Starting phenix.real_space_refine on Mon Feb 19 01:04:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3a_25652/02_2024/7t3a_25652_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3a_25652/02_2024/7t3a_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_25652/02_2024/7t3a_25652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3a_25652/02_2024/7t3a_25652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3a_25652/02_2024/7t3a_25652_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3a_25652/02_2024/7t3a_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-dev-5238/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: 11.98, 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: 8.55 Conformation dependent library (CDL) restraints added in 4.1 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: 5.09 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: 7.72 Time building geometry restraints manager: 9.27 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: 12477 17.39 - 34.78: 1542 34.78 - 52.18: 260 52.18 - 69.57: 54 69.57 - 86.96: 26 Dihedral angle restraints: 14359 sinusoidal: 5830 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 14356 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: 3.840 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: 18.770 Check model and map are aligned: 0.370 Set scattering table: 0.210 Process input model: 59.450 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.190 ------------------------------------------------------------------------------- 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 : 15.610 86.959 8808 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP M 102 HIS 0.017 0.002 HIS A1375 PHE 0.060 0.003 PHE B 282 TYR 0.034 0.003 TYR B 351 ARG 0.018 0.001 ARG L 193 *********************** 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 : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8596 (pmm) cc_final: 0.8258 (pmm) REVERT: B 255 VAL cc_start: 0.8637 (t) cc_final: 0.8220 (p) REVERT: B 319 MET cc_start: 0.8309 (mmp) cc_final: 0.8098 (mmm) REVERT: B 329 TYR cc_start: 0.7799 (m-80) cc_final: 0.7554 (m-80) REVERT: B 360 MET cc_start: 0.8202 (tpt) cc_final: 0.7965 (tpp) REVERT: C 79 MET cc_start: 0.8424 (mpp) cc_final: 0.8080 (mpp) REVERT: C 89 ASP cc_start: 0.8292 (p0) cc_final: 0.7842 (m-30) REVERT: C 90 ASN cc_start: 0.8696 (p0) cc_final: 0.8394 (p0) REVERT: C 308 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8291 (tm-30) REVERT: C 368 PHE cc_start: 0.9245 (m-80) cc_final: 0.9043 (m-80) REVERT: K 139 LEU cc_start: 0.9398 (tt) cc_final: 0.9172 (mm) REVERT: K 273 MET cc_start: 0.9160 (tpt) cc_final: 0.8936 (tpt) REVERT: L 67 MET cc_start: 0.2687 (pmm) cc_final: 0.2263 (pmm) REVERT: L 192 GLN cc_start: 0.8921 (pp30) cc_final: 0.8491 (pp30) REVERT: L 288 MET cc_start: 0.9142 (tmm) cc_final: 0.8851 (tmm) REVERT: L 294 ASP cc_start: 0.8419 (p0) cc_final: 0.8197 (p0) REVERT: M 88 TYR cc_start: 0.7918 (m-10) cc_final: 0.7584 (m-80) REVERT: O 79 GLN cc_start: 0.7763 (mp10) cc_final: 0.7238 (mp10) REVERT: O 109 GLU cc_start: 0.8549 (tp30) cc_final: 0.7891 (pt0) REVERT: Q 24 THR cc_start: 0.7129 (t) cc_final: 0.6707 (t) REVERT: Q 37 LEU cc_start: 0.6536 (mt) cc_final: 0.6327 (mt) outliers start: 1 outliers final: 1 residues processed: 318 average time/residue: 0.3425 time to fit residues: 172.3615 Evaluate side-chains 229 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 30 ASN 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: 10.0000 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: 0.4980 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN ** A 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 GLN ** 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** Q 7 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 23807 Z= 0.313 Angle : 0.722 11.117 32248 Z= 0.377 Chirality : 0.046 0.204 3647 Planarity : 0.005 0.058 4109 Dihedral : 6.913 54.743 3162 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.52 % Favored : 91.41 % Rotamer: Outliers : 1.16 % Allowed : 10.11 % Favored : 88.73 % 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: -2.22 (0.15), residues: 2851 helix: -0.85 (0.15), residues: 1000 sheet: -1.25 (0.23), residues: 518 loop : -2.01 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 379 HIS 0.008 0.001 HIS Q 79 PHE 0.022 0.002 PHE B 282 TYR 0.028 0.002 TYR L 299 ARG 0.005 0.000 ARG A 422 *********************** 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 268 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 238 time to evaluate : 2.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8768 (pmm) cc_final: 0.8224 (pmm) REVERT: A 780 GLU cc_start: 0.7691 (tp30) cc_final: 0.7414 (tp30) REVERT: A 856 MET cc_start: 0.8396 (tmm) cc_final: 0.8120 (tmm) REVERT: A 915 GLU cc_start: 0.8677 (tp30) cc_final: 0.8476 (tp30) REVERT: A 979 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7894 (pm20) REVERT: A 1385 GLU cc_start: 0.8894 (pp20) cc_final: 0.8688 (pp20) REVERT: B 182 GLU cc_start: 0.8688 (pp20) cc_final: 0.8457 (pp20) REVERT: B 208 LYS cc_start: 0.5017 (OUTLIER) cc_final: 0.4387 (tttt) REVERT: B 321 ASN cc_start: 0.8641 (t0) cc_final: 0.8418 (t0) REVERT: B 323 ILE cc_start: 0.9362 (mm) cc_final: 0.8886 (tp) REVERT: C 79 MET cc_start: 0.8432 (mpp) cc_final: 0.8144 (mpp) REVERT: C 312 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8900 (pt) REVERT: C 368 PHE cc_start: 0.9315 (m-80) cc_final: 0.9052 (m-80) REVERT: C 393 MET cc_start: 0.9117 (mmp) cc_final: 0.8765 (mmm) REVERT: C 397 MET cc_start: 0.9388 (mpp) cc_final: 0.9169 (mpp) REVERT: L 67 MET cc_start: 0.2518 (pmm) cc_final: 0.2243 (pmm) REVERT: L 132 MET cc_start: 0.8123 (ttt) cc_final: 0.7795 (tpp) REVERT: L 288 MET cc_start: 0.9127 (tmm) cc_final: 0.8798 (tmm) REVERT: M 88 TYR cc_start: 0.7939 (m-10) cc_final: 0.7712 (m-80) REVERT: O 109 GLU cc_start: 0.8554 (tp30) cc_final: 0.7979 (pt0) REVERT: Q 37 LEU cc_start: 0.6546 (mt) cc_final: 0.6344 (mt) outliers start: 30 outliers final: 20 residues processed: 250 average time/residue: 0.3573 time to fit residues: 147.2518 Evaluate side-chains 234 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 211 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 898 ASP Chi-restraints excluded: chain A residue 979 GLU Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 289 ILE Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 5 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 259 optimal weight: 20.0000 chunk 280 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 208 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 205 HIS L 192 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 23807 Z= 0.370 Angle : 0.735 9.749 32248 Z= 0.383 Chirality : 0.046 0.242 3647 Planarity : 0.004 0.051 4109 Dihedral : 6.542 56.111 3160 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.54 % Favored : 90.39 % Rotamer: Outliers : 2.32 % Allowed : 15.67 % Favored : 82.01 % 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: -1.98 (0.16), residues: 2851 helix: -0.50 (0.16), residues: 1000 sheet: -1.15 (0.23), residues: 528 loop : -2.00 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 379 HIS 0.010 0.001 HIS A 896 PHE 0.026 0.002 PHE B 11 TYR 0.030 0.002 TYR L 299 ARG 0.005 0.001 ARG A 422 *********************** 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 281 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 221 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 856 MET cc_start: 0.8574 (tmm) cc_final: 0.8244 (tmm) REVERT: B 182 GLU cc_start: 0.8793 (pp20) cc_final: 0.8555 (pp20) REVERT: B 208 LYS cc_start: 0.5069 (OUTLIER) cc_final: 0.4316 (tttt) REVERT: B 319 MET cc_start: 0.8073 (mmp) cc_final: 0.7715 (mmm) REVERT: C 79 MET cc_start: 0.8406 (mpp) cc_final: 0.8196 (mpp) REVERT: C 312 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9026 (pt) REVERT: C 368 PHE cc_start: 0.9363 (m-80) cc_final: 0.9100 (m-80) REVERT: L 288 MET cc_start: 0.9118 (tmm) cc_final: 0.8797 (tmm) REVERT: M 88 TYR cc_start: 0.7903 (m-10) cc_final: 0.7652 (m-80) REVERT: O 79 GLN cc_start: 0.7867 (mp10) cc_final: 0.7180 (mp10) outliers start: 60 outliers final: 37 residues processed: 257 average time/residue: 0.3268 time to fit residues: 137.4663 Evaluate side-chains 245 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 206 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 979 GLU Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 183 ASN Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 289 ILE Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 306 SER Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 28 optimal weight: 0.0970 chunk 123 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 260 optimal weight: 0.3980 chunk 275 optimal weight: 40.0000 chunk 135 optimal weight: 0.7980 chunk 246 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.8582 ------------------------------------------------------------------------------- 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 ** A 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN A1375 HIS ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS L 192 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23807 Z= 0.203 Angle : 0.644 10.283 32248 Z= 0.332 Chirality : 0.044 0.206 3647 Planarity : 0.004 0.054 4109 Dihedral : 6.043 57.387 3160 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.24 % Favored : 91.72 % Rotamer: Outliers : 1.97 % Allowed : 18.26 % Favored : 79.78 % 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: -1.71 (0.16), residues: 2851 helix: -0.24 (0.16), residues: 1006 sheet: -0.96 (0.23), residues: 522 loop : -1.89 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 379 HIS 0.013 0.001 HIS A1375 PHE 0.016 0.001 PHE K 206 TYR 0.019 0.001 TYR A 775 ARG 0.004 0.000 ARG A 422 *********************** 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 284 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 233 time to evaluate : 4.108 Fit side-chains revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8151 (t0) cc_final: 0.7877 (t0) REVERT: A 856 MET cc_start: 0.8481 (tmm) cc_final: 0.8125 (tmm) REVERT: A 1553 MET cc_start: 0.8301 (ptm) cc_final: 0.8012 (ptp) REVERT: B 182 GLU cc_start: 0.8757 (pp20) cc_final: 0.8538 (pp20) REVERT: B 226 ASN cc_start: 0.8615 (t0) cc_final: 0.8272 (t0) REVERT: B 319 MET cc_start: 0.8161 (mmp) cc_final: 0.7782 (mmm) REVERT: B 321 ASN cc_start: 0.8774 (t0) cc_final: 0.8435 (t0) REVERT: B 323 ILE cc_start: 0.9334 (mm) cc_final: 0.8918 (tp) REVERT: C 73 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9046 (mm) REVERT: C 79 MET cc_start: 0.8480 (mpp) cc_final: 0.8074 (mpp) REVERT: C 312 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.9006 (pt) REVERT: C 368 PHE cc_start: 0.9354 (m-80) cc_final: 0.9030 (m-80) REVERT: C 397 MET cc_start: 0.9394 (mpp) cc_final: 0.9142 (mpp) REVERT: K 110 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9324 (tt) REVERT: L 288 MET cc_start: 0.9096 (tmm) cc_final: 0.8797 (tmm) REVERT: M 88 TYR cc_start: 0.7840 (m-10) cc_final: 0.7611 (m-80) REVERT: M 99 LEU cc_start: 0.4742 (OUTLIER) cc_final: 0.4413 (tt) REVERT: O 79 GLN cc_start: 0.7769 (mp10) cc_final: 0.7119 (mp10) REVERT: O 109 GLU cc_start: 0.8629 (tp30) cc_final: 0.8060 (tt0) outliers start: 51 outliers final: 34 residues processed: 267 average time/residue: 0.3373 time to fit residues: 148.0377 Evaluate side-chains 243 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 205 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 898 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1356 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 235 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 247 optimal weight: 30.0000 chunk 69 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS L 192 GLN ** 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 ** 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: 0.8213 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23807 Z= 0.190 Angle : 0.621 8.842 32248 Z= 0.317 Chirality : 0.044 0.199 3647 Planarity : 0.003 0.050 4109 Dihedral : 5.766 57.962 3160 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 2.39 % Allowed : 19.64 % Favored : 77.96 % 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: -1.55 (0.16), residues: 2851 helix: -0.06 (0.17), residues: 1004 sheet: -0.87 (0.23), residues: 520 loop : -1.84 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 379 HIS 0.007 0.001 HIS K 47 PHE 0.020 0.001 PHE B 177 TYR 0.016 0.001 TYR A 775 ARG 0.003 0.000 ARG A 263 *********************** 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 290 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 228 time to evaluate : 3.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8811 (pmm) cc_final: 0.8332 (pmm) REVERT: A 180 GLU cc_start: 0.8354 (mp0) cc_final: 0.7859 (mp0) REVERT: A 856 MET cc_start: 0.8482 (tmm) cc_final: 0.8107 (tmm) REVERT: A 1465 TYR cc_start: 0.7027 (m-80) cc_final: 0.6408 (t80) REVERT: A 1553 MET cc_start: 0.8283 (ptm) cc_final: 0.7981 (ptp) REVERT: B 182 GLU cc_start: 0.8771 (pp20) cc_final: 0.8539 (pp20) REVERT: B 226 ASN cc_start: 0.8574 (t0) cc_final: 0.8197 (t0) REVERT: B 319 MET cc_start: 0.8167 (mmp) cc_final: 0.7790 (mmm) REVERT: B 323 ILE cc_start: 0.9340 (mm) cc_final: 0.9015 (tp) REVERT: C 73 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9037 (mm) REVERT: C 79 MET cc_start: 0.8478 (mpp) cc_final: 0.8086 (mpp) REVERT: C 312 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9013 (pt) REVERT: C 368 PHE cc_start: 0.9365 (m-80) cc_final: 0.9040 (m-80) REVERT: K 13 MET cc_start: 0.9141 (mmm) cc_final: 0.8905 (mmm) REVERT: K 110 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9315 (tt) REVERT: K 129 MET cc_start: 0.8603 (pmm) cc_final: 0.8302 (pmm) REVERT: K 168 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8354 (p) REVERT: L 67 MET cc_start: 0.2322 (pmm) cc_final: 0.1988 (pmm) REVERT: L 171 MET cc_start: 0.8295 (tmm) cc_final: 0.7636 (tmm) REVERT: L 288 MET cc_start: 0.9053 (tmm) cc_final: 0.8799 (tmm) REVERT: M 88 TYR cc_start: 0.7860 (m-10) cc_final: 0.7632 (m-80) REVERT: M 134 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.6458 (pmt-80) REVERT: N 37 TYR cc_start: 0.5095 (p90) cc_final: 0.4890 (p90) REVERT: O 79 GLN cc_start: 0.7744 (mp10) cc_final: 0.7513 (mp10) REVERT: O 109 GLU cc_start: 0.8623 (tp30) cc_final: 0.8042 (tt0) outliers start: 62 outliers final: 41 residues processed: 271 average time/residue: 0.3310 time to fit residues: 145.8952 Evaluate side-chains 255 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 209 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 898 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 183 ASN Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 13 MET Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 60 THR 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: 9.9990 chunk 54 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 68 optimal weight: 0.0870 chunk 275 optimal weight: 30.0000 chunk 228 optimal weight: 8.9990 chunk 127 optimal weight: 0.0270 chunk 22 optimal weight: 3.9990 chunk 91 optimal weight: 0.0980 chunk 144 optimal weight: 5.9990 overall best weight: 0.8218 ------------------------------------------------------------------------------- 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 ** A 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1375 HIS ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS C 407 HIS ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 GLN ** N 59 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 23807 Z= 0.151 Angle : 0.616 11.637 32248 Z= 0.311 Chirality : 0.044 0.277 3647 Planarity : 0.003 0.053 4109 Dihedral : 5.468 55.000 3160 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.32 % Allowed : 20.61 % Favored : 77.07 % 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: -1.41 (0.16), residues: 2851 helix: 0.06 (0.17), residues: 1003 sheet: -0.85 (0.23), residues: 524 loop : -1.73 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 102 HIS 0.005 0.001 HIS Q 79 PHE 0.013 0.001 PHE K 206 TYR 0.017 0.001 TYR A 775 ARG 0.002 0.000 ARG A 263 *********************** 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 298 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 238 time to evaluate : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 856 MET cc_start: 0.8413 (tmm) cc_final: 0.8046 (tmm) REVERT: A 991 GLU cc_start: 0.8393 (pp20) cc_final: 0.7991 (pp20) REVERT: A 1553 MET cc_start: 0.8207 (ptm) cc_final: 0.7979 (ptt) REVERT: B 182 GLU cc_start: 0.8758 (pp20) cc_final: 0.8530 (pp20) REVERT: B 226 ASN cc_start: 0.8547 (t0) cc_final: 0.8193 (t0) REVERT: B 319 MET cc_start: 0.8234 (mmp) cc_final: 0.7858 (mmm) REVERT: B 321 ASN cc_start: 0.8800 (t0) cc_final: 0.8396 (t0) REVERT: C 79 MET cc_start: 0.8474 (mpp) cc_final: 0.8100 (mpp) REVERT: C 312 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9011 (pt) REVERT: C 368 PHE cc_start: 0.9362 (m-80) cc_final: 0.9013 (m-80) REVERT: K 13 MET cc_start: 0.9102 (mmm) cc_final: 0.8860 (mmm) REVERT: K 23 MET cc_start: 0.8768 (ptp) cc_final: 0.8447 (mtt) REVERT: K 110 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9327 (tt) REVERT: K 129 MET cc_start: 0.8454 (pmm) cc_final: 0.8240 (pmm) REVERT: K 168 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.8347 (p) REVERT: L 130 TYR cc_start: 0.2750 (p90) cc_final: 0.1674 (m-10) REVERT: L 288 MET cc_start: 0.9028 (tmm) cc_final: 0.8776 (tmm) REVERT: M 88 TYR cc_start: 0.7811 (m-10) cc_final: 0.7601 (m-80) REVERT: M 134 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6486 (pmt-80) REVERT: O 79 GLN cc_start: 0.7670 (mp10) cc_final: 0.7446 (mp10) REVERT: O 109 GLU cc_start: 0.8605 (tp30) cc_final: 0.8022 (tt0) outliers start: 60 outliers final: 37 residues processed: 285 average time/residue: 0.3138 time to fit residues: 147.0467 Evaluate side-chains 256 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 215 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 898 ASP Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 183 ASN Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain Q residue 13 MET Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 201 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 232 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 274 optimal weight: 40.0000 chunk 171 optimal weight: 9.9990 chunk 167 optimal weight: 20.0000 chunk 126 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS B 252 GLN ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 524 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 250 GLN ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 ASN ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.140 23807 Z= 0.442 Angle : 0.782 9.641 32248 Z= 0.405 Chirality : 0.047 0.248 3647 Planarity : 0.004 0.066 4109 Dihedral : 6.157 58.853 3160 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 3.59 % Allowed : 21.42 % Favored : 74.99 % 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: -1.67 (0.16), residues: 2851 helix: -0.17 (0.16), residues: 994 sheet: -1.08 (0.23), residues: 535 loop : -1.81 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1548 HIS 0.007 0.001 HIS A 32 PHE 0.030 0.002 PHE A 802 TYR 0.019 0.002 TYR B 230 ARG 0.007 0.001 ARG A 958 *********************** 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 303 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 210 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 808 MET cc_start: 0.9358 (OUTLIER) cc_final: 0.9110 (tpp) REVERT: A 856 MET cc_start: 0.8626 (tmm) cc_final: 0.8350 (tmm) REVERT: A 1465 TYR cc_start: 0.6911 (m-80) cc_final: 0.6426 (t80) REVERT: A 1553 MET cc_start: 0.8391 (ptm) cc_final: 0.7979 (ptp) REVERT: B 208 LYS cc_start: 0.5243 (OUTLIER) cc_final: 0.4262 (tttt) REVERT: B 319 MET cc_start: 0.8297 (mmp) cc_final: 0.7836 (mmm) REVERT: C 79 MET cc_start: 0.8455 (mpp) cc_final: 0.8099 (mpp) REVERT: K 110 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9324 (tt) REVERT: K 129 MET cc_start: 0.8795 (pmm) cc_final: 0.8576 (pmm) REVERT: K 250 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8385 (pp30) REVERT: L 69 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8036 (mt) REVERT: L 171 MET cc_start: 0.8227 (tmm) cc_final: 0.7887 (tmm) REVERT: L 288 MET cc_start: 0.9028 (tmm) cc_final: 0.8819 (tmm) REVERT: M 88 TYR cc_start: 0.7952 (m-10) cc_final: 0.7688 (m-80) REVERT: M 134 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.6476 (pmt-80) REVERT: O 79 GLN cc_start: 0.7893 (mp10) cc_final: 0.7650 (mp10) outliers start: 93 outliers final: 60 residues processed: 284 average time/residue: 0.3125 time to fit residues: 146.0515 Evaluate side-chains 265 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 199 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 898 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1385 GLU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 183 ASN Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 250 GLN Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 226 PHE Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 289 ILE Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 306 SER Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 249 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1232 GLN ** 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 L 168 ASN ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23807 Z= 0.185 Angle : 0.660 12.346 32248 Z= 0.334 Chirality : 0.045 0.293 3647 Planarity : 0.003 0.057 4109 Dihedral : 5.703 55.473 3160 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.72 % Favored : 92.25 % Rotamer: Outliers : 2.66 % Allowed : 22.46 % Favored : 74.87 % 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: 0.07 (0.17), residues: 1002 sheet: -0.91 (0.23), residues: 524 loop : -1.69 (0.18), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 102 HIS 0.005 0.001 HIS K 47 PHE 0.020 0.001 PHE A1482 TYR 0.021 0.001 TYR B 230 ARG 0.004 0.000 ARG A 422 *********************** 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 294 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 225 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8773 (pmm) cc_final: 0.8251 (pmm) REVERT: A 856 MET cc_start: 0.8464 (tmm) cc_final: 0.8054 (tmm) REVERT: A 991 GLU cc_start: 0.8423 (pp20) cc_final: 0.8018 (pp20) REVERT: A 1465 TYR cc_start: 0.6719 (m-80) cc_final: 0.6317 (t80) REVERT: A 1553 MET cc_start: 0.8271 (ptm) cc_final: 0.7989 (ptp) REVERT: B 226 ASN cc_start: 0.8576 (t0) cc_final: 0.8140 (t0) REVERT: B 319 MET cc_start: 0.8295 (mmp) cc_final: 0.7849 (mmm) REVERT: B 323 ILE cc_start: 0.9273 (tp) cc_final: 0.8965 (tp) REVERT: C 79 MET cc_start: 0.8473 (mpp) cc_final: 0.8150 (mpp) REVERT: K 13 MET cc_start: 0.9066 (mmm) cc_final: 0.8815 (mmm) REVERT: K 110 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9301 (tt) REVERT: K 129 MET cc_start: 0.8610 (pmm) cc_final: 0.8353 (pmm) REVERT: K 168 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8367 (p) REVERT: L 67 MET cc_start: 0.3337 (pmm) cc_final: 0.2811 (pmm) REVERT: L 69 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.7875 (mt) REVERT: L 130 TYR cc_start: 0.2822 (p90) cc_final: 0.1673 (m-10) REVERT: L 171 MET cc_start: 0.8229 (tmm) cc_final: 0.7113 (tmm) REVERT: L 279 MET cc_start: 0.7026 (ptp) cc_final: 0.6795 (pmm) REVERT: M 88 TYR cc_start: 0.7837 (m-10) cc_final: 0.7603 (m-80) REVERT: M 134 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6524 (pmt-80) REVERT: O 109 GLU cc_start: 0.8635 (tp30) cc_final: 0.8081 (tt0) outliers start: 69 outliers final: 56 residues processed: 278 average time/residue: 0.3148 time to fit residues: 143.7095 Evaluate side-chains 266 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 206 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 898 ASP Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1354 VAL Chi-restraints excluded: chain A residue 1385 GLU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 183 ASN Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 226 PHE Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 306 SER Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain L residue 340 ILE Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 13 MET Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 9.9990 chunk 240 optimal weight: 20.0000 chunk 255 optimal weight: 0.9990 chunk 154 optimal weight: 20.0000 chunk 111 optimal weight: 0.9980 chunk 201 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 231 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 chunk 168 optimal weight: 0.6980 chunk 270 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1232 GLN ** 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 K 250 GLN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23807 Z= 0.194 Angle : 0.670 17.104 32248 Z= 0.336 Chirality : 0.045 0.280 3647 Planarity : 0.003 0.056 4109 Dihedral : 5.553 58.220 3160 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 2.62 % Allowed : 23.16 % Favored : 74.22 % 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: 0.07 (0.17), residues: 997 sheet: -0.90 (0.23), residues: 519 loop : -1.70 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M 102 HIS 0.005 0.001 HIS Q 79 PHE 0.028 0.001 PHE B 282 TYR 0.020 0.001 TYR A 775 ARG 0.006 0.000 ARG A 422 *********************** 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 288 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 220 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8794 (pmm) cc_final: 0.8269 (pmm) REVERT: A 856 MET cc_start: 0.8452 (tmm) cc_final: 0.8023 (tmm) REVERT: A 991 GLU cc_start: 0.8419 (pp20) cc_final: 0.7912 (pp20) REVERT: A 1391 MET cc_start: 0.8304 (tpt) cc_final: 0.8072 (tpt) REVERT: A 1465 TYR cc_start: 0.6735 (m-80) cc_final: 0.6321 (t80) REVERT: A 1553 MET cc_start: 0.8289 (ptm) cc_final: 0.7996 (ptp) REVERT: B 78 ARG cc_start: 0.8339 (ptt-90) cc_final: 0.8053 (ptt-90) REVERT: B 319 MET cc_start: 0.8352 (mmp) cc_final: 0.7885 (mmm) REVERT: B 323 ILE cc_start: 0.9288 (tp) cc_final: 0.8973 (tp) REVERT: C 79 MET cc_start: 0.8471 (mpp) cc_final: 0.8144 (mpp) REVERT: K 13 MET cc_start: 0.9071 (mmm) cc_final: 0.8801 (mmm) REVERT: K 110 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9309 (tt) REVERT: K 129 MET cc_start: 0.8558 (pmm) cc_final: 0.8314 (pmm) REVERT: K 168 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8415 (p) REVERT: K 250 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8626 (pp30) REVERT: L 67 MET cc_start: 0.3204 (pmm) cc_final: 0.2907 (pmm) REVERT: L 69 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.7847 (mt) REVERT: L 130 TYR cc_start: 0.2913 (p90) cc_final: 0.1759 (m-10) REVERT: L 171 MET cc_start: 0.8208 (tmm) cc_final: 0.7161 (tmm) REVERT: L 279 MET cc_start: 0.7031 (ptp) cc_final: 0.6773 (pmm) REVERT: L 288 MET cc_start: 0.8920 (tmm) cc_final: 0.8635 (tmm) REVERT: M 88 TYR cc_start: 0.7854 (m-10) cc_final: 0.7652 (m-80) REVERT: M 134 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6527 (pmt-80) REVERT: O 75 TYR cc_start: 0.8339 (m-80) cc_final: 0.8099 (m-80) REVERT: O 109 GLU cc_start: 0.8622 (tp30) cc_final: 0.8068 (tt0) outliers start: 68 outliers final: 56 residues processed: 272 average time/residue: 0.3137 time to fit residues: 140.4105 Evaluate side-chains 270 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 209 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 898 ASP Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1354 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 183 ASN Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 250 GLN Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 226 PHE Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain L residue 340 ILE Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 60 THR 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: 4.9990 chunk 188 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 226 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 138 optimal weight: 0.1980 chunk 179 optimal weight: 4.9990 chunk 240 optimal weight: 8.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- 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 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 250 GLN ** L 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2932 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= 0.305 Angle : 0.723 14.750 32248 Z= 0.367 Chirality : 0.045 0.274 3647 Planarity : 0.004 0.062 4109 Dihedral : 5.762 58.342 3160 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.61 % Favored : 90.35 % Rotamer: Outliers : 2.70 % Allowed : 23.16 % Favored : 74.14 % 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: -1.47 (0.16), residues: 2851 helix: 0.01 (0.17), residues: 998 sheet: -0.90 (0.24), residues: 518 loop : -1.75 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP M 102 HIS 0.005 0.001 HIS K 47 PHE 0.027 0.002 PHE B 177 TYR 0.020 0.002 TYR A 775 ARG 0.007 0.000 ARG A 422 ********************** 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 276 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 206 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 808 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.9088 (tpp) REVERT: A 856 MET cc_start: 0.8548 (tmm) cc_final: 0.8067 (tmm) REVERT: A 921 LEU cc_start: 0.9206 (tt) cc_final: 0.8980 (tp) REVERT: A 1231 MET cc_start: 0.8633 (tpp) cc_final: 0.8424 (tpp) REVERT: A 1375 HIS cc_start: 0.9210 (OUTLIER) cc_final: 0.8993 (m90) REVERT: A 1465 TYR cc_start: 0.6865 (m-80) cc_final: 0.6380 (t80) REVERT: A 1553 MET cc_start: 0.8308 (ptm) cc_final: 0.7955 (ptp) REVERT: B 78 ARG cc_start: 0.8370 (ptt-90) cc_final: 0.8081 (ptt-90) REVERT: B 208 LYS cc_start: 0.5277 (OUTLIER) cc_final: 0.4353 (tttt) REVERT: B 319 MET cc_start: 0.8304 (mmp) cc_final: 0.7817 (mmm) REVERT: B 323 ILE cc_start: 0.9342 (tp) cc_final: 0.9032 (tp) REVERT: C 79 MET cc_start: 0.8460 (mpp) cc_final: 0.8131 (mpp) REVERT: K 13 MET cc_start: 0.9111 (mmm) cc_final: 0.8860 (mmm) REVERT: K 110 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9309 (tt) REVERT: K 129 MET cc_start: 0.8667 (pmm) cc_final: 0.8381 (pmm) REVERT: K 168 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8531 (p) REVERT: L 67 MET cc_start: 0.3230 (pmm) cc_final: 0.3003 (pmm) REVERT: L 69 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.7907 (mt) REVERT: L 130 TYR cc_start: 0.2973 (p90) cc_final: 0.1805 (m-10) REVERT: L 279 MET cc_start: 0.7137 (ptp) cc_final: 0.6861 (pmm) REVERT: L 288 MET cc_start: 0.8931 (tmm) cc_final: 0.8655 (tmm) REVERT: M 88 TYR cc_start: 0.7905 (m-10) cc_final: 0.7691 (m-80) REVERT: M 134 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6549 (pmt-80) REVERT: O 75 TYR cc_start: 0.8515 (m-80) cc_final: 0.8225 (m-80) REVERT: Q 37 LEU cc_start: 0.5875 (mt) cc_final: 0.5671 (mt) outliers start: 70 outliers final: 52 residues processed: 261 average time/residue: 0.3174 time to fit residues: 135.6617 Evaluate side-chains 262 residues out of total 2592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 203 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 898 ASP Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1354 VAL Chi-restraints excluded: chain A residue 1375 HIS Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 124 CYS Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 183 ASN Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 226 PHE Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 290 ASP Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain L residue 340 ILE Chi-restraints excluded: chain M residue 57 ILE Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 60 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 5.9990 chunk 208 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 226 optimal weight: 7.9990 chunk 94 optimal weight: 0.0570 chunk 232 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.0370 chunk 198 optimal weight: 0.9990 chunk 12 optimal weight: 0.0060 overall best weight: 0.2392 ------------------------------------------------------------------------------- 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 383 HIS ** A 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1232 GLN ** 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 195 GLN B 205 HIS K 250 GLN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.093379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.074026 restraints weight = 110398.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.072687 restraints weight = 71485.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.073354 restraints weight = 56573.441| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 23807 Z= 0.160 Angle : 0.679 16.500 32248 Z= 0.337 Chirality : 0.045 0.285 3647 Planarity : 0.003 0.052 4109 Dihedral : 5.328 55.045 3160 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.08 % Allowed : 23.77 % Favored : 74.14 % 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: -1.29 (0.16), residues: 2851 helix: 0.13 (0.17), residues: 1001 sheet: -0.84 (0.24), residues: 525 loop : -1.60 (0.18), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP M 102 HIS 0.006 0.001 HIS A1504 PHE 0.031 0.001 PHE B 282 TYR 0.014 0.001 TYR L 165 ARG 0.006 0.000 ARG L 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4453.03 seconds wall clock time: 83 minutes 4.28 seconds (4984.28 seconds total)