Starting phenix.real_space_refine on Fri Mar 15 14:57:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb5_20287/03_2024/6pb5_20287_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb5_20287/03_2024/6pb5_20287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb5_20287/03_2024/6pb5_20287.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb5_20287/03_2024/6pb5_20287.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb5_20287/03_2024/6pb5_20287_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb5_20287/03_2024/6pb5_20287_trim_updated.pdb" } resolution = 4.52 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= -0.020 sd= 0.262 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 158 5.49 5 Mg 1 5.21 5 S 147 5.16 5 C 21701 2.51 5 N 6264 2.21 5 O 7104 1.98 5 H 34319 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 268": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 872": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 795": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 999": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1325": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 1355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 69696 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3599 Classifications: {'peptide': 230} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 219} Chain: "B" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3556 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 21054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 21054 Classifications: {'peptide': 1334} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1276} Chain breaks: 1 Chain: "D" Number of atoms: 21012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 21012 Classifications: {'peptide': 1337} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1281} Chain breaks: 2 Chain: "E" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1261 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 7892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 7892 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 15, 'TRANS': 466} Chain breaks: 1 Chain: "G" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3154 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "H" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3155 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "1" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 2480 Classifications: {'DNA': 78} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 77} Chain: "2" Number of atoms: 2486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 2486 Classifications: {'DNA': 78} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 77} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29109 SG CYS D 70 122.914 125.710 67.439 1.00 20.00 S ATOM 29138 SG CYS D 72 124.561 126.693 70.401 1.00 20.00 S ATOM 29416 SG CYS D 88 125.925 122.311 69.136 1.00 20.00 S ATOM 40950 SG CYS D 814 90.491 80.871 20.327 1.00 20.00 S ATOM 42088 SG CYS D 888 91.542 81.732 23.612 1.00 20.00 S ATOM 42179 SG CYS D 895 88.248 82.581 22.524 1.00 20.00 S ATOM 42216 SG CYS D 898 87.814 79.356 23.550 1.00 20.00 S Time building chain proxies: 22.74, per 1000 atoms: 0.33 Number of scatterers: 69696 At special positions: 0 Unit cell: (201.6, 204.3, 184.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 147 16.00 P 158 15.00 Mg 1 11.99 O 7104 8.00 N 6264 7.00 C 21701 6.00 H 34319 1.00 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: 47.88 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " Number of angles added : 6 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 32 sheets defined 35.6% alpha, 6.9% beta 47 base pairs and 121 stacking pairs defined. Time for finding SS restraints: 31.76 Creating SS restraints... Processing helix chain 'A' and resid 38 through 49 removed outlier: 3.538A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 213 through 230 removed outlier: 4.125A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 78 through 85 Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 213 through 230 removed outlier: 4.727A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 8 No H-bonds generated for 'chain 'C' and resid 5 through 8' Processing helix chain 'C' and resid 30 through 39 Processing helix chain 'C' and resid 49 through 56 Processing helix chain 'C' and resid 82 through 87 Processing helix chain 'C' and resid 208 through 212 Processing helix chain 'C' and resid 217 through 222 Processing helix chain 'C' and resid 271 through 279 Processing helix chain 'C' and resid 289 through 292 Processing helix chain 'C' and resid 319 through 328 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 359 through 370 Processing helix chain 'C' and resid 378 through 390 removed outlier: 4.792A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 407 Processing helix chain 'C' and resid 422 through 437 Processing helix chain 'C' and resid 458 through 481 removed outlier: 3.587A pdb=" N GLN C 463 " --> pdb=" O ALA C 460 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG C 473 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 478 " --> pdb=" O VAL C 475 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER C 480 " --> pdb=" O GLU C 477 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU C 481 " --> pdb=" O ARG C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 492 No H-bonds generated for 'chain 'C' and resid 490 through 492' Processing helix chain 'C' and resid 497 through 505 Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 608 through 613 removed outlier: 4.295A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 666 No H-bonds generated for 'chain 'C' and resid 664 through 666' Processing helix chain 'C' and resid 671 through 673 No H-bonds generated for 'chain 'C' and resid 671 through 673' Processing helix chain 'C' and resid 676 through 688 removed outlier: 3.879A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 711 Processing helix chain 'C' and resid 821 through 824 No H-bonds generated for 'chain 'C' and resid 821 through 824' Processing helix chain 'C' and resid 862 through 864 No H-bonds generated for 'chain 'C' and resid 862 through 864' Processing helix chain 'C' and resid 872 through 875 No H-bonds generated for 'chain 'C' and resid 872 through 875' Processing helix chain 'C' and resid 897 through 905 Processing helix chain 'C' and resid 943 through 969 Processing helix chain 'C' and resid 971 through 980 removed outlier: 3.695A pdb=" N ILE C 975 " --> pdb=" O PHE C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 1008 through 1037 removed outlier: 4.008A pdb=" N LYS C1022 " --> pdb=" O TYR C1018 " (cutoff:3.500A) Processing helix chain 'C' and resid 1103 through 1106 No H-bonds generated for 'chain 'C' and resid 1103 through 1106' Processing helix chain 'C' and resid 1110 through 1134 removed outlier: 3.589A pdb=" N ALA C1121 " --> pdb=" O LEU C1117 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1149 Processing helix chain 'C' and resid 1166 through 1175 Processing helix chain 'C' and resid 1192 through 1202 Processing helix chain 'C' and resid 1239 through 1242 No H-bonds generated for 'chain 'C' and resid 1239 through 1242' Processing helix chain 'C' and resid 1272 through 1281 removed outlier: 3.719A pdb=" N LEU C1278 " --> pdb=" O GLU C1274 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1299 through 1309 Processing helix chain 'C' and resid 1321 through 1332 Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 59 through 62 No H-bonds generated for 'chain 'D' and resid 59 through 62' Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 125 through 128 No H-bonds generated for 'chain 'D' and resid 125 through 128' Processing helix chain 'D' and resid 133 through 140 Processing helix chain 'D' and resid 165 through 172 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 195 through 207 removed outlier: 3.595A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 230 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 264 through 284 removed outlier: 3.764A pdb=" N LEU D 283 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 307 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 337 through 340 No H-bonds generated for 'chain 'D' and resid 337 through 340' Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 378 through 388 Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 406 through 416 removed outlier: 3.501A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 451 through 454 Processing helix chain 'D' and resid 474 through 482 Processing helix chain 'D' and resid 506 through 513 Processing helix chain 'D' and resid 530 through 539 Processing helix chain 'D' and resid 574 through 582 removed outlier: 4.061A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 592 No H-bonds generated for 'chain 'D' and resid 590 through 592' Processing helix chain 'D' and resid 598 through 612 Processing helix chain 'D' and resid 615 through 635 Processing helix chain 'D' and resid 641 through 643 No H-bonds generated for 'chain 'D' and resid 641 through 643' Processing helix chain 'D' and resid 651 through 669 Processing helix chain 'D' and resid 676 through 699 Processing helix chain 'D' and resid 722 through 727 Processing helix chain 'D' and resid 734 through 741 Processing helix chain 'D' and resid 769 through 787 removed outlier: 3.531A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 802 Processing helix chain 'D' and resid 835 through 838 No H-bonds generated for 'chain 'D' and resid 835 through 838' Processing helix chain 'D' and resid 866 through 874 Processing helix chain 'D' and resid 896 through 899 No H-bonds generated for 'chain 'D' and resid 896 through 899' Processing helix chain 'D' and resid 917 through 927 Proline residue: D 926 - end of helix Processing helix chain 'D' and resid 1139 through 1146 Processing helix chain 'D' and resid 1217 through 1223 Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 3.808A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1251 through 1258 removed outlier: 3.692A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1287 Processing helix chain 'D' and resid 1309 through 1314 Processing helix chain 'D' and resid 1328 through 1338 removed outlier: 4.099A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1352 Processing helix chain 'D' and resid 1360 through 1374 removed outlier: 4.175A pdb=" N ALA D1364 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 13 Processing helix chain 'E' and resid 16 through 31 removed outlier: 3.743A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 61 through 79 Processing helix chain 'F' and resid 97 through 107 Processing helix chain 'F' and resid 115 through 135 Processing helix chain 'F' and resid 144 through 151 removed outlier: 4.073A pdb=" N TYR F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 235 removed outlier: 3.955A pdb=" N ALA F 222 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 254 Processing helix chain 'F' and resid 265 through 292 removed outlier: 3.697A pdb=" N MET F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL F 280 " --> pdb=" O MET F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 309 removed outlier: 4.121A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY F 308 " --> pdb=" O THR F 304 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN F 309 " --> pdb=" O LEU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 319 Processing helix chain 'F' and resid 325 through 328 No H-bonds generated for 'chain 'F' and resid 325 through 328' Processing helix chain 'F' and resid 334 through 351 removed outlier: 3.807A pdb=" N HIS F 338 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU F 348 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU F 349 " --> pdb=" O GLN F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 393 removed outlier: 3.523A pdb=" N GLY F 368 " --> pdb=" O ARG F 364 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS F 377 " --> pdb=" O ARG F 373 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 418 Processing helix chain 'F' and resid 421 through 423 No H-bonds generated for 'chain 'F' and resid 421 through 423' Processing helix chain 'F' and resid 427 through 445 removed outlier: 4.035A pdb=" N ALA F 444 " --> pdb=" O THR F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 474 removed outlier: 4.922A pdb=" N ARG F 468 " --> pdb=" O ASN F 464 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN F 469 " --> pdb=" O ARG F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 487 No H-bonds generated for 'chain 'F' and resid 484 through 487' Processing helix chain 'F' and resid 491 through 500 Processing helix chain 'F' and resid 519 through 521 No H-bonds generated for 'chain 'F' and resid 519 through 521' Processing helix chain 'F' and resid 531 through 550 removed outlier: 4.487A pdb=" N GLY F 550 " --> pdb=" O ASP F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 562 Processing helix chain 'F' and resid 573 through 579 Processing helix chain 'F' and resid 585 through 598 Processing helix chain 'F' and resid 608 through 610 No H-bonds generated for 'chain 'F' and resid 608 through 610' Processing helix chain 'G' and resid 10 through 17 removed outlier: 3.562A pdb=" N HIS G 17 " --> pdb=" O TRP G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 108 Processing helix chain 'G' and resid 113 through 135 Processing helix chain 'G' and resid 139 through 152 Processing helix chain 'G' and resid 171 through 176 Processing helix chain 'G' and resid 180 through 192 Processing helix chain 'H' and resid 10 through 15 Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'H' and resid 99 through 108 removed outlier: 3.858A pdb=" N GLN H 104 " --> pdb=" O LYS H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 136 removed outlier: 4.181A pdb=" N ARG H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 150 Processing helix chain 'H' and resid 170 through 176 Processing helix chain 'H' and resid 181 through 192 Processing sheet with id= A, first strand: chain 'A' and resid 170 through 172 Processing sheet with id= B, first strand: chain 'A' and resid 108 through 110 Processing sheet with id= C, first strand: chain 'A' and resid 182 through 187 Processing sheet with id= D, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.546A pdb=" N GLU A 29 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 14 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 16 through 18 Processing sheet with id= F, first strand: chain 'B' and resid 52 through 56 Processing sheet with id= G, first strand: chain 'B' and resid 59 through 61 Processing sheet with id= H, first strand: chain 'C' and resid 120 through 123 removed outlier: 3.666A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 184 through 188 Processing sheet with id= J, first strand: chain 'C' and resid 333 through 335 Processing sheet with id= K, first strand: chain 'C' and resid 603 through 605 Processing sheet with id= L, first strand: chain 'C' and resid 634 through 638 removed outlier: 3.852A pdb=" N PHE C 645 " --> pdb=" O VAL C 634 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS C 636 " --> pdb=" O SER C 643 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER C 643 " --> pdb=" O CYS C 636 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER C 638 " --> pdb=" O GLU C 641 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 798 through 803 removed outlier: 3.559A pdb=" N GLN C 798 " --> pdb=" O MET C1232 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET C1232 " --> pdb=" O GLN C 798 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET C1230 " --> pdb=" O MET C 800 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY C1228 " --> pdb=" O VAL C 802 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 835 through 840 Processing sheet with id= O, first strand: chain 'C' and resid 301 through 303 removed outlier: 7.118A pdb=" N ASP C 303 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU C 309 " --> pdb=" O ASP C 303 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 722 through 726 removed outlier: 6.094A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 103 through 106 Processing sheet with id= R, first strand: chain 'D' and resid 252 through 254 Processing sheet with id= S, first strand: chain 'D' and resid 351 through 354 removed outlier: 3.636A pdb=" N VAL D 421 " --> pdb=" O PHE D 437 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 365 through 369 removed outlier: 6.228A pdb=" N GLU D 438 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU D 368 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL D 440 " --> pdb=" O LEU D 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'D' and resid 547 through 552 Processing sheet with id= V, first strand: chain 'D' and resid 820 through 822 Processing sheet with id= W, first strand: chain 'D' and resid 965 through 967 Processing sheet with id= X, first strand: chain 'D' and resid 1034 through 1036 removed outlier: 3.608A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 1105 through 1107 Processing sheet with id= Z, first strand: chain 'D' and resid 981 through 985 Processing sheet with id= AA, first strand: chain 'G' and resid 21 through 23 removed outlier: 5.804A pdb=" N ALA G 95 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE G 42 " --> pdb=" O ALA G 95 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE G 97 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TYR G 40 " --> pdb=" O ILE G 97 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 63 through 65 Processing sheet with id= AC, first strand: chain 'G' and resid 197 through 199 Processing sheet with id= AD, first strand: chain 'H' and resid 21 through 23 Processing sheet with id= AE, first strand: chain 'H' and resid 85 through 88 removed outlier: 6.371A pdb=" N ILE H 51 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE H 60 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 163 through 165 1032 hydrogen bonds defined for protein. 2814 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 111 hydrogen bonds 222 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 121 stacking parallelities Total time for adding SS restraints: 26.27 Time building geometry restraints manager: 50.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 34287 1.01 - 1.21: 43 1.21 - 1.42: 14716 1.42 - 1.62: 21254 1.62 - 1.83: 261 Bond restraints: 70561 Sorted by residual: bond pdb=" C ILE C1079 " pdb=" N ASN C1080 " ideal model delta sigma weight residual 1.333 1.229 0.104 1.61e-02 3.86e+03 4.16e+01 bond pdb=" C ARG B 91 " pdb=" N VAL B 92 " ideal model delta sigma weight residual 1.334 1.277 0.057 1.29e-02 6.01e+03 1.98e+01 bond pdb=" CG LEU C 979 " pdb=" CD2 LEU C 979 " ideal model delta sigma weight residual 1.521 1.383 0.138 3.30e-02 9.18e+02 1.76e+01 bond pdb=" N ASN D 792 " pdb=" CA ASN D 792 " ideal model delta sigma weight residual 1.459 1.508 -0.049 1.19e-02 7.06e+03 1.67e+01 bond pdb=" CG HIS H 31 " pdb=" ND1 HIS H 31 " ideal model delta sigma weight residual 1.378 1.420 -0.042 1.10e-02 8.26e+03 1.45e+01 ... (remaining 70556 not shown) Histogram of bond angle deviations from ideal: 96.26 - 104.31: 1312 104.31 - 112.35: 81045 112.35 - 120.40: 25866 120.40 - 128.44: 19372 128.44 - 136.49: 410 Bond angle restraints: 128005 Sorted by residual: angle pdb=" C GLN A 147 " pdb=" N ARG A 148 " pdb=" CA ARG A 148 " ideal model delta sigma weight residual 121.54 134.81 -13.27 1.91e+00 2.74e-01 4.83e+01 angle pdb=" N LEU C 246 " pdb=" CA LEU C 246 " pdb=" C LEU C 246 " ideal model delta sigma weight residual 109.71 100.71 9.00 1.41e+00 5.03e-01 4.07e+01 angle pdb=" N LEU D 672 " pdb=" CA LEU D 672 " pdb=" C LEU D 672 " ideal model delta sigma weight residual 110.80 98.52 12.28 2.13e+00 2.20e-01 3.32e+01 angle pdb=" C PRO F 263 " pdb=" N LYS F 264 " pdb=" CA LYS F 264 " ideal model delta sigma weight residual 121.54 132.43 -10.89 1.91e+00 2.74e-01 3.25e+01 angle pdb=" N GLY D1308 " pdb=" CA GLY D1308 " pdb=" C GLY D1308 " ideal model delta sigma weight residual 111.85 117.86 -6.01 1.06e+00 8.90e-01 3.22e+01 ... (remaining 128000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.09: 30519 34.09 - 68.18: 1623 68.18 - 102.27: 34 102.27 - 136.36: 4 136.36 - 170.45: 6 Dihedral angle restraints: 32186 sinusoidal: 19113 harmonic: 13073 Sorted by residual: dihedral pdb=" CA VAL A 153 " pdb=" C VAL A 153 " pdb=" N PRO A 154 " pdb=" CA PRO A 154 " ideal model delta harmonic sigma weight residual -180.00 -108.33 -71.67 0 5.00e+00 4.00e-02 2.05e+02 dihedral pdb=" CA ILE H 167 " pdb=" C ILE H 167 " pdb=" N THR H 168 " pdb=" CA THR H 168 " ideal model delta harmonic sigma weight residual -180.00 -122.05 -57.95 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual -180.00 -124.81 -55.19 0 5.00e+00 4.00e-02 1.22e+02 ... (remaining 32183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4050 0.061 - 0.122: 1326 0.122 - 0.183: 222 0.183 - 0.244: 41 0.244 - 0.305: 9 Chirality restraints: 5648 Sorted by residual: chirality pdb=" CG LEU F 471 " pdb=" CB LEU F 471 " pdb=" CD1 LEU F 471 " pdb=" CD2 LEU F 471 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CG LEU C 989 " pdb=" CB LEU C 989 " pdb=" CD1 LEU C 989 " pdb=" CD2 LEU C 989 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA ALA D 178 " pdb=" N ALA D 178 " pdb=" C ALA D 178 " pdb=" CB ALA D 178 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 5645 not shown) Planarity restraints: 9932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C1034 " -0.828 9.50e-02 1.11e+02 2.76e-01 8.07e+01 pdb=" NE ARG C1034 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG C1034 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG C1034 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C1034 " -0.003 2.00e-02 2.50e+03 pdb="HH11 ARG C1034 " 0.011 2.00e-02 2.50e+03 pdb="HH12 ARG C1034 " -0.010 2.00e-02 2.50e+03 pdb="HH21 ARG C1034 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG C1034 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 178 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO A 179 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 179 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 179 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 128 " -0.043 2.00e-02 2.50e+03 2.54e-02 1.45e+01 pdb=" CG HIS B 128 " 0.059 2.00e-02 2.50e+03 pdb=" ND1 HIS B 128 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS B 128 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS B 128 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS B 128 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 HIS B 128 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 HIS B 128 " -0.007 2.00e-02 2.50e+03 pdb=" HE2 HIS B 128 " -0.013 2.00e-02 2.50e+03 ... (remaining 9929 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 3128 2.15 - 2.76: 136290 2.76 - 3.38: 199308 3.38 - 3.99: 252935 3.99 - 4.60: 386109 Nonbonded interactions: 977770 Sorted by model distance: nonbonded pdb=" H ALA D1157 " pdb=" O ASP D1208 " model vdw 1.538 1.850 nonbonded pdb=" H ALA C 617 " pdb=" O TYR C 652 " model vdw 1.543 1.850 nonbonded pdb=" OD2 ASP C 14 " pdb="HH21 ARG C1156 " model vdw 1.546 1.850 nonbonded pdb=" O ASP D 304 " pdb=" H ASP D 308 " model vdw 1.557 1.850 nonbonded pdb=" O TYR C 291 " pdb=" HZ3 LYS C 295 " model vdw 1.577 1.850 ... (remaining 977765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 233) selection = chain 'B' } ncs_group { reference = (chain 'G' and (resid 9 through 113 or (resid 114 and (name N or name CA or name \ C or name O or name CB or name CG or name SD or name CE or name HA or name HB2 \ or name HB3 or name HG2 or name HG3 or name HE1 or name HE2 or name HE3)) or res \ id 115 through 205 or resid 301)) selection = (chain 'H' and (resid 9 through 122 or (resid 123 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21)) or \ resid 124 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or \ name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 o \ r name HD3 or name HE or name HH11 or name HH12 or name HH21)) or resid 170 thro \ ugh 205 or resid 301)) } 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: 2.960 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: 0.760 Extract box with map and model: 13.770 Check model and map are aligned: 0.790 Set scattering table: 0.490 Process input model: 214.640 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.190 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 237.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1321 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 : 0.011 0.138 36242 Z= 0.707 Angle : 1.310 16.964 49608 Z= 0.728 Chirality : 0.061 0.305 5648 Planarity : 0.009 0.357 5910 Dihedral : 16.366 170.445 14327 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.69 % Allowed : 11.60 % Favored : 87.71 % Rotamer: Outliers : 0.26 % Allowed : 3.72 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.03 % Twisted Proline : 3.90 % Twisted General : 1.20 % 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: -4.55 (0.10), residues: 4060 helix: -2.89 (0.10), residues: 1485 sheet: -3.06 (0.23), residues: 377 loop : -3.17 (0.11), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP H 85 HIS 0.025 0.004 HIS D 113 PHE 0.051 0.005 PHE D 763 TYR 0.057 0.005 TYR D 679 ARG 0.036 0.003 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 466 time to evaluate : 3.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: C 82 VAL cc_start: -0.0817 (p) cc_final: -0.1024 (p) REVERT: C 88 ARG cc_start: -0.0574 (mmp80) cc_final: -0.1569 (mtt180) REVERT: C 704 MET cc_start: -0.0606 (mmm) cc_final: -0.0957 (ttm) REVERT: C 1230 MET cc_start: -0.3302 (ttm) cc_final: -0.3555 (tpp) REVERT: D 614 LEU cc_start: 0.5529 (pt) cc_final: 0.5306 (pt) REVERT: D 625 MET cc_start: 0.4547 (ttp) cc_final: 0.4049 (tpp) REVERT: D 801 VAL cc_start: 0.6510 (t) cc_final: 0.6285 (t) REVERT: D 857 LEU cc_start: -0.0579 (OUTLIER) cc_final: -0.0794 (pp) REVERT: E 30 MET cc_start: -0.1666 (mtp) cc_final: -0.2779 (mmt) REVERT: F 456 MET cc_start: 0.4208 (mpt) cc_final: 0.3968 (mpp) REVERT: G 157 MET cc_start: -0.0569 (mpp) cc_final: -0.1145 (mpp) REVERT: H 157 MET cc_start: 0.0384 (mpp) cc_final: -0.0684 (mtt) outliers start: 9 outliers final: 7 residues processed: 474 average time/residue: 1.1160 time to fit residues: 801.5737 Evaluate side-chains 336 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 328 time to evaluate : 3.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 352 optimal weight: 2.9990 chunk 316 optimal weight: 30.0000 chunk 175 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 213 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 327 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 chunk 379 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN C 339 ASN C 686 GLN ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1017 GLN C1244 HIS C1288 GLN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN D 817 HIS D1023 HIS D1279 GLN D1350 ASN H 65 ASN H 149 ASN H 174 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1186 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 36242 Z= 0.230 Angle : 0.770 11.613 49608 Z= 0.420 Chirality : 0.044 0.199 5648 Planarity : 0.006 0.079 5910 Dihedral : 19.617 175.155 6234 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.19 % Favored : 90.30 % Rotamer: Outliers : 0.06 % Allowed : 2.20 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.05 % Twisted Proline : 3.90 % Twisted General : 0.69 % 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: -3.63 (0.11), residues: 4060 helix: -1.83 (0.11), residues: 1525 sheet: -2.84 (0.23), residues: 392 loop : -2.80 (0.12), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 183 HIS 0.014 0.002 HIS C1244 PHE 0.019 0.002 PHE C 505 TYR 0.037 0.002 TYR D 679 ARG 0.012 0.001 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 387 time to evaluate : 3.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: -0.2517 (mmt) cc_final: -0.2900 (tpp) REVERT: C 88 ARG cc_start: -0.0748 (mmp80) cc_final: -0.1737 (mtt180) REVERT: C 704 MET cc_start: -0.1135 (mmm) cc_final: -0.1384 (mtt) REVERT: C 1230 MET cc_start: -0.3484 (ttm) cc_final: -0.3922 (tpp) REVERT: C 1315 MET cc_start: 0.1574 (tpt) cc_final: 0.1260 (tpt) REVERT: D 614 LEU cc_start: 0.5328 (pt) cc_final: 0.4916 (pt) REVERT: D 801 VAL cc_start: 0.6464 (t) cc_final: 0.6149 (t) REVERT: E 30 MET cc_start: -0.1925 (mtp) cc_final: -0.2877 (mmt) REVERT: G 157 MET cc_start: -0.0011 (mpp) cc_final: -0.0559 (mpp) REVERT: H 157 MET cc_start: 0.0260 (mpp) cc_final: -0.0866 (mtt) outliers start: 2 outliers final: 1 residues processed: 389 average time/residue: 1.0795 time to fit residues: 636.1621 Evaluate side-chains 321 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 320 time to evaluate : 3.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 210 optimal weight: 9.9990 chunk 117 optimal weight: 0.0970 chunk 315 optimal weight: 30.0000 chunk 258 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 380 optimal weight: 0.8980 chunk 410 optimal weight: 10.0000 chunk 338 optimal weight: 9.9990 chunk 377 optimal weight: 0.7980 chunk 129 optimal weight: 0.4980 chunk 305 optimal weight: 9.9990 overall best weight: 1.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 GLN ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1193 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 36242 Z= 0.210 Angle : 0.702 11.583 49608 Z= 0.385 Chirality : 0.043 0.195 5648 Planarity : 0.005 0.079 5910 Dihedral : 19.372 179.134 6234 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.22 % Favored : 89.38 % Rotamer: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.05 % Twisted Proline : 3.25 % Twisted General : 0.51 % 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: -3.15 (0.12), residues: 4060 helix: -1.27 (0.12), residues: 1535 sheet: -2.78 (0.24), residues: 370 loop : -2.64 (0.12), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 183 HIS 0.006 0.001 HIS D 777 PHE 0.017 0.001 PHE D 620 TYR 0.030 0.002 TYR D 679 ARG 0.005 0.000 ARG C 557 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 374 time to evaluate : 3.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: -0.2366 (mmp) cc_final: -0.2609 (tpt) REVERT: C 88 ARG cc_start: -0.0812 (mmp80) cc_final: -0.1903 (mtt180) REVERT: C 704 MET cc_start: -0.1095 (mmm) cc_final: -0.1500 (mtt) REVERT: D 513 MET cc_start: 0.2745 (tmm) cc_final: 0.2475 (tmm) REVERT: D 625 MET cc_start: 0.4973 (tpp) cc_final: 0.4767 (tpp) REVERT: D 698 MET cc_start: 0.3883 (tpp) cc_final: 0.2969 (tpp) REVERT: E 30 MET cc_start: -0.1930 (mtp) cc_final: -0.2941 (mmt) REVERT: F 409 ASN cc_start: 0.2895 (m110) cc_final: 0.2671 (m110) REVERT: G 157 MET cc_start: 0.0211 (mpp) cc_final: -0.0655 (mpp) REVERT: H 157 MET cc_start: 0.0243 (mpp) cc_final: -0.0796 (mtt) outliers start: 1 outliers final: 1 residues processed: 375 average time/residue: 1.0592 time to fit residues: 608.9107 Evaluate side-chains 315 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 314 time to evaluate : 3.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 375 optimal weight: 6.9990 chunk 285 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 255 optimal weight: 30.0000 chunk 381 optimal weight: 0.6980 chunk 404 optimal weight: 30.0000 chunk 199 optimal weight: 7.9990 chunk 361 optimal weight: 9.9990 chunk 108 optimal weight: 0.5980 overall best weight: 4.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN C 688 GLN ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN G 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1335 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 36242 Z= 0.245 Angle : 0.703 11.650 49608 Z= 0.388 Chirality : 0.043 0.194 5648 Planarity : 0.005 0.083 5910 Dihedral : 19.333 179.082 6234 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.54 % Favored : 89.09 % Rotamer: Outliers : 0.03 % Allowed : 1.49 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.05 % Twisted Proline : 3.25 % Twisted General : 0.46 % 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: -2.99 (0.12), residues: 4060 helix: -1.03 (0.12), residues: 1522 sheet: -2.82 (0.22), residues: 402 loop : -2.58 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D1193 HIS 0.006 0.001 HIS D 777 PHE 0.015 0.002 PHE C 225 TYR 0.025 0.002 TYR D 679 ARG 0.012 0.001 ARG D 692 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 355 time to evaluate : 3.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: C 88 ARG cc_start: -0.0888 (mmp80) cc_final: -0.1891 (mtt-85) REVERT: C 1230 MET cc_start: -0.1744 (tpp) cc_final: -0.4344 (tpt) REVERT: D 698 MET cc_start: 0.4014 (tpp) cc_final: 0.2855 (tpp) REVERT: G 157 MET cc_start: 0.0381 (mpp) cc_final: -0.0349 (mpp) REVERT: H 157 MET cc_start: 0.0263 (mpp) cc_final: -0.0968 (mtt) outliers start: 1 outliers final: 0 residues processed: 356 average time/residue: 1.0509 time to fit residues: 571.5351 Evaluate side-chains 299 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 3.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 336 optimal weight: 9.9990 chunk 229 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 300 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 344 optimal weight: 5.9990 chunk 279 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 362 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 580 GLN ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 GLN ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN D 865 HIS D 951 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 271 ASN ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 HIS ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 GLN H 174 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1820 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.125 36242 Z= 0.453 Angle : 0.929 12.928 49608 Z= 0.508 Chirality : 0.049 0.337 5648 Planarity : 0.007 0.137 5910 Dihedral : 19.735 179.120 6234 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 51.67 Ramachandran Plot: Outliers : 0.37 % Allowed : 14.26 % Favored : 85.37 % Rotamer: Outliers : 0.14 % Allowed : 3.83 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.05 % Twisted Proline : 4.55 % Twisted General : 0.51 % 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: -3.59 (0.11), residues: 4060 helix: -1.57 (0.12), residues: 1493 sheet: -3.00 (0.25), residues: 350 loop : -2.95 (0.12), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 183 HIS 0.014 0.002 HIS D1366 PHE 0.030 0.003 PHE G 14 TYR 0.043 0.003 TYR C 756 ARG 0.018 0.001 ARG G 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 336 time to evaluate : 3.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: -0.1578 (mmt) cc_final: -0.1831 (tpp) REVERT: C 369 MET cc_start: 0.8199 (ptm) cc_final: 0.7320 (tpt) REVERT: C 1230 MET cc_start: -0.1206 (tpp) cc_final: -0.3860 (tpt) REVERT: D 797 THR cc_start: 0.7787 (p) cc_final: 0.7548 (p) REVERT: G 157 MET cc_start: 0.0496 (mpp) cc_final: -0.0038 (mpp) REVERT: H 157 MET cc_start: 0.1375 (mpp) cc_final: -0.0081 (mtt) outliers start: 5 outliers final: 4 residues processed: 341 average time/residue: 1.0153 time to fit residues: 533.2643 Evaluate side-chains 296 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 292 time to evaluate : 3.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 135 optimal weight: 20.0000 chunk 363 optimal weight: 0.4980 chunk 79 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 99 optimal weight: 0.0470 chunk 404 optimal weight: 20.0000 chunk 335 optimal weight: 20.0000 chunk 187 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 212 optimal weight: 0.9990 overall best weight: 2.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN ** D 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 720 ASN D1289 ASN F 345 GLN G 17 HIS ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1565 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 36242 Z= 0.238 Angle : 0.730 10.608 49608 Z= 0.399 Chirality : 0.045 0.259 5648 Planarity : 0.006 0.103 5910 Dihedral : 19.576 176.295 6234 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 26.12 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.84 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.05 % Twisted Proline : 4.55 % Twisted General : 0.38 % 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: -3.23 (0.12), residues: 4060 helix: -1.16 (0.12), residues: 1500 sheet: -3.06 (0.23), residues: 388 loop : -2.76 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 183 HIS 0.013 0.002 HIS C1023 PHE 0.017 0.002 PHE F 580 TYR 0.035 0.002 TYR C 179 ARG 0.018 0.001 ARG D 799 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 3.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: -0.1946 (mmt) cc_final: -0.2364 (tpp) REVERT: C 1230 MET cc_start: -0.1684 (tpp) cc_final: -0.3409 (tpt) REVERT: D 513 MET cc_start: 0.3293 (tmm) cc_final: 0.3089 (tmm) REVERT: D 797 THR cc_start: 0.7787 (p) cc_final: 0.7564 (p) REVERT: H 157 MET cc_start: 0.1337 (mpp) cc_final: -0.0133 (mtt) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 1.0072 time to fit residues: 525.0291 Evaluate side-chains 296 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 3.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 389 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 230 optimal weight: 5.9990 chunk 295 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 chunk 340 optimal weight: 10.0000 chunk 225 optimal weight: 20.0000 chunk 402 optimal weight: 9.9990 chunk 252 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS F 147 GLN ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1660 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 36242 Z= 0.269 Angle : 0.728 13.694 49608 Z= 0.400 Chirality : 0.044 0.223 5648 Planarity : 0.006 0.079 5910 Dihedral : 19.516 175.374 6234 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 30.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.05 % Favored : 86.72 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.05 % Twisted Proline : 2.60 % Twisted General : 0.43 % 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: -3.15 (0.12), residues: 4060 helix: -1.06 (0.12), residues: 1508 sheet: -3.05 (0.23), residues: 387 loop : -2.74 (0.12), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 183 HIS 0.009 0.001 HIS D1366 PHE 0.040 0.002 PHE D 338 TYR 0.041 0.002 TYR F 430 ARG 0.011 0.001 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 3.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: C 1119 MET cc_start: -0.2142 (ttt) cc_final: -0.3143 (ttt) REVERT: C 1230 MET cc_start: -0.1773 (tpp) cc_final: -0.3693 (tpt) REVERT: D 697 MET cc_start: -0.0665 (ppp) cc_final: -0.1491 (ppp) REVERT: D 698 MET cc_start: 0.3542 (tpp) cc_final: 0.1967 (mmt) REVERT: H 157 MET cc_start: 0.1475 (mpp) cc_final: 0.0001 (mtt) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 1.0292 time to fit residues: 529.6832 Evaluate side-chains 289 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 3.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 249 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 chunk 240 optimal weight: 20.0000 chunk 121 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 256 optimal weight: 10.0000 chunk 274 optimal weight: 8.9990 chunk 199 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 316 optimal weight: 10.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS C1288 GLN ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 GLN D1289 ASN D1350 ASN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1840 moved from start: 0.6486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 36242 Z= 0.350 Angle : 0.817 11.877 49608 Z= 0.448 Chirality : 0.047 0.291 5648 Planarity : 0.007 0.156 5910 Dihedral : 19.702 175.357 6234 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 41.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 14.16 % Favored : 85.62 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.05 % Twisted Proline : 2.60 % Twisted General : 0.43 % 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: -3.45 (0.12), residues: 4060 helix: -1.35 (0.12), residues: 1482 sheet: -3.20 (0.24), residues: 364 loop : -2.88 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 434 HIS 0.014 0.002 HIS B 37 PHE 0.024 0.003 PHE D 172 TYR 0.042 0.003 TYR F 228 ARG 0.013 0.001 ARG D 744 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 3.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: C 1119 MET cc_start: -0.2038 (ttt) cc_final: -0.3254 (ttt) REVERT: C 1230 MET cc_start: -0.1489 (tpp) cc_final: -0.3309 (tpt) REVERT: D 797 THR cc_start: 0.7875 (p) cc_final: 0.7592 (p) REVERT: H 157 MET cc_start: 0.1967 (mpp) cc_final: 0.0608 (mtt) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.9997 time to fit residues: 497.7664 Evaluate side-chains 286 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 3.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 366 optimal weight: 8.9990 chunk 385 optimal weight: 20.0000 chunk 352 optimal weight: 6.9990 chunk 375 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 294 optimal weight: 20.0000 chunk 115 optimal weight: 3.9990 chunk 339 optimal weight: 10.0000 chunk 355 optimal weight: 10.0000 chunk 374 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 GLN ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1759 moved from start: 0.6703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 36242 Z= 0.265 Angle : 0.730 12.040 49608 Z= 0.401 Chirality : 0.045 0.242 5648 Planarity : 0.006 0.079 5910 Dihedral : 19.649 174.073 6234 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 33.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.20 % Favored : 86.63 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.05 % Twisted Proline : 1.95 % Twisted General : 0.36 % 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: -3.29 (0.12), residues: 4060 helix: -1.18 (0.12), residues: 1516 sheet: -3.21 (0.24), residues: 364 loop : -2.81 (0.12), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 409 HIS 0.008 0.001 HIS C1070 PHE 0.017 0.002 PHE D 338 TYR 0.039 0.002 TYR F 430 ARG 0.009 0.001 ARG C 378 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 3.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: C 1230 MET cc_start: -0.1607 (tpp) cc_final: -0.3591 (tpt) REVERT: E 30 MET cc_start: -0.0858 (mtt) cc_final: -0.1067 (mtp) REVERT: H 157 MET cc_start: 0.1919 (mpp) cc_final: 0.0640 (mtt) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 1.0153 time to fit residues: 503.9777 Evaluate side-chains 289 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 3.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 246 optimal weight: 8.9990 chunk 397 optimal weight: 20.0000 chunk 242 optimal weight: 30.0000 chunk 188 optimal weight: 7.9990 chunk 275 optimal weight: 0.0060 chunk 416 optimal weight: 9.9990 chunk 383 optimal weight: 10.0000 chunk 331 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 256 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 overall best weight: 5.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1832 moved from start: 0.7252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 36242 Z= 0.297 Angle : 0.752 11.229 49608 Z= 0.414 Chirality : 0.045 0.240 5648 Planarity : 0.007 0.219 5910 Dihedral : 19.674 175.413 6234 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 35.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 14.04 % Favored : 85.74 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.05 % Twisted Proline : 1.95 % Twisted General : 0.41 % 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: -3.36 (0.12), residues: 4060 helix: -1.21 (0.12), residues: 1511 sheet: -3.07 (0.24), residues: 389 loop : -2.91 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D1020 HIS 0.010 0.001 HIS B 37 PHE 0.021 0.002 PHE C 38 TYR 0.038 0.003 TYR F 430 ARG 0.011 0.001 ARG B 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8120 Ramachandran restraints generated. 4060 Oldfield, 0 Emsley, 4060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 3.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: -0.1880 (mmt) cc_final: -0.2136 (tpp) REVERT: C 1230 MET cc_start: -0.1760 (tpp) cc_final: -0.3466 (tpt) REVERT: E 30 MET cc_start: -0.0862 (mtt) cc_final: -0.1107 (mtp) REVERT: H 157 MET cc_start: 0.2116 (mpp) cc_final: 0.1059 (mtt) outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 1.0091 time to fit residues: 513.1022 Evaluate side-chains 293 residues out of total 3499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 3.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 263 optimal weight: 0.8980 chunk 353 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 305 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 332 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 341 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 GLN ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.134156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.108129 restraints weight = 1414783.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.108585 restraints weight = 1405201.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.108566 restraints weight = 1235208.223| |-----------------------------------------------------------------------------| r_work (final): 0.4494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6018 moved from start: 0.7272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 36242 Z= 0.204 Angle : 0.676 10.261 49608 Z= 0.370 Chirality : 0.044 0.223 5648 Planarity : 0.005 0.079 5910 Dihedral : 19.528 174.924 6234 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 24.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.54 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.05 % Twisted Proline : 1.95 % Twisted General : 0.28 % 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: -2.93 (0.12), residues: 4060 helix: -0.85 (0.13), residues: 1522 sheet: -2.77 (0.25), residues: 384 loop : -2.68 (0.12), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 85 HIS 0.008 0.001 HIS D 545 PHE 0.019 0.002 PHE D 620 TYR 0.034 0.002 TYR F 430 ARG 0.009 0.001 ARG C 378 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13034.58 seconds wall clock time: 227 minutes 16.64 seconds (13636.64 seconds total)