Starting phenix.real_space_refine on Sat Feb 17 20:10:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opl_13020/02_2024/7opl_13020_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opl_13020/02_2024/7opl_13020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opl_13020/02_2024/7opl_13020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opl_13020/02_2024/7opl_13020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opl_13020/02_2024/7opl_13020_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opl_13020/02_2024/7opl_13020_updated.pdb" } resolution = 4.12 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= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 3 6.06 5 S 105 5.16 5 C 12633 2.51 5 N 3352 2.21 5 O 3646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 524": "OD1" <-> "OD2" Residue "A PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 630": "OD1" <-> "OD2" Residue "A GLU 643": "OE1" <-> "OE2" Residue "A TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 871": "OE1" <-> "OE2" Residue "A PHE 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A GLU 1121": "OE1" <-> "OE2" Residue "A PHE 1296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1406": "OE1" <-> "OE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 390": "OE1" <-> "OE2" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 582": "OD1" <-> "OD2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "D TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 243": "OD1" <-> "OD2" Residue "D TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19743 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8641 Classifications: {'peptide': 1070} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1014} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3451 Classifications: {'peptide': 444} Modifications used: {'COO': 1} Link IDs: {'PCIS': 5, 'PTRANS': 26, 'TRANS': 412} Chain: "C" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3261 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 16, 'TRANS': 372} Chain breaks: 2 Chain: "D" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3562 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 20, 'TRANS': 413} Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7229 SG CYS A1283 112.373 17.705 58.207 1.00135.57 S ATOM 7249 SG CYS A1286 111.889 15.123 60.842 1.00147.72 S ATOM 7435 SG CYS A1310 113.695 18.494 61.673 1.00149.57 S ATOM 7471 SG CYS A1315 115.418 15.846 59.618 1.00171.25 S ATOM 7749 SG CYS A1348 83.298 50.604 69.806 1.00 90.83 S ATOM 7787 SG CYS A1353 80.639 47.930 70.287 1.00 93.60 S ATOM 7937 SG CYS A1371 80.342 50.706 67.461 1.00 91.47 S ATOM 7955 SG CYS A1374 79.873 51.104 71.398 1.00 94.18 S ATOM 13140 SG CYS C 121 125.948 135.610 55.829 1.00275.08 S ATOM 13146 SG CYS C 122 122.661 136.917 54.444 1.00275.04 S ATOM 13185 SG CYS C 128 125.718 137.241 52.329 1.00274.28 S ATOM 13207 SG CYS C 131 124.419 133.886 52.725 1.00274.93 S ATOM 18208 SG CYS D 367 118.684 61.213 83.318 1.00 94.23 S ATOM 18336 SG CYS D 384 117.254 67.057 87.000 1.00100.01 S ATOM 18652 SG CYS D 424 122.851 64.361 86.683 1.00114.38 S ATOM 17537 SG CYS D 287 117.830 61.835 89.046 1.00111.07 S Time building chain proxies: 10.35, per 1000 atoms: 0.52 Number of scatterers: 19743 At special positions: 0 Unit cell: (160.308, 153.738, 118.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 Fe 4 26.01 S 105 16.00 O 3646 8.00 N 3352 7.00 C 12633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 8.14 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 D 601 " pdb="FE3 SF4 D 601 " - pdb=" SG CYS D 424 " pdb="FE1 SF4 D 601 " - pdb=" SG CYS D 367 " pdb="FE2 SF4 D 601 " - pdb=" SG CYS D 384 " pdb="FE4 SF4 D 601 " - pdb=" SG CYS D 287 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1283 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1315 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1286 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1310 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A1353 " pdb="ZN ZN A1502 " - pdb=" SG CYS A1374 " pdb="ZN ZN A1502 " - pdb=" SG CYS A1348 " pdb="ZN ZN A1502 " - pdb=" SG CYS A1371 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 128 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 131 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 122 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 121 " Number of angles added : 18 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 17 sheets defined 41.0% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.41 Creating SS restraints... Processing helix chain 'A' and resid 410 through 425 removed outlier: 4.475A pdb=" N ALA A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 490 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 598 through 605 Processing helix chain 'A' and resid 615 through 629 Processing helix chain 'A' and resid 643 through 653 Processing helix chain 'A' and resid 659 through 662 removed outlier: 3.559A pdb=" N ILE A 662 " --> pdb=" O TRP A 659 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 659 through 662' Processing helix chain 'A' and resid 693 through 700 Processing helix chain 'A' and resid 708 through 714 Processing helix chain 'A' and resid 728 through 733 removed outlier: 4.558A pdb=" N SER A 733 " --> pdb=" O GLN A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 759 Processing helix chain 'A' and resid 761 through 772 Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 784 through 798 Processing helix chain 'A' and resid 864 through 872 Processing helix chain 'A' and resid 910 through 930 Processing helix chain 'A' and resid 936 through 960 removed outlier: 4.218A pdb=" N TYR A 957 " --> pdb=" O ALA A 953 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY A 958 " --> pdb=" O ASN A 954 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 960 " --> pdb=" O MET A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 993 Processing helix chain 'A' and resid 1015 through 1032 Processing helix chain 'A' and resid 1064 through 1066 No H-bonds generated for 'chain 'A' and resid 1064 through 1066' Processing helix chain 'A' and resid 1086 through 1099 Processing helix chain 'A' and resid 1105 through 1125 Processing helix chain 'A' and resid 1130 through 1133 Processing helix chain 'A' and resid 1143 through 1145 No H-bonds generated for 'chain 'A' and resid 1143 through 1145' Processing helix chain 'A' and resid 1153 through 1164 Processing helix chain 'A' and resid 1188 through 1191 Processing helix chain 'A' and resid 1195 through 1200 Processing helix chain 'A' and resid 1208 through 1214 Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 4.297A pdb=" N ILE A1223 " --> pdb=" O VAL A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1239 Processing helix chain 'A' and resid 1243 through 1248 Processing helix chain 'A' and resid 1269 through 1272 No H-bonds generated for 'chain 'A' and resid 1269 through 1272' Processing helix chain 'A' and resid 1300 through 1302 No H-bonds generated for 'chain 'A' and resid 1300 through 1302' Processing helix chain 'A' and resid 1306 through 1308 No H-bonds generated for 'chain 'A' and resid 1306 through 1308' Processing helix chain 'A' and resid 1319 through 1321 No H-bonds generated for 'chain 'A' and resid 1319 through 1321' Processing helix chain 'A' and resid 1323 through 1342 Processing helix chain 'A' and resid 1385 through 1398 Processing helix chain 'A' and resid 1401 through 1406 removed outlier: 3.858A pdb=" N GLU A1406 " --> pdb=" O GLU A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1420 Processing helix chain 'A' and resid 1424 through 1441 removed outlier: 3.899A pdb=" N ALA A1437 " --> pdb=" O LEU A1433 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE A1440 " --> pdb=" O THR A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1455 No H-bonds generated for 'chain 'A' and resid 1452 through 1455' Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 213 through 235 Processing helix chain 'B' and resid 276 through 279 No H-bonds generated for 'chain 'B' and resid 276 through 279' Processing helix chain 'B' and resid 332 through 335 No H-bonds generated for 'chain 'B' and resid 332 through 335' Processing helix chain 'B' and resid 358 through 370 Processing helix chain 'B' and resid 387 through 390 No H-bonds generated for 'chain 'B' and resid 387 through 390' Processing helix chain 'B' and resid 398 through 413 Processing helix chain 'B' and resid 447 through 452 Processing helix chain 'B' and resid 476 through 483 removed outlier: 4.026A pdb=" N GLU B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 504 Processing helix chain 'B' and resid 522 through 528 Processing helix chain 'C' and resid 6 through 19 removed outlier: 3.549A pdb=" N LEU C 9 " --> pdb=" O PRO C 6 " (cutoff:3.500A) Proline residue: C 10 - end of helix removed outlier: 4.565A pdb=" N LEU C 13 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR C 17 " --> pdb=" O LYS C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 34 removed outlier: 6.453A pdb=" N GLY C 33 " --> pdb=" O TRP C 29 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 52 No H-bonds generated for 'chain 'C' and resid 50 through 52' Processing helix chain 'C' and resid 63 through 73 removed outlier: 3.596A pdb=" N MET C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 93 removed outlier: 5.530A pdb=" N ASN C 92 " --> pdb=" O ASN C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 129 through 148 removed outlier: 4.822A pdb=" N THR C 133 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU C 134 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C 148 " --> pdb=" O ALA C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 179 through 188 Processing helix chain 'C' and resid 210 through 226 removed outlier: 4.323A pdb=" N LYS C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR C 222 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLU C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU C 225 " --> pdb=" O LYS C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 246 removed outlier: 3.887A pdb=" N LYS C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 261 removed outlier: 4.785A pdb=" N ASP C 253 " --> pdb=" O THR C 250 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 261 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 282 Processing helix chain 'C' and resid 292 through 301 removed outlier: 3.600A pdb=" N MET C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 311 Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 389 through 411 Processing helix chain 'D' and resid 39 through 62 Processing helix chain 'D' and resid 68 through 81 Processing helix chain 'D' and resid 89 through 110 removed outlier: 4.518A pdb=" N TYR D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU D 94 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Proline residue: D 95 - end of helix Processing helix chain 'D' and resid 114 through 134 Processing helix chain 'D' and resid 137 through 146 removed outlier: 4.449A pdb=" N GLN D 141 " --> pdb=" O LYS D 137 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP D 142 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 168 removed outlier: 5.053A pdb=" N GLN D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLU D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 197 removed outlier: 4.146A pdb=" N LEU D 192 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ASP D 193 " --> pdb=" O ASP D 190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG D 196 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY D 197 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 242 Proline residue: D 238 - end of helix removed outlier: 4.388A pdb=" N SER D 242 " --> pdb=" O PRO D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 250 Proline residue: D 248 - end of helix No H-bonds generated for 'chain 'D' and resid 244 through 250' Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.979A pdb=" N ASP D 277 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS D 282 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER D 283 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 298 Processing helix chain 'D' and resid 303 through 315 Processing helix chain 'D' and resid 320 through 332 Processing helix chain 'D' and resid 338 through 353 removed outlier: 4.728A pdb=" N TYR D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN D 348 " --> pdb=" O GLY D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 385 through 388 No H-bonds generated for 'chain 'D' and resid 385 through 388' Processing helix chain 'D' and resid 391 through 400 Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 420 through 431 Processing helix chain 'D' and resid 444 through 454 Processing helix chain 'E' and resid 23 through 25 No H-bonds generated for 'chain 'E' and resid 23 through 25' Processing helix chain 'E' and resid 35 through 48 removed outlier: 3.502A pdb=" N LEU E 39 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER E 40 " --> pdb=" O GLU E 36 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 63 No H-bonds generated for 'chain 'E' and resid 61 through 63' Processing sheet with id= A, first strand: chain 'A' and resid 526 through 528 removed outlier: 3.521A pdb=" N PHE A 341 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N HIS A 342 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP A 366 " --> pdb=" O HIS A 342 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE A 362 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ALA A 348 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE A 360 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 363 " --> pdb=" O CYS A 376 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 434 through 436 removed outlier: 3.519A pdb=" N VAL A 435 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLU A 451 " --> pdb=" O PRO A 391 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS A 475 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 690 through 692 removed outlier: 6.735A pdb=" N ILE A 634 " --> pdb=" O CYS A 691 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A 583 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 581 " --> pdb=" O VAL A 564 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 850 through 852 removed outlier: 3.767A pdb=" N LEU A1050 " --> pdb=" O LYS A1054 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LYS A1054 " --> pdb=" O LEU A1050 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA A1057 " --> pdb=" O GLU A1073 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU A1073 " --> pdb=" O ALA A1057 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A1061 " --> pdb=" O VAL A1069 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 856 through 859 removed outlier: 4.030A pdb=" N TYR A1000 " --> pdb=" O MET A1007 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN A1009 " --> pdb=" O VAL A 998 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL A 998 " --> pdb=" O ASN A1009 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1135 through 1138 Processing sheet with id= G, first strand: chain 'A' and resid 1279 through 1282 removed outlier: 3.520A pdb=" N TYR A1292 " --> pdb=" O PHE A1279 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1346 through 1348 Processing sheet with id= I, first strand: chain 'B' and resid 193 through 195 removed outlier: 7.071A pdb=" N VAL B 537 " --> pdb=" O GLY B 470 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR B 472 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE B 539 " --> pdb=" O THR B 472 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL B 555 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ILE B 540 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B 557 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE B 547 " --> pdb=" O ASN B 558 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 256 through 259 Processing sheet with id= K, first strand: chain 'B' and resid 453 through 456 removed outlier: 6.564A pdb=" N LEU B 420 " --> pdb=" O GLN B 454 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL B 456 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE B 422 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL B 374 " --> pdb=" O MET B 341 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 574 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 572 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N CYS B 346 " --> pdb=" O THR B 570 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N THR B 570 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 172 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG B 597 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL B 170 " --> pdb=" O ARG B 597 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 45 through 48 removed outlier: 3.620A pdb=" N LYS C 77 " --> pdb=" O THR C 48 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 109 through 111 removed outlier: 4.050A pdb=" N ILE C 110 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 165 " --> pdb=" O ILE C 110 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 184 through 187 removed outlier: 3.708A pdb=" N TYR D 184 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL D 209 " --> pdb=" O TYR D 184 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 14 through 19 removed outlier: 4.169A pdb=" N VAL E 14 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 51 through 55 Processing sheet with id= Q, first strand: chain 'E' and resid 70 through 73 713 hydrogen bonds defined for protein. 1977 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: 6.23 Time building geometry restraints manager: 8.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 8369 1.43 - 1.64: 11656 1.64 - 1.86: 146 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 20183 Sorted by residual: bond pdb=" N ILE D 371 " pdb=" CA ILE D 371 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 9.04e+00 bond pdb=" N LEU D 372 " pdb=" CA LEU D 372 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.33e-02 5.65e+03 8.55e+00 bond pdb=" CA SER D 366 " pdb=" CB SER D 366 " ideal model delta sigma weight residual 1.530 1.488 0.042 1.58e-02 4.01e+03 7.23e+00 bond pdb=" N CYS D 367 " pdb=" CA CYS D 367 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.62e+00 bond pdb=" C CYS D 367 " pdb=" O CYS D 367 " ideal model delta sigma weight residual 1.237 1.267 -0.030 1.17e-02 7.31e+03 6.62e+00 ... (remaining 20178 not shown) Histogram of bond angle deviations from ideal: 73.70 - 85.77: 12 85.77 - 97.84: 3 97.84 - 109.91: 2632 109.91 - 121.97: 20859 121.97 - 134.04: 3776 Bond angle restraints: 27282 Sorted by residual: angle pdb=" CA PRO C 333 " pdb=" N PRO C 333 " pdb=" CD PRO C 333 " ideal model delta sigma weight residual 112.00 104.35 7.65 1.40e+00 5.10e-01 2.98e+01 angle pdb=" CA PRO C 22 " pdb=" N PRO C 22 " pdb=" CD PRO C 22 " ideal model delta sigma weight residual 112.00 104.58 7.42 1.40e+00 5.10e-01 2.81e+01 angle pdb=" N PRO C 22 " pdb=" CD PRO C 22 " pdb=" CG PRO C 22 " ideal model delta sigma weight residual 103.20 95.83 7.37 1.50e+00 4.44e-01 2.42e+01 angle pdb=" CA SER D 366 " pdb=" C SER D 366 " pdb=" O SER D 366 " ideal model delta sigma weight residual 121.28 115.94 5.34 1.18e+00 7.18e-01 2.05e+01 angle pdb=" N VAL A 607 " pdb=" CA VAL A 607 " pdb=" C VAL A 607 " ideal model delta sigma weight residual 110.05 105.30 4.75 1.09e+00 8.42e-01 1.90e+01 ... (remaining 27277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 11110 18.00 - 35.99: 967 35.99 - 53.99: 165 53.99 - 71.99: 37 71.99 - 89.98: 26 Dihedral angle restraints: 12305 sinusoidal: 5137 harmonic: 7168 Sorted by residual: dihedral pdb=" CA GLU D 356 " pdb=" C GLU D 356 " pdb=" N GLY D 357 " pdb=" CA GLY D 357 " ideal model delta harmonic sigma weight residual -180.00 -150.07 -29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA SER A1444 " pdb=" C SER A1444 " pdb=" N GLY A1445 " pdb=" CA GLY A1445 " ideal model delta harmonic sigma weight residual 180.00 152.22 27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ASP A1242 " pdb=" C ASP A1242 " pdb=" N PRO A1243 " pdb=" CA PRO A1243 " ideal model delta harmonic sigma weight residual -180.00 -153.24 -26.76 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 12302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2726 0.082 - 0.165: 266 0.165 - 0.247: 7 0.247 - 0.330: 0 0.330 - 0.412: 1 Chirality restraints: 3000 Sorted by residual: chirality pdb=" CA CYS D 367 " pdb=" N CYS D 367 " pdb=" C CYS D 367 " pdb=" CB CYS D 367 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CB THR A1410 " pdb=" CA THR A1410 " pdb=" OG1 THR A1410 " pdb=" CG2 THR A1410 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA PRO B 199 " pdb=" N PRO B 199 " pdb=" C PRO B 199 " pdb=" CB PRO B 199 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2997 not shown) Planarity restraints: 3505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 332 " 0.090 5.00e-02 4.00e+02 1.32e-01 2.77e+01 pdb=" N PRO C 333 " -0.227 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 534 " 0.079 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO A 535 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 588 " -0.077 5.00e-02 4.00e+02 1.15e-01 2.10e+01 pdb=" N PRO B 589 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO B 589 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO B 589 " -0.062 5.00e-02 4.00e+02 ... (remaining 3502 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 423 2.67 - 3.23: 20426 3.23 - 3.79: 32306 3.79 - 4.34: 42351 4.34 - 4.90: 66518 Nonbonded interactions: 162024 Sorted by model distance: nonbonded pdb=" OH TYR A1383 " pdb=" OE1 GLN A1391 " model vdw 2.116 2.440 nonbonded pdb=" OE1 GLU D 57 " pdb=" NE1 TRP D 119 " model vdw 2.155 2.520 nonbonded pdb=" NE2 GLN B 211 " pdb=" OD1 ASP B 521 " model vdw 2.158 2.520 nonbonded pdb=" O ILE D 166 " pdb=" OG SER D 170 " model vdw 2.162 2.440 nonbonded pdb=" NE2 GLN D 425 " pdb=" O PHE D 439 " model vdw 2.167 2.520 ... (remaining 162019 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: 0.240 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: 2.190 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 59.000 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.004 0.102 20183 Z= 0.223 Angle : 0.775 9.106 27282 Z= 0.422 Chirality : 0.048 0.412 3000 Planarity : 0.007 0.132 3505 Dihedral : 14.343 89.982 7673 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.46 % Favored : 95.45 % Rotamer: Outliers : 0.05 % Allowed : 0.41 % Favored : 99.55 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.17), residues: 2420 helix: 0.23 (0.16), residues: 1030 sheet: -0.74 (0.31), residues: 279 loop : -1.19 (0.19), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP A1238 HIS 0.009 0.001 HIS B 278 PHE 0.029 0.002 PHE A 796 TYR 0.023 0.001 TYR A1342 ARG 0.012 0.001 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.7369 (tpt) cc_final: 0.6760 (tpp) REVERT: A 731 MET cc_start: 0.9224 (tmm) cc_final: 0.8824 (tmm) REVERT: A 1047 LEU cc_start: 0.8418 (tt) cc_final: 0.8122 (tt) REVERT: A 1052 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7817 (mmtt) REVERT: B 464 ILE cc_start: 0.9151 (mm) cc_final: 0.8924 (mm) REVERT: B 469 PHE cc_start: 0.7237 (m-80) cc_final: 0.6894 (m-80) REVERT: C 45 PHE cc_start: 0.9105 (m-80) cc_final: 0.8857 (m-80) REVERT: C 70 MET cc_start: 0.8343 (mmm) cc_final: 0.7827 (mmm) REVERT: C 112 MET cc_start: 0.8811 (mmp) cc_final: 0.8438 (mmm) REVERT: C 146 LEU cc_start: 0.9761 (mp) cc_final: 0.9531 (pp) REVERT: C 297 MET cc_start: 0.9015 (ppp) cc_final: 0.8708 (ppp) REVERT: C 300 TYR cc_start: 0.6853 (t80) cc_final: 0.5710 (t80) REVERT: D 74 LEU cc_start: 0.9030 (tp) cc_final: 0.8682 (tp) REVERT: E 70 PHE cc_start: 0.8513 (m-80) cc_final: 0.8279 (m-80) outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.3523 time to fit residues: 116.5551 Evaluate side-chains 133 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 30.0000 chunk 183 optimal weight: 50.0000 chunk 101 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 219 optimal weight: 9.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 505 GLN A 713 GLN A 880 GLN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN A1154 HIS ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20183 Z= 0.235 Angle : 0.633 9.599 27282 Z= 0.328 Chirality : 0.044 0.210 3000 Planarity : 0.006 0.104 3505 Dihedral : 4.994 27.812 2657 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 0.27 % Allowed : 4.71 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2420 helix: 0.33 (0.16), residues: 1027 sheet: -0.92 (0.30), residues: 297 loop : -1.10 (0.20), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 29 HIS 0.007 0.001 HIS B 278 PHE 0.016 0.001 PHE A 796 TYR 0.016 0.001 TYR A 957 ARG 0.006 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 155 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 LEU cc_start: 0.8547 (mm) cc_final: 0.8310 (mm) REVERT: A 394 MET cc_start: 0.7679 (tpt) cc_final: 0.7227 (tpp) REVERT: A 428 MET cc_start: 0.8984 (pmm) cc_final: 0.8588 (pmm) REVERT: A 731 MET cc_start: 0.9271 (tmm) cc_final: 0.8852 (tmm) REVERT: A 985 MET cc_start: 0.8985 (tmm) cc_final: 0.8784 (tmm) REVERT: A 989 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8624 (pm20) REVERT: A 1047 LEU cc_start: 0.8452 (tt) cc_final: 0.8213 (tt) REVERT: C 45 PHE cc_start: 0.9196 (m-80) cc_final: 0.8841 (m-80) REVERT: C 70 MET cc_start: 0.8581 (mmm) cc_final: 0.8123 (mmm) REVERT: C 112 MET cc_start: 0.8618 (mmp) cc_final: 0.8116 (mmm) REVERT: C 297 MET cc_start: 0.8965 (ppp) cc_final: 0.8715 (ppp) REVERT: C 300 TYR cc_start: 0.7009 (t80) cc_final: 0.5937 (t80) REVERT: D 74 LEU cc_start: 0.8843 (tp) cc_final: 0.8431 (tp) outliers start: 6 outliers final: 3 residues processed: 161 average time/residue: 0.3228 time to fit residues: 81.5581 Evaluate side-chains 124 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 122 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 182 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 220 optimal weight: 9.9990 chunk 237 optimal weight: 30.0000 chunk 196 optimal weight: 6.9990 chunk 218 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN A 946 GLN ** A 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 ASN ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN C 260 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 20183 Z= 0.248 Angle : 0.621 7.593 27282 Z= 0.321 Chirality : 0.043 0.215 3000 Planarity : 0.005 0.108 3505 Dihedral : 4.977 26.321 2657 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.46 % Rotamer: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.17), residues: 2420 helix: 0.38 (0.16), residues: 1020 sheet: -0.81 (0.29), residues: 304 loop : -1.13 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 29 HIS 0.008 0.001 HIS B 419 PHE 0.015 0.002 PHE D 447 TYR 0.015 0.001 TYR D 309 ARG 0.005 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 153 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 LEU cc_start: 0.8638 (mm) cc_final: 0.8378 (mm) REVERT: A 428 MET cc_start: 0.8998 (pmm) cc_final: 0.8561 (pmm) REVERT: A 519 MET cc_start: 0.8311 (ttp) cc_final: 0.7966 (ttp) REVERT: A 731 MET cc_start: 0.9321 (tmm) cc_final: 0.9006 (tmm) REVERT: A 1047 LEU cc_start: 0.8505 (tt) cc_final: 0.8211 (tt) REVERT: A 1052 LYS cc_start: 0.8744 (mmtt) cc_final: 0.8328 (mmtt) REVERT: C 45 PHE cc_start: 0.9280 (m-80) cc_final: 0.8894 (m-80) REVERT: C 112 MET cc_start: 0.8716 (mmp) cc_final: 0.8208 (mmm) REVERT: C 297 MET cc_start: 0.8987 (ppp) cc_final: 0.8758 (ppp) REVERT: C 300 TYR cc_start: 0.7067 (t80) cc_final: 0.6027 (t80) REVERT: D 74 LEU cc_start: 0.8890 (tp) cc_final: 0.8471 (tp) outliers start: 2 outliers final: 1 residues processed: 155 average time/residue: 0.3314 time to fit residues: 80.3220 Evaluate side-chains 119 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 217 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 147 optimal weight: 20.0000 chunk 220 optimal weight: 20.0000 chunk 233 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 ASN ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN C 257 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 20183 Z= 0.244 Angle : 0.613 7.155 27282 Z= 0.317 Chirality : 0.043 0.225 3000 Planarity : 0.005 0.109 3505 Dihedral : 4.937 24.886 2657 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.58 % Favored : 94.34 % Rotamer: Outliers : 0.18 % Allowed : 4.44 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2420 helix: 0.36 (0.16), residues: 1025 sheet: -0.79 (0.29), residues: 303 loop : -1.18 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 29 HIS 0.009 0.001 HIS B 419 PHE 0.016 0.002 PHE D 447 TYR 0.013 0.001 TYR A 957 ARG 0.012 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 149 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.9012 (pmm) cc_final: 0.8556 (pmm) REVERT: A 519 MET cc_start: 0.8250 (ttp) cc_final: 0.7930 (ttp) REVERT: A 731 MET cc_start: 0.9317 (tmm) cc_final: 0.8930 (tmm) REVERT: A 1052 LYS cc_start: 0.8665 (mmtt) cc_final: 0.8205 (mmtt) REVERT: C 45 PHE cc_start: 0.9146 (m-80) cc_final: 0.8656 (m-80) REVERT: C 112 MET cc_start: 0.8728 (mmp) cc_final: 0.8216 (mmm) REVERT: C 297 MET cc_start: 0.9019 (ppp) cc_final: 0.8780 (ppp) REVERT: C 300 TYR cc_start: 0.7129 (t80) cc_final: 0.6091 (t80) REVERT: D 74 LEU cc_start: 0.8880 (tp) cc_final: 0.8439 (tp) outliers start: 4 outliers final: 2 residues processed: 153 average time/residue: 0.3327 time to fit residues: 79.7057 Evaluate side-chains 118 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 194 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 174 optimal weight: 50.0000 chunk 96 optimal weight: 9.9990 chunk 199 optimal weight: 0.9990 chunk 161 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 209 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1380 GLN ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 20183 Z= 0.222 Angle : 0.611 7.396 27282 Z= 0.314 Chirality : 0.043 0.210 3000 Planarity : 0.005 0.109 3505 Dihedral : 4.887 24.021 2657 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.46 % Rotamer: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.17), residues: 2420 helix: 0.42 (0.16), residues: 1015 sheet: -0.83 (0.29), residues: 303 loop : -1.14 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 29 HIS 0.007 0.001 HIS B 419 PHE 0.015 0.001 PHE D 447 TYR 0.013 0.001 TYR A 957 ARG 0.010 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 3.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.8897 (pmm) cc_final: 0.8514 (pmm) REVERT: A 519 MET cc_start: 0.8292 (ttp) cc_final: 0.8049 (ttp) REVERT: A 731 MET cc_start: 0.9329 (tmm) cc_final: 0.8912 (tmm) REVERT: A 1052 LYS cc_start: 0.8669 (mmtt) cc_final: 0.8219 (mmtt) REVERT: C 45 PHE cc_start: 0.9191 (m-80) cc_final: 0.8698 (m-80) REVERT: C 112 MET cc_start: 0.8862 (mmp) cc_final: 0.8275 (mmm) REVERT: C 297 MET cc_start: 0.9026 (ppp) cc_final: 0.8785 (ppp) REVERT: C 300 TYR cc_start: 0.7109 (t80) cc_final: 0.6017 (t80) REVERT: D 74 LEU cc_start: 0.8859 (tp) cc_final: 0.8383 (tp) outliers start: 2 outliers final: 1 residues processed: 151 average time/residue: 0.3323 time to fit residues: 79.0874 Evaluate side-chains 118 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 78 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 chunk 46 optimal weight: 0.2980 chunk 137 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 234 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 overall best weight: 6.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 ASN ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 20183 Z= 0.266 Angle : 0.635 7.802 27282 Z= 0.327 Chirality : 0.043 0.223 3000 Planarity : 0.005 0.110 3505 Dihedral : 4.969 24.596 2657 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.16 % Favored : 93.76 % Rotamer: Outliers : 0.05 % Allowed : 3.21 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2420 helix: 0.37 (0.16), residues: 1008 sheet: -1.00 (0.28), residues: 318 loop : -1.09 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 29 HIS 0.007 0.001 HIS B 419 PHE 0.018 0.002 PHE D 447 TYR 0.021 0.002 TYR A 344 ARG 0.005 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.8984 (pmm) cc_final: 0.8601 (pmm) REVERT: A 731 MET cc_start: 0.9359 (tmm) cc_final: 0.9048 (tmm) REVERT: C 45 PHE cc_start: 0.9229 (m-80) cc_final: 0.8727 (m-80) REVERT: C 112 MET cc_start: 0.8930 (mmp) cc_final: 0.8217 (mmm) REVERT: C 297 MET cc_start: 0.9089 (ppp) cc_final: 0.8879 (ppp) REVERT: C 300 TYR cc_start: 0.7124 (t80) cc_final: 0.6070 (t80) REVERT: D 74 LEU cc_start: 0.8876 (tp) cc_final: 0.8502 (tp) outliers start: 1 outliers final: 1 residues processed: 140 average time/residue: 0.3039 time to fit residues: 67.5511 Evaluate side-chains 112 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 225 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 170 optimal weight: 40.0000 chunk 132 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 20183 Z= 0.278 Angle : 0.650 8.097 27282 Z= 0.335 Chirality : 0.044 0.274 3000 Planarity : 0.005 0.111 3505 Dihedral : 5.072 25.069 2657 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 24.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.16 % Favored : 93.76 % Rotamer: Outliers : 0.05 % Allowed : 1.99 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.17), residues: 2420 helix: 0.31 (0.16), residues: 993 sheet: -1.07 (0.28), residues: 317 loop : -1.08 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 29 HIS 0.007 0.001 HIS B 278 PHE 0.017 0.002 PHE D 447 TYR 0.014 0.002 TYR A 344 ARG 0.013 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.8961 (pmm) cc_final: 0.8636 (pmm) REVERT: A 519 MET cc_start: 0.8363 (ttt) cc_final: 0.7935 (ttp) REVERT: A 731 MET cc_start: 0.9361 (tmm) cc_final: 0.9050 (tmm) REVERT: A 1047 LEU cc_start: 0.8235 (tt) cc_final: 0.8016 (tt) REVERT: C 45 PHE cc_start: 0.9290 (m-80) cc_final: 0.8878 (m-80) REVERT: C 112 MET cc_start: 0.8740 (mmp) cc_final: 0.8393 (mmm) REVERT: C 297 MET cc_start: 0.9108 (ppp) cc_final: 0.8893 (ppp) REVERT: C 300 TYR cc_start: 0.7152 (t80) cc_final: 0.6133 (t80) REVERT: D 74 LEU cc_start: 0.8894 (tp) cc_final: 0.8459 (tp) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.3131 time to fit residues: 69.8365 Evaluate side-chains 106 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 144 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 115 optimal weight: 0.3980 chunk 21 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 212 optimal weight: 0.4980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN A 505 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 ASN A1164 GLN ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN C 257 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 20183 Z= 0.178 Angle : 0.629 9.230 27282 Z= 0.318 Chirality : 0.044 0.236 3000 Planarity : 0.005 0.110 3505 Dihedral : 4.905 23.628 2657 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.12 % Rotamer: Outliers : 0.14 % Allowed : 1.58 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2420 helix: 0.51 (0.16), residues: 1004 sheet: -0.80 (0.30), residues: 294 loop : -1.12 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 29 HIS 0.005 0.001 HIS B 278 PHE 0.016 0.001 PHE A 542 TYR 0.013 0.001 TYR A 957 ARG 0.009 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 MET cc_start: 0.8262 (ttt) cc_final: 0.7925 (ttp) REVERT: A 731 MET cc_start: 0.9341 (tmm) cc_final: 0.8991 (tmm) REVERT: A 985 MET cc_start: 0.8897 (tmm) cc_final: 0.8559 (tmm) REVERT: C 45 PHE cc_start: 0.9238 (m-80) cc_final: 0.8863 (m-80) REVERT: C 112 MET cc_start: 0.8687 (mmp) cc_final: 0.8292 (mmm) REVERT: C 300 TYR cc_start: 0.7118 (t80) cc_final: 0.6076 (t80) REVERT: D 43 GLU cc_start: 0.7160 (pp20) cc_final: 0.6959 (pp20) REVERT: D 74 LEU cc_start: 0.8846 (tp) cc_final: 0.8365 (tp) outliers start: 3 outliers final: 0 residues processed: 151 average time/residue: 0.3294 time to fit residues: 81.9287 Evaluate side-chains 112 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 223 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 217 optimal weight: 0.2980 chunk 130 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 170 optimal weight: 30.0000 chunk 66 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 205 optimal weight: 20.0000 chunk 216 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN C 257 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 20183 Z= 0.197 Angle : 0.623 8.372 27282 Z= 0.314 Chirality : 0.043 0.213 3000 Planarity : 0.005 0.111 3505 Dihedral : 4.859 23.394 2657 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.33 % Favored : 94.59 % Rotamer: Outliers : 0.09 % Allowed : 0.63 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.17), residues: 2420 helix: 0.52 (0.16), residues: 1010 sheet: -0.77 (0.30), residues: 292 loop : -1.08 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 29 HIS 0.006 0.001 HIS A 553 PHE 0.020 0.001 PHE A 861 TYR 0.014 0.001 TYR A 957 ARG 0.007 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 MET cc_start: 0.8466 (ttt) cc_final: 0.7933 (ttp) REVERT: A 731 MET cc_start: 0.9340 (tmm) cc_final: 0.9007 (tmm) REVERT: A 985 MET cc_start: 0.8870 (tmm) cc_final: 0.8641 (tmm) REVERT: A 1047 LEU cc_start: 0.8199 (tt) cc_final: 0.7980 (tt) REVERT: A 1333 ASP cc_start: 0.8037 (p0) cc_final: 0.7827 (p0) REVERT: C 45 PHE cc_start: 0.9240 (m-80) cc_final: 0.8827 (m-80) REVERT: C 112 MET cc_start: 0.8704 (mmp) cc_final: 0.8238 (mmm) REVERT: C 297 MET cc_start: 0.9183 (ppp) cc_final: 0.8966 (ppp) REVERT: C 300 TYR cc_start: 0.7130 (t80) cc_final: 0.6085 (t80) REVERT: D 74 LEU cc_start: 0.8851 (tp) cc_final: 0.8376 (tp) outliers start: 2 outliers final: 1 residues processed: 144 average time/residue: 0.3149 time to fit residues: 76.0219 Evaluate side-chains 108 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 229 optimal weight: 7.9990 chunk 140 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 159 optimal weight: 8.9990 chunk 241 optimal weight: 30.0000 chunk 221 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 chunk 19 optimal weight: 0.2980 chunk 148 optimal weight: 20.0000 chunk 117 optimal weight: 7.9990 chunk 152 optimal weight: 30.0000 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 20183 Z= 0.229 Angle : 0.641 8.428 27282 Z= 0.325 Chirality : 0.043 0.208 3000 Planarity : 0.005 0.112 3505 Dihedral : 4.903 23.628 2657 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 0.05 % Allowed : 0.36 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.17), residues: 2420 helix: 0.51 (0.16), residues: 1008 sheet: -0.82 (0.29), residues: 298 loop : -1.04 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 29 HIS 0.006 0.001 HIS B 278 PHE 0.016 0.001 PHE D 447 TYR 0.019 0.001 TYR A 344 ARG 0.010 0.000 ARG C 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 2.360 Fit side-chains revert: symmetry clash REVERT: A 519 MET cc_start: 0.8424 (ttt) cc_final: 0.8045 (ttp) REVERT: A 731 MET cc_start: 0.9351 (tmm) cc_final: 0.9016 (tmm) REVERT: A 985 MET cc_start: 0.8883 (tmm) cc_final: 0.8469 (tmm) REVERT: A 1047 LEU cc_start: 0.8244 (tt) cc_final: 0.8033 (tt) REVERT: A 1333 ASP cc_start: 0.8098 (p0) cc_final: 0.7877 (p0) REVERT: C 45 PHE cc_start: 0.9302 (m-80) cc_final: 0.8881 (m-80) REVERT: C 112 MET cc_start: 0.8674 (mmp) cc_final: 0.8346 (mmm) REVERT: C 300 TYR cc_start: 0.7119 (t80) cc_final: 0.6104 (t80) REVERT: D 74 LEU cc_start: 0.8844 (tp) cc_final: 0.8357 (tp) REVERT: E 43 ARG cc_start: 0.8050 (ptp-110) cc_final: 0.7394 (mtm110) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.3141 time to fit residues: 69.4202 Evaluate side-chains 104 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 0.1980 chunk 58 optimal weight: 8.9990 chunk 177 optimal weight: 50.0000 chunk 28 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 197 optimal weight: 0.9990 chunk 24 optimal weight: 30.0000 chunk 35 optimal weight: 8.9990 chunk 168 optimal weight: 40.0000 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.044535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.030215 restraints weight = 166821.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.031017 restraints weight = 111990.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.031643 restraints weight = 84101.378| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 20183 Z= 0.185 Angle : 0.621 8.279 27282 Z= 0.312 Chirality : 0.043 0.207 3000 Planarity : 0.005 0.112 3505 Dihedral : 4.819 22.552 2657 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 0.05 % Allowed : 0.45 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.17), residues: 2420 helix: 0.57 (0.16), residues: 1009 sheet: -0.69 (0.30), residues: 288 loop : -1.01 (0.19), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 29 HIS 0.005 0.001 HIS B 278 PHE 0.015 0.001 PHE D 447 TYR 0.014 0.001 TYR A 344 ARG 0.011 0.000 ARG C 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3244.43 seconds wall clock time: 61 minutes 43.52 seconds (3703.52 seconds total)