-chains 219 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 196 time to evaluate : 2.966 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2249 time to fit residues: 13.3458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 176 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 259 optimal weight: 4.9990 chunk 280 optimal weight: 30.0000 chunk 230 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 GLN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS ** L 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 23807 Z= 0.300 Angle : 0.693 10.151 32248 Z= 0.361 Chirality : 0.045 0.226 3647 Planarity : 0.004 0.049 4109 Dihedral : 6.440 57.952 3132 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.19 % Favored : 90.74 % Rotamer: Outliers : 1.39 % Allowed : 15.67 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.15), residues: 2851 helix: -0.50 (0.16), residues: 991 sheet: -1.22 (0.23), residues: 530 loop : -1.95 (0.17), residues: 1330 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 225 time to evaluate : 2.792 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 13 residues processed: 250 average time/residue: 0.3344 time to fit residues: 136.9174 Evaluate side-chains 216 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 203 time to evaluate : 2.691 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2119 time to fit residues: 8.6919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 0.0000 chunk 194 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 123 optimal weight: 0.0670 chunk 174 optimal weight: 0.9990 chunk 260 optimal weight: 20.0000 chunk 275 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 246 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 23807 Z= 0.189 Angle : 0.643 11.016 32248 Z= 0.331 Chirality : 0.044 0.254 3647 Planarity : 0.004 0.053 4109 Dihedral : 5.987 59.797 3132 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 1.35 % Allowed : 17.68 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.16), residues: 2851 helix: -0.27 (0.16), residues: 1002 sheet: -1.00 (0.23), residues: 526 loop : -1.89 (0.17), residues: 1323 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 237 time to evaluate : 2.833 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 20 residues processed: 259 average time/residue: 0.3351 time to fit residues: 142.3135 Evaluate side-chains 222 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 202 time to evaluate : 2.801 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2297 time to fit residues: 12.1919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 4 optimal weight: 0.4980 chunk 205 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 chunk 190 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 chunk 247 optimal weight: 20.0000 chunk 69 optimal weight: 0.0670 overall best weight: 1.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 168 ASN ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23807 Z= 0.188 Angle : 0.631 8.484 32248 Z= 0.323 Chirality : 0.044 0.223 3647 Planarity : 0.003 0.050 4109 Dihedral : 5.741 59.997 3132 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 1.08 % Allowed : 19.95 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.16), residues: 2851 helix: -0.10 (0.17), residues: 1001 sheet: -0.84 (0.23), residues: 529 loop : -1.86 (0.17), residues: 1321 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 222 time to evaluate : 3.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 243 average time/residue: 0.3365 time to fit residues: 133.8165 Evaluate side-chains 214 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 202 time to evaluate : 3.013 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2316 time to fit residues: 8.8857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 275 optimal weight: 30.0000 chunk 228 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 144 optimal weight: 20.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 GLN ** N 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 23807 Z= 0.323 Angle : 0.704 11.772 32248 Z= 0.362 Chirality : 0.045 0.209 3647 Planarity : 0.004 0.061 4109 Dihedral : 5.945 55.993 3132 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 1.74 % Allowed : 21.27 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.16), residues: 2851 helix: -0.14 (0.17), residues: 1001 sheet: -0.95 (0.23), residues: 527 loop : -1.91 (0.17), residues: 1323 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 205 time to evaluate : 3.460 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 22 residues processed: 231 average time/residue: 0.3361 time to fit residues: 127.2611 Evaluate side-chains 220 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 198 time to evaluate : 3.620 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2228 time to fit residues: 12.8170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 157 optimal weight: 9.9990 chunk 201 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 232 optimal weight: 0.0570 chunk 153 optimal weight: 0.9990 chunk 274 optimal weight: 40.0000 chunk 171 optimal weight: 10.0000 chunk 167 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 205 HIS B 226 ASN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23807 Z= 0.173 Angle : 0.644 11.778 32248 Z= 0.325 Chirality : 0.044 0.290 3647 Planarity : 0.003 0.057 4109 Dihedral : 5.611 57.623 3132 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 1.00 % Allowed : 21.57 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.16), residues: 2851 helix: 0.07 (0.17), residues: 994 sheet: -0.83 (0.23), residues: 527 loop : -1.78 (0.17), residues: 1330 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 234 time to evaluate : 3.127 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 249 average time/residue: 0.3475 time to fit residues: 142.3282 Evaluate side-chains 217 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 206 time to evaluate : 2.671 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2400 time to fit residues: 8.4199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 8.9990 chunk 109 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 174 optimal weight: 0.0870 chunk 187 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 215 optimal weight: 10.0000 chunk 249 optimal weight: 2.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 383 HIS ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 87 GLN ** N 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 23807 Z= 0.161 Angle : 0.661 11.822 32248 Z= 0.332 Chirality : 0.045 0.280 3647 Planarity : 0.003 0.055 4109 Dihedral : 5.443 58.863 3132 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.69 % Allowed : 22.73 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.16), residues: 2851 helix: 0.12 (0.17), residues: 991 sheet: -0.81 (0.23), residues: 520 loop : -1.70 (0.17), residues: 1340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 234 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 246 average time/residue: 0.3453 time to fit residues: 138.9263 Evaluate side-chains 215 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 209 time to evaluate : 3.282 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2491 time to fit residues: 6.6578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 10.0000 chunk 240 optimal weight: 9.9990 chunk 255 optimal weight: 4.9990 chunk 154 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 78 optimal weight: 0.5980 chunk 231 optimal weight: 9.9990 chunk 242 optimal weight: 9.9990 chunk 168 optimal weight: 0.0870 chunk 270 optimal weight: 1.9990 overall best weight: 2.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 GLN N 59 ASN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23807 Z= 0.237 Angle : 0.675 10.942 32248 Z= 0.342 Chirality : 0.045 0.251 3647 Planarity : 0.004 0.059 4109 Dihedral : 5.490 55.093 3132 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 0.62 % Allowed : 23.47 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.16), residues: 2851 helix: 0.09 (0.17), residues: 994 sheet: -0.87 (0.23), residues: 526 loop : -1.72 (0.18), residues: 1331 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 218 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 227 average time/residue: 0.3429 time to fit residues: 128.2482 Evaluate side-chains 217 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 210 time to evaluate : 2.794 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2288 time to fit residues: 6.8349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 chunk 188 optimal weight: 4.9990 chunk 283 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 226 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 179 optimal weight: 0.9990 chunk 240 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 GLN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23807 Z= 0.239 Angle : 0.687 10.796 32248 Z= 0.348 Chirality : 0.045 0.250 3647 Planarity : 0.004 0.059 4109 Dihedral : 5.543 54.405 3132 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.54 % Allowed : 23.58 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.16), residues: 2851 helix: 0.08 (0.17), residues: 996 sheet: -0.91 (0.23), residues: 529 loop : -1.75 (0.18), residues: 1326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5702 Ramachandran restraints generated. 2851 Oldfield, 0 Emsley, 2851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 219 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 227 average time/residue: 0.3690 time to fit residues: 137.3641 Evaluate side-chains 218 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 208 time to evaluate : 2.918 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2377 time to fit residues: 8.2044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 226 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 232 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.0670 chunk 198 optimal weight: 6.9990 chunk 12 optimal weight: 0.0470 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 205 HIS ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.092814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.073082 restraints weight = 109761.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.071988 restraints weight = 70239.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.072703 restraints weight = 53814.013| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23807 Z= 0.167 Angle : 0.667 11.780 32248 Z= 0.333 Chirality : 0.045 0.254 3647 Planarity : 0.003 0.054 4109 Dihedral : 5.334 56.983 3132 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.19 % Allowed : 23.89 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.16), residues: 2851 helix: 0.16 (0.17), residues: 997 sheet: -0.85 (0.23), residues: 529 loop : -1.66 (0.18), residues: 1325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4268.34 seconds wall clock time: 79 minutes 49.16 seconds (4789.16 seconds total)