Starting phenix.real_space_refine on Tue Mar 19 14:01:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmi_0452/03_2024/6nmi_0452_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmi_0452/03_2024/6nmi_0452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmi_0452/03_2024/6nmi_0452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmi_0452/03_2024/6nmi_0452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmi_0452/03_2024/6nmi_0452_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmi_0452/03_2024/6nmi_0452_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 6 6.06 5 S 141 5.16 5 C 15472 2.51 5 N 4259 2.21 5 O 4497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 542": "NH1" <-> "NH2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24379 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5190 Classifications: {'peptide': 653} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 4, 'PTRANS': 25, 'TRANS': 623} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 6040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6040 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 729} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'UNK:plan-1': 27} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 2657 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 206} Link IDs: {'PTRANS': 9, 'TRANS': 398} Chain breaks: 2 Unresolved non-hydrogen bonds: 480 Unresolved non-hydrogen angles: 688 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'UNK:plan-1': 169, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 258 Chain: "D" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3589 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 429} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2710 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 349} Chain breaks: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'UNK:plan-1': 56} Unresolved non-hydrogen planarities: 56 Chain: "F" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2065 Classifications: {'peptide': 263} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 253} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "H" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1592 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 7, 'TRANS': 202} Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6122 SG CYS B 116 31.188 92.936 92.618 1.00 57.98 S ATOM 6431 SG CYS B 155 25.509 94.811 95.777 1.00 71.14 S ATOM 6262 SG CYS B 134 29.804 98.669 94.897 1.00 58.64 S ATOM 6720 SG CYS B 190 29.808 93.756 99.287 1.00 60.71 S ATOM 19864 SG CYS E 345 106.926 53.182 92.189 1.00 75.65 S ATOM 19886 SG CYS E 348 108.467 51.856 88.413 1.00 64.83 S ATOM 20043 SG CYS E 368 106.401 56.196 89.757 1.00 71.71 S ATOM 20064 SG CYS E 371 104.697 52.665 89.750 1.00 71.32 S ATOM 19984 SG CYS E 360 96.585 51.420 99.170 1.00 84.88 S ATOM 20002 SG CYS E 363 99.750 48.979 100.284 1.00 87.91 S ATOM 20151 SG CYS E 382 98.330 48.895 96.556 1.00 71.58 S ATOM 20168 SG CYS E 385 95.940 47.256 99.392 1.00 74.09 S ATOM 19428 SG CYS E 291 71.907 29.161 73.434 1.00 79.05 S ATOM 19450 SG CYS E 294 69.682 28.269 70.220 1.00 89.45 S ATOM 19539 SG CYS E 305 69.598 31.885 71.534 1.00 81.96 S ATOM 19562 SG CYS E 308 66.943 29.397 72.226 1.00 86.60 S ATOM 22072 SG CYS F 268 71.653 40.558 91.347 1.00 65.95 S ATOM 22091 SG CYS F 271 74.687 39.238 92.484 1.00 64.03 S ATOM 22176 SG CYS F 282 71.860 38.166 94.531 1.00 77.32 S ATOM 22196 SG CYS F 285 73.237 41.680 95.218 1.00 82.61 S ATOM 22803 SG CYS H 6 23.507 133.253 59.350 1.00200.73 S ATOM 22821 SG CYS H 9 23.606 136.318 57.013 1.00206.24 S ATOM 22939 SG CYS H 31 26.156 135.891 60.585 1.00212.05 S ATOM 22955 SG CYS H 34 22.538 136.118 60.764 1.00219.26 S ATOM 22909 SG CYS H 26 15.011 138.561 70.710 1.00197.12 S ATOM 23016 SG CYS H 46 14.560 138.076 67.402 1.00221.32 S ATOM 23034 SG CYS H 49 12.266 136.988 69.848 1.00223.19 S Time building chain proxies: 12.39, per 1000 atoms: 0.51 Number of scatterers: 24379 At special positions: 0 Unit cell: (165.6, 165.6, 131.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 S 141 16.00 O 4497 8.00 N 4259 7.00 C 15472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 255 " - pdb=" SG CYS F 257 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.74 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 371 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 345 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 368 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 348 " pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 363 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 385 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 382 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 360 " pdb=" ZN E 403 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 308 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 305 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 294 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 291 " pdb=" ZN F 401 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 271 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 268 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 282 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 285 " pdb=" ZN H 400 " pdb="ZN ZN H 400 " - pdb=" SG CYS H 34 " pdb="ZN ZN H 400 " - pdb=" SG CYS H 6 " pdb="ZN ZN H 400 " - pdb=" SG CYS H 31 " pdb="ZN ZN H 400 " - pdb=" SG CYS H 9 " pdb=" ZN H 401 " pdb="ZN ZN H 401 " - pdb=" ND1 HIS H 28 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 46 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 26 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 49 " Number of angles added : 33 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6072 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 122 helices and 17 sheets defined 46.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.20 Creating SS restraints... Processing helix chain 'A' and resid 38 through 41 No H-bonds generated for 'chain 'A' and resid 38 through 41' Processing helix chain 'A' and resid 93 through 103 Processing helix chain 'A' and resid 120 through 129 Processing helix chain 'A' and resid 133 through 141 Processing helix chain 'A' and resid 150 through 159 removed outlier: 3.559A pdb=" N CYS A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 249 through 261 Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 346 through 357 removed outlier: 4.172A pdb=" N GLY A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 480 through 483 Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 516 through 524 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 586 through 597 Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 633 through 643 Processing helix chain 'A' and resid 669 through 683 Processing helix chain 'A' and resid 707 through 717 Processing helix chain 'B' and resid 19 through 33 Processing helix chain 'B' and resid 48 through 62 Processing helix chain 'B' and resid 77 through 97 Processing helix chain 'B' and resid 127 through 137 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.532A pdb=" N GLN B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'B' and resid 223 through 228 removed outlier: 4.422A pdb=" N LYS B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 247 Processing helix chain 'B' and resid 253 through 276 Processing helix chain 'B' and resid 279 through 289 Processing helix chain 'B' and resid 326 through 345 Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 370 through 373 No H-bonds generated for 'chain 'B' and resid 370 through 373' Processing helix chain 'B' and resid 375 through 385 Processing helix chain 'B' and resid 391 through 407 Proline residue: B 396 - end of helix Processing helix chain 'B' and resid 441 through 450 Proline residue: B 446 - end of helix Processing helix chain 'B' and resid 467 through 470 No H-bonds generated for 'chain 'B' and resid 467 through 470' Processing helix chain 'B' and resid 514 through 530 Processing helix chain 'B' and resid 542 through 551 Processing helix chain 'B' and resid 558 through 564 Processing helix chain 'B' and resid 576 through 587 Processing helix chain 'B' and resid 603 through 605 No H-bonds generated for 'chain 'B' and resid 603 through 605' Processing helix chain 'B' and resid 631 through 642 Processing helix chain 'B' and resid 648 through 664 removed outlier: 3.645A pdb=" N THR B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 685 Processing helix chain 'B' and resid 690 through 692 No H-bonds generated for 'chain 'B' and resid 690 through 692' Processing helix chain 'B' and resid 695 through 700 removed outlier: 4.981A pdb=" N HIS B 700 " --> pdb=" O TRP B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 723 Processing helix chain 'B' and resid 730 through 732 No H-bonds generated for 'chain 'B' and resid 730 through 732' Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'C' and resid 109 through 120 Processing helix chain 'C' and resid 122 through 131 Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 190 through 199 Processing helix chain 'C' and resid 201 through 209 Processing helix chain 'C' and resid 217 through 222 Processing helix chain 'C' and resid 241 through 255 Processing helix chain 'C' and resid 296 through 317 Processing helix chain 'C' and resid 347 through 358 Processing helix chain 'C' and resid 379 through 383 Processing helix chain 'C' and resid 398 through 410 Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 455 through 479 Processing helix chain 'C' and resid 486 through 514 Processing helix chain 'C' and resid 523 through 545 Processing helix chain 'D' and resid 20 through 23 No H-bonds generated for 'chain 'D' and resid 20 through 23' Processing helix chain 'D' and resid 28 through 34 Processing helix chain 'D' and resid 38 through 45 Processing helix chain 'D' and resid 50 through 59 Processing helix chain 'D' and resid 68 through 73 Processing helix chain 'D' and resid 77 through 79 No H-bonds generated for 'chain 'D' and resid 77 through 79' Processing helix chain 'D' and resid 84 through 92 Processing helix chain 'D' and resid 112 through 122 Processing helix chain 'D' and resid 145 through 164 Processing helix chain 'D' and resid 175 through 181 Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 208 through 220 Processing helix chain 'D' and resid 230 through 240 Processing helix chain 'D' and resid 256 through 268 Processing helix chain 'D' and resid 285 through 288 No H-bonds generated for 'chain 'D' and resid 285 through 288' Processing helix chain 'D' and resid 322 through 331 Processing helix chain 'D' and resid 348 through 356 Processing helix chain 'D' and resid 363 through 370 Processing helix chain 'D' and resid 385 through 398 Processing helix chain 'D' and resid 416 through 427 Processing helix chain 'D' and resid 448 through 455 Processing helix chain 'E' and resid 18 through 21 Processing helix chain 'E' and resid 30 through 41 Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 80 through 98 Processing helix chain 'E' and resid 124 through 136 removed outlier: 4.627A pdb=" N ASP E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 156 Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 225 through 236 Processing helix chain 'E' and resid 369 through 377 Processing helix chain 'E' and resid 383 through 386 No H-bonds generated for 'chain 'E' and resid 383 through 386' Processing helix chain 'F' and resid 19 through 27 Processing helix chain 'F' and resid 34 through 51 Processing helix chain 'F' and resid 102 through 119 Processing helix chain 'F' and resid 134 through 149 Processing helix chain 'F' and resid 171 through 186 removed outlier: 5.063A pdb=" N MET F 175 " --> pdb=" O LEU F 172 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N MET F 178 " --> pdb=" O MET F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 209 Processing helix chain 'F' and resid 220 through 230 removed outlier: 4.975A pdb=" N LEU F 224 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU F 228 " --> pdb=" O GLN F 225 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP F 229 " --> pdb=" O TYR F 226 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL F 230 " --> pdb=" O LEU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 238 No H-bonds generated for 'chain 'F' and resid 235 through 238' Processing helix chain 'G' and resid 14 through 26 Processing helix chain 'G' and resid 47 through 64 removed outlier: 3.632A pdb=" N VAL G 50 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASN G 51 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU G 55 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL G 57 " --> pdb=" O GLN G 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 15 No H-bonds generated for 'chain 'H' and resid 12 through 15' Processing helix chain 'H' and resid 32 through 39 Processing helix chain 'H' and resid 66 through 79 Processing helix chain 'H' and resid 92 through 111 Processing helix chain 'H' and resid 114 through 129 Processing helix chain 'H' and resid 132 through 188 Processing helix chain 'H' and resid 194 through 209 Processing sheet with id= A, first strand: chain 'A' and resid 76 through 79 removed outlier: 5.750A pdb=" N LYS A 117 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 291 through 293 removed outlier: 6.380A pdb=" N VAL A 166 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR A 175 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 336 through 339 removed outlier: 5.804A pdb=" N MET A 438 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 466 " --> pdb=" O MET A 438 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU A 440 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA A 406 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N GLY A 365 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N SER A 408 " --> pdb=" O GLY A 365 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 505 through 512 removed outlier: 6.452A pdb=" N ALA A 657 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ALA A 508 " --> pdb=" O ALA A 657 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE A 659 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL A 510 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N SER A 661 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N CYS A 512 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL A 663 " --> pdb=" O CYS A 512 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 2 through 4 Processing sheet with id= F, first strand: chain 'B' and resid 229 through 233 removed outlier: 6.240A pdb=" N LYS B 69 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL B 232 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE B 71 " --> pdb=" O VAL B 232 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 249 through 252 Processing sheet with id= H, first strand: chain 'B' and resid 490 through 494 removed outlier: 7.150A pdb=" N GLY B 675 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N MET B 493 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET B 677 " --> pdb=" O MET B 493 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 536 " --> pdb=" O ALA B 617 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU B 566 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU B 597 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N VAL B 599 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 96 through 100 Processing sheet with id= J, first strand: chain 'D' and resid 271 through 273 Processing sheet with id= K, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.366A pdb=" N GLN D 345 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N MET D 334 " --> pdb=" O GLN D 345 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 407 through 410 Processing sheet with id= M, first strand: chain 'E' and resid 219 through 221 removed outlier: 9.103A pdb=" N HIS E 220 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL E 198 " --> pdb=" O HIS E 220 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLN E 103 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL E 63 " --> pdb=" O GLN E 103 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLY E 105 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL E 65 " --> pdb=" O GLY E 105 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE E 107 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL E 108 " --> pdb=" O LYS E 116 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LYS E 116 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LYS E 110 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 332 through 334 Processing sheet with id= O, first strand: chain 'F' and resid 213 through 216 removed outlier: 6.223A pdb=" N LEU F 10 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU F 162 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL F 12 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE F 164 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL F 14 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS F 56 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE F 13 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA F 58 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL F 15 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE F 60 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ALA F 61 " --> pdb=" O PHE F 69 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N PHE F 69 " --> pdb=" O ALA F 61 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 8 through 10 Processing sheet with id= Q, first strand: chain 'H' and resid 21 through 23 994 hydrogen bonds defined for protein. 2784 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.65 Time building geometry restraints manager: 9.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 10378 1.43 - 1.64: 14250 1.64 - 1.86: 204 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 24844 Sorted by residual: bond pdb=" C VAL C 211 " pdb=" N PRO C 212 " ideal model delta sigma weight residual 1.334 1.414 -0.080 2.34e-02 1.83e+03 1.18e+01 bond pdb=" CA PRO H 17 " pdb=" CB PRO H 17 " ideal model delta sigma weight residual 1.531 1.552 -0.020 6.20e-03 2.60e+04 1.07e+01 bond pdb=" C CYS E 177 " pdb=" N ASP E 178 " ideal model delta sigma weight residual 1.331 1.247 0.084 2.83e-02 1.25e+03 8.75e+00 bond pdb=" C MET C 117 " pdb=" N LEU C 118 " ideal model delta sigma weight residual 1.332 1.363 -0.031 1.40e-02 5.10e+03 4.90e+00 bond pdb=" C SER B 395 " pdb=" N PRO B 396 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.58e+00 ... (remaining 24839 not shown) Histogram of bond angle deviations from ideal: 73.15 - 85.66: 12 85.66 - 98.17: 5 98.17 - 110.68: 7943 110.68 - 123.19: 24308 123.19 - 135.70: 1425 Bond angle restraints: 33693 Sorted by residual: angle pdb=" N VAL A 92 " pdb=" CA VAL A 92 " pdb=" C VAL A 92 " ideal model delta sigma weight residual 111.77 105.15 6.62 1.04e+00 9.25e-01 4.05e+01 angle pdb=" C TYR C 414 " pdb=" N THR C 415 " pdb=" CA THR C 415 " ideal model delta sigma weight residual 121.80 135.70 -13.90 2.44e+00 1.68e-01 3.25e+01 angle pdb=" CA GLN C 442 " pdb=" C GLN C 442 " pdb=" O GLN C 442 " ideal model delta sigma weight residual 120.80 111.48 9.32 1.70e+00 3.46e-01 3.00e+01 angle pdb=" C SER C 227 " pdb=" N HIS C 228 " pdb=" CA HIS C 228 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C UNK C 154 " pdb=" N UNK C 155 " pdb=" CA UNK C 155 " ideal model delta sigma weight residual 121.70 130.72 -9.02 1.80e+00 3.09e-01 2.51e+01 ... (remaining 33688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 14383 16.09 - 32.19: 577 32.19 - 48.28: 102 48.28 - 64.38: 13 64.38 - 80.47: 9 Dihedral angle restraints: 15084 sinusoidal: 5742 harmonic: 9342 Sorted by residual: dihedral pdb=" CA PRO C 212 " pdb=" C PRO C 212 " pdb=" N HIS C 213 " pdb=" CA HIS C 213 " ideal model delta harmonic sigma weight residual -180.00 -99.53 -80.47 0 5.00e+00 4.00e-02 2.59e+02 dihedral pdb=" CA LEU B 102 " pdb=" C LEU B 102 " pdb=" N PRO B 103 " pdb=" CA PRO B 103 " ideal model delta harmonic sigma weight residual -180.00 -123.78 -56.22 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA ALA E 315 " pdb=" C ALA E 315 " pdb=" N PRO E 316 " pdb=" CA PRO E 316 " ideal model delta harmonic sigma weight residual 180.00 125.62 54.38 0 5.00e+00 4.00e-02 1.18e+02 ... (remaining 15081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3174 0.077 - 0.155: 627 0.155 - 0.232: 59 0.232 - 0.309: 1 0.309 - 0.387: 2 Chirality restraints: 3863 Sorted by residual: chirality pdb=" CB ILE B 595 " pdb=" CA ILE B 595 " pdb=" CG1 ILE B 595 " pdb=" CG2 ILE B 595 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CB ILE B 417 " pdb=" CA ILE B 417 " pdb=" CG1 ILE B 417 " pdb=" CG2 ILE B 417 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CG LEU A 455 " pdb=" CB LEU A 455 " pdb=" CD1 LEU A 455 " pdb=" CD2 LEU A 455 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 3860 not shown) Planarity restraints: 4354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 315 " 0.065 5.00e-02 4.00e+02 9.85e-02 1.55e+01 pdb=" N PRO E 316 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO E 316 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO E 316 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 228 " 0.032 2.00e-02 2.50e+03 2.73e-02 1.49e+01 pdb=" CG TYR E 228 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR E 228 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR E 228 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR E 228 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 228 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR E 228 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 228 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 102 " 0.058 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO B 103 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO B 103 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 103 " 0.049 5.00e-02 4.00e+02 ... (remaining 4351 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4574 2.77 - 3.30: 22362 3.30 - 3.84: 38953 3.84 - 4.37: 44853 4.37 - 4.90: 76898 Nonbonded interactions: 187640 Sorted by model distance: nonbonded pdb=" OG1 THR C 430 " pdb=" OG SER F 222 " model vdw 2.240 2.440 nonbonded pdb=" O GLU A 48 " pdb=" OG1 THR A 51 " model vdw 2.265 2.440 nonbonded pdb=" O ILE A 531 " pdb=" OG1 THR A 535 " model vdw 2.278 2.440 nonbonded pdb=" NH2 ARG B 280 " pdb=" OE1 GLU B 387 " model vdw 2.290 2.520 nonbonded pdb=" O ILE D 328 " pdb=" OG SER D 332 " model vdw 2.290 2.440 ... (remaining 187635 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.180 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 70.360 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.100 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 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 : 0.008 0.084 24844 Z= 0.494 Angle : 1.126 13.903 33693 Z= 0.611 Chirality : 0.059 0.387 3863 Planarity : 0.008 0.099 4354 Dihedral : 9.846 80.473 9009 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.56 % Favored : 89.23 % Rotamer: Outliers : 0.16 % Allowed : 2.01 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 5.88 % Twisted General : 0.32 % 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: -4.24 (0.13), residues: 2870 helix: -2.47 (0.10), residues: 1393 sheet: -2.34 (0.27), residues: 329 loop : -3.25 (0.16), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP A 77 HIS 0.022 0.002 HIS D 161 PHE 0.044 0.004 PHE A 451 TYR 0.068 0.004 TYR E 228 ARG 0.008 0.001 ARG B 616 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 775 time to evaluate : 2.953 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 TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8615 (mttt) cc_final: 0.8218 (mttm) REVERT: A 425 ARG cc_start: 0.7217 (ttt180) cc_final: 0.6188 (tmt170) REVERT: A 489 TYR cc_start: 0.7961 (t80) cc_final: 0.7130 (t80) REVERT: A 511 TRP cc_start: 0.6804 (m-10) cc_final: 0.5990 (m100) REVERT: A 564 ASN cc_start: 0.7787 (t0) cc_final: 0.7486 (t0) REVERT: A 679 PHE cc_start: 0.7282 (t80) cc_final: 0.6773 (t80) REVERT: A 715 LYS cc_start: 0.6796 (ttmt) cc_final: 0.6526 (ttpt) REVERT: B 32 LEU cc_start: 0.8261 (mp) cc_final: 0.7815 (tt) REVERT: B 42 MET cc_start: 0.8558 (tpp) cc_final: 0.8243 (tpt) REVERT: B 146 TYR cc_start: 0.8542 (t80) cc_final: 0.8037 (t80) REVERT: B 211 TYR cc_start: 0.8038 (t80) cc_final: 0.7167 (t80) REVERT: B 259 CYS cc_start: 0.7925 (t) cc_final: 0.7244 (t) REVERT: B 338 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6569 (mm-30) REVERT: B 344 LEU cc_start: 0.8980 (tp) cc_final: 0.8723 (tt) REVERT: B 478 MET cc_start: 0.8257 (tpp) cc_final: 0.7821 (ttp) REVERT: B 505 SER cc_start: 0.8625 (p) cc_final: 0.8387 (t) REVERT: B 520 TYR cc_start: 0.7835 (m-80) cc_final: 0.7592 (m-80) REVERT: C 216 THR cc_start: 0.7668 (m) cc_final: 0.7454 (t) REVERT: C 346 GLN cc_start: 0.5094 (mt0) cc_final: 0.4624 (pm20) REVERT: C 384 HIS cc_start: 0.7047 (p-80) cc_final: 0.6661 (p-80) REVERT: C 473 ARG cc_start: 0.7359 (ttt180) cc_final: 0.7050 (tmt170) REVERT: C 474 HIS cc_start: 0.5364 (m-70) cc_final: 0.5144 (m170) REVERT: C 527 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6721 (tp30) REVERT: D 140 LYS cc_start: 0.7989 (mttt) cc_final: 0.7704 (tmtt) REVERT: D 173 GLN cc_start: 0.7849 (pt0) cc_final: 0.7494 (tm-30) REVERT: D 215 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7833 (t80) REVERT: D 247 LYS cc_start: 0.7116 (mttt) cc_final: 0.6273 (pttp) REVERT: D 249 TYR cc_start: 0.6387 (m-80) cc_final: 0.6109 (m-80) REVERT: D 268 PHE cc_start: 0.8213 (m-10) cc_final: 0.7945 (m-80) REVERT: E 66 ASP cc_start: 0.8558 (m-30) cc_final: 0.8248 (m-30) REVERT: E 138 THR cc_start: 0.8363 (m) cc_final: 0.8157 (m) REVERT: E 229 LYS cc_start: 0.8306 (mttt) cc_final: 0.8048 (mttm) REVERT: E 249 LEU cc_start: 0.8871 (tp) cc_final: 0.8298 (mp) REVERT: E 306 LYS cc_start: 0.8103 (mmtt) cc_final: 0.7364 (pttm) REVERT: F 133 LEU cc_start: 0.8682 (tp) cc_final: 0.8352 (mm) REVERT: F 147 MET cc_start: 0.7843 (mmt) cc_final: 0.7305 (mmm) REVERT: F 266 TYR cc_start: 0.8172 (m-80) cc_final: 0.7808 (m-80) REVERT: H 108 ASN cc_start: 0.7515 (m-40) cc_final: 0.7003 (m110) REVERT: H 155 ARG cc_start: 0.7568 (mtt180) cc_final: 0.6989 (ttp80) REVERT: H 168 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7588 (mt-10) REVERT: H 171 LEU cc_start: 0.8410 (tp) cc_final: 0.8162 (tt) outliers start: 4 outliers final: 2 residues processed: 778 average time/residue: 0.4262 time to fit residues: 482.7527 Evaluate side-chains 412 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 409 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain F residue 157 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 140 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 249 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 HIS A 366 ASN A 591 GLN A 595 ASN B 164 HIS ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN B 384 HIS ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 GLN B 562 GLN B 715 GLN B 726 GLN C 228 HIS C 384 HIS C 398 GLN D 18 ASN D 54 ASN D 116 GLN D 141 HIS D 181 GLN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 HIS E 257 HIS ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 GLN G 36 GLN G 64 ASN H 28 HIS ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24844 Z= 0.208 Angle : 0.691 11.022 33693 Z= 0.356 Chirality : 0.043 0.214 3863 Planarity : 0.005 0.085 4354 Dihedral : 6.565 73.535 3439 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.98 % Favored : 91.95 % Rotamer: Outliers : 3.14 % Allowed : 10.49 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 3.36 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.14), residues: 2870 helix: -0.82 (0.13), residues: 1378 sheet: -2.11 (0.27), residues: 334 loop : -3.01 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 493 HIS 0.006 0.001 HIS D 97 PHE 0.022 0.002 PHE B 104 TYR 0.039 0.002 TYR A 581 ARG 0.007 0.001 ARG A 639 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 493 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8604 (mttt) cc_final: 0.8241 (mttm) REVERT: A 277 ILE cc_start: 0.8762 (mm) cc_final: 0.8345 (pt) REVERT: A 291 LEU cc_start: 0.6875 (mt) cc_final: 0.6626 (mt) REVERT: A 399 LYS cc_start: 0.7527 (mmmm) cc_final: 0.7114 (mmtm) REVERT: A 425 ARG cc_start: 0.7108 (ttt180) cc_final: 0.6078 (tmt170) REVERT: A 429 TRP cc_start: 0.7414 (t60) cc_final: 0.6871 (t-100) REVERT: A 489 TYR cc_start: 0.7885 (t80) cc_final: 0.7050 (t80) REVERT: A 529 LYS cc_start: 0.8053 (tttt) cc_final: 0.7633 (mttp) REVERT: A 564 ASN cc_start: 0.8018 (t0) cc_final: 0.7486 (t0) REVERT: A 639 ARG cc_start: 0.8001 (ptp-170) cc_final: 0.7661 (mtp180) REVERT: A 655 TYR cc_start: 0.7297 (m-80) cc_final: 0.7094 (m-80) REVERT: A 715 LYS cc_start: 0.6367 (ttmt) cc_final: 0.6091 (ttpt) REVERT: B 22 PHE cc_start: 0.7552 (t80) cc_final: 0.7274 (t80) REVERT: B 211 TYR cc_start: 0.8066 (t80) cc_final: 0.7304 (t80) REVERT: B 220 LEU cc_start: 0.4641 (OUTLIER) cc_final: 0.4297 (pp) REVERT: B 273 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8250 (tp) REVERT: B 274 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7852 (tptp) REVERT: B 338 GLU cc_start: 0.6773 (mm-30) cc_final: 0.6517 (mm-30) REVERT: B 344 LEU cc_start: 0.9057 (tp) cc_final: 0.8813 (tt) REVERT: B 421 PHE cc_start: 0.7506 (p90) cc_final: 0.6977 (p90) REVERT: B 478 MET cc_start: 0.8239 (tpp) cc_final: 0.7893 (ttp) REVERT: B 629 GLN cc_start: 0.6492 (tp-100) cc_final: 0.5331 (tt0) REVERT: B 641 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6615 (ttt180) REVERT: C 346 GLN cc_start: 0.5046 (mt0) cc_final: 0.4771 (pt0) REVERT: C 527 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6749 (tp30) REVERT: D 140 LYS cc_start: 0.7931 (mttt) cc_final: 0.7670 (tmtt) REVERT: D 215 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7922 (t80) REVERT: D 247 LYS cc_start: 0.7051 (mttt) cc_final: 0.6377 (pttp) REVERT: D 268 PHE cc_start: 0.8220 (m-10) cc_final: 0.7832 (m-10) REVERT: D 433 PHE cc_start: 0.6571 (t80) cc_final: 0.6175 (t80) REVERT: E 66 ASP cc_start: 0.8516 (m-30) cc_final: 0.8218 (m-30) REVERT: E 174 LEU cc_start: 0.8676 (mt) cc_final: 0.8446 (mp) REVERT: E 186 ILE cc_start: 0.9045 (mt) cc_final: 0.8733 (mt) REVERT: E 249 LEU cc_start: 0.8795 (tp) cc_final: 0.8302 (mp) REVERT: E 331 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.7019 (m-10) REVERT: F 8 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7796 (tp) REVERT: F 147 MET cc_start: 0.7843 (mmt) cc_final: 0.7348 (mmm) REVERT: F 160 ARG cc_start: 0.8488 (ptt90) cc_final: 0.8213 (ptt90) REVERT: H 71 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7962 (pt0) REVERT: H 108 ASN cc_start: 0.7414 (m-40) cc_final: 0.6996 (m110) REVERT: H 154 GLU cc_start: 0.7998 (tt0) cc_final: 0.7444 (tp30) REVERT: H 155 ARG cc_start: 0.7437 (mtt180) cc_final: 0.6940 (ttp80) REVERT: H 168 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7404 (mt-10) REVERT: H 169 GLU cc_start: 0.7526 (pt0) cc_final: 0.7291 (pp20) outliers start: 78 outliers final: 38 residues processed: 544 average time/residue: 0.3762 time to fit residues: 314.4619 Evaluate side-chains 412 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 367 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 189 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 138 optimal weight: 0.1980 chunk 77 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 170 optimal weight: 30.0000 chunk 68 optimal weight: 8.9990 chunk 250 optimal weight: 9.9990 chunk 270 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 chunk 248 optimal weight: 0.0040 chunk 85 optimal weight: 4.9990 chunk 200 optimal weight: 0.0970 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 HIS A 665 GLN B 237 HIS B 241 ASN B 434 HIS B 613 HIS C 384 HIS C 398 GLN C 474 HIS D 181 GLN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 HIS ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 ASN ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24844 Z= 0.171 Angle : 0.632 11.235 33693 Z= 0.322 Chirality : 0.042 0.272 3863 Planarity : 0.004 0.073 4354 Dihedral : 5.836 67.976 3436 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.35 % Favored : 92.54 % Rotamer: Outliers : 3.34 % Allowed : 13.30 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 2.52 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.15), residues: 2870 helix: 0.06 (0.13), residues: 1380 sheet: -1.95 (0.28), residues: 329 loop : -2.71 (0.17), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 129 HIS 0.033 0.001 HIS H 28 PHE 0.038 0.002 PHE D 331 TYR 0.029 0.002 TYR A 581 ARG 0.006 0.000 ARG D 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 455 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7763 (ttmm) REVERT: A 167 LYS cc_start: 0.8560 (mttt) cc_final: 0.8301 (mttm) REVERT: A 291 LEU cc_start: 0.6940 (mt) cc_final: 0.6691 (mt) REVERT: A 399 LYS cc_start: 0.7506 (mmmm) cc_final: 0.7233 (mmtm) REVERT: A 425 ARG cc_start: 0.6875 (ttt180) cc_final: 0.5944 (tmt170) REVERT: A 427 MET cc_start: 0.7410 (mmt) cc_final: 0.6852 (mmt) REVERT: A 429 TRP cc_start: 0.7406 (t60) cc_final: 0.6811 (t-100) REVERT: A 529 LYS cc_start: 0.8060 (tttt) cc_final: 0.7630 (mttp) REVERT: A 564 ASN cc_start: 0.7937 (t0) cc_final: 0.7537 (t0) REVERT: B 1 MET cc_start: 0.6848 (ttm) cc_final: 0.6648 (ttm) REVERT: B 25 MET cc_start: 0.7882 (mmm) cc_final: 0.7447 (mmp) REVERT: B 42 MET cc_start: 0.8380 (tpp) cc_final: 0.7456 (tpp) REVERT: B 211 TYR cc_start: 0.8033 (t80) cc_final: 0.7291 (t80) REVERT: B 274 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7752 (tptp) REVERT: B 329 PHE cc_start: 0.8014 (t80) cc_final: 0.7631 (t80) REVERT: B 338 GLU cc_start: 0.6704 (mm-30) cc_final: 0.6338 (mm-30) REVERT: B 344 LEU cc_start: 0.9034 (tp) cc_final: 0.8812 (tt) REVERT: B 421 PHE cc_start: 0.7390 (p90) cc_final: 0.6928 (p90) REVERT: B 478 MET cc_start: 0.8094 (tpp) cc_final: 0.7813 (ttp) REVERT: B 629 GLN cc_start: 0.6495 (tp-100) cc_final: 0.5242 (tt0) REVERT: C 313 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6598 (mmt) REVERT: C 346 GLN cc_start: 0.4979 (mt0) cc_final: 0.4449 (pm20) REVERT: D 37 HIS cc_start: 0.7269 (OUTLIER) cc_final: 0.6638 (t-90) REVERT: D 57 MET cc_start: 0.8197 (tpp) cc_final: 0.7641 (mpp) REVERT: D 188 THR cc_start: 0.6723 (OUTLIER) cc_final: 0.6359 (t) REVERT: D 247 LYS cc_start: 0.6911 (mttt) cc_final: 0.6296 (ptmm) REVERT: D 268 PHE cc_start: 0.8125 (m-10) cc_final: 0.7739 (m-10) REVERT: E 62 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7910 (t80) REVERT: E 66 ASP cc_start: 0.8493 (m-30) cc_final: 0.8285 (m-30) REVERT: E 249 LEU cc_start: 0.8831 (tp) cc_final: 0.8355 (mp) REVERT: F 147 MET cc_start: 0.7801 (mmt) cc_final: 0.7269 (mmm) REVERT: F 160 ARG cc_start: 0.8481 (ptt90) cc_final: 0.8237 (ptt90) REVERT: H 108 ASN cc_start: 0.7534 (m-40) cc_final: 0.7015 (m110) REVERT: H 154 GLU cc_start: 0.7955 (tt0) cc_final: 0.7433 (tp30) REVERT: H 155 ARG cc_start: 0.7356 (mtt180) cc_final: 0.6937 (ttp80) REVERT: H 168 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7412 (mt-10) REVERT: H 171 LEU cc_start: 0.8130 (tt) cc_final: 0.7845 (mm) outliers start: 83 outliers final: 40 residues processed: 512 average time/residue: 0.3725 time to fit residues: 295.4644 Evaluate side-chains 422 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 376 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 474 HIS Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 144 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 247 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 chunk 129 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 chunk 251 optimal weight: 0.1980 chunk 265 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 237 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 551 HIS ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 GLN C 384 HIS C 398 GLN ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24844 Z= 0.198 Angle : 0.633 12.529 33693 Z= 0.320 Chirality : 0.042 0.268 3863 Planarity : 0.004 0.074 4354 Dihedral : 5.493 60.661 3434 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.91 % Favored : 92.06 % Rotamer: Outliers : 3.70 % Allowed : 14.79 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.15), residues: 2870 helix: 0.44 (0.14), residues: 1387 sheet: -1.94 (0.28), residues: 329 loop : -2.60 (0.17), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 129 HIS 0.019 0.001 HIS C 474 PHE 0.030 0.002 PHE D 331 TYR 0.024 0.002 TYR E 339 ARG 0.005 0.000 ARG D 371 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 409 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7923 (ttmm) REVERT: A 167 LYS cc_start: 0.8560 (mttt) cc_final: 0.8282 (mttm) REVERT: A 266 GLN cc_start: 0.7537 (tp-100) cc_final: 0.7043 (tp-100) REVERT: A 399 LYS cc_start: 0.7495 (mmmm) cc_final: 0.7217 (mmtm) REVERT: A 425 ARG cc_start: 0.6891 (ttt180) cc_final: 0.5961 (tmt170) REVERT: A 495 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6664 (tm-30) REVERT: A 529 LYS cc_start: 0.8070 (tttt) cc_final: 0.7696 (mttp) REVERT: A 564 ASN cc_start: 0.8045 (t0) cc_final: 0.7472 (t0) REVERT: B 1 MET cc_start: 0.7123 (ttm) cc_final: 0.6857 (ttm) REVERT: B 29 LYS cc_start: 0.7656 (tptt) cc_final: 0.7133 (tttt) REVERT: B 42 MET cc_start: 0.8486 (tpp) cc_final: 0.8118 (tpt) REVERT: B 211 TYR cc_start: 0.8252 (t80) cc_final: 0.7416 (t80) REVERT: B 274 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7788 (tptp) REVERT: B 338 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6380 (mm-30) REVERT: B 344 LEU cc_start: 0.9068 (tp) cc_final: 0.8851 (tt) REVERT: B 478 MET cc_start: 0.8192 (tpp) cc_final: 0.7858 (ttp) REVERT: B 542 TYR cc_start: 0.7533 (m-80) cc_final: 0.7260 (m-80) REVERT: B 629 GLN cc_start: 0.6444 (tp-100) cc_final: 0.5270 (tt0) REVERT: C 313 MET cc_start: 0.7074 (OUTLIER) cc_final: 0.6664 (mmt) REVERT: C 346 GLN cc_start: 0.4971 (mt0) cc_final: 0.4452 (pm20) REVERT: C 405 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.8015 (mp10) REVERT: D 37 HIS cc_start: 0.7313 (OUTLIER) cc_final: 0.6703 (t-90) REVERT: D 54 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8058 (t160) REVERT: D 115 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6614 (ttm170) REVERT: D 127 LYS cc_start: 0.7632 (pttm) cc_final: 0.7310 (mtmm) REVERT: D 188 THR cc_start: 0.6613 (OUTLIER) cc_final: 0.6362 (t) REVERT: D 247 LYS cc_start: 0.6878 (mttt) cc_final: 0.6300 (ptmm) REVERT: D 268 PHE cc_start: 0.8193 (m-10) cc_final: 0.7784 (m-80) REVERT: D 341 MET cc_start: 0.8016 (ptm) cc_final: 0.7267 (ptp) REVERT: E 249 LEU cc_start: 0.8789 (tp) cc_final: 0.8346 (mp) REVERT: E 331 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.6806 (m-10) REVERT: F 8 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7542 (tp) REVERT: F 147 MET cc_start: 0.7776 (mmt) cc_final: 0.7239 (mmm) REVERT: F 160 ARG cc_start: 0.8531 (ptt90) cc_final: 0.8180 (ptt90) REVERT: F 213 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7328 (tt) REVERT: H 71 GLU cc_start: 0.7995 (tt0) cc_final: 0.7663 (tt0) REVERT: H 108 ASN cc_start: 0.7504 (m-40) cc_final: 0.6948 (m110) REVERT: H 154 GLU cc_start: 0.7957 (tt0) cc_final: 0.7391 (tp30) REVERT: H 155 ARG cc_start: 0.7285 (mtt180) cc_final: 0.6787 (ttp80) REVERT: H 168 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7332 (mt-10) outliers start: 92 outliers final: 51 residues processed: 482 average time/residue: 0.3517 time to fit residues: 265.4763 Evaluate side-chains 441 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 378 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain C residue 212 PRO Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 189 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 221 optimal weight: 5.9990 chunk 150 optimal weight: 0.5980 chunk 3 optimal weight: 8.9990 chunk 197 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 226 optimal weight: 6.9990 chunk 183 optimal weight: 0.0370 chunk 0 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 chunk 238 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS A 551 HIS A 665 GLN A 677 GLN ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS C 474 HIS ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 HIS ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 24844 Z= 0.261 Angle : 0.657 10.335 33693 Z= 0.334 Chirality : 0.043 0.295 3863 Planarity : 0.005 0.071 4354 Dihedral : 5.508 54.869 3434 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.89 % Favored : 91.08 % Rotamer: Outliers : 4.30 % Allowed : 15.15 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.16), residues: 2870 helix: 0.55 (0.14), residues: 1384 sheet: -2.00 (0.28), residues: 332 loop : -2.53 (0.17), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 129 HIS 0.010 0.001 HIS H 28 PHE 0.031 0.002 PHE D 331 TYR 0.036 0.002 TYR A 581 ARG 0.006 0.001 ARG F 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 405 time to evaluate : 2.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7984 (ttmm) REVERT: A 54 ASP cc_start: 0.7999 (m-30) cc_final: 0.7245 (t0) REVERT: A 167 LYS cc_start: 0.8618 (mttt) cc_final: 0.8338 (mttm) REVERT: A 399 LYS cc_start: 0.7505 (mmmm) cc_final: 0.7222 (mmtm) REVERT: A 425 ARG cc_start: 0.6920 (ttt180) cc_final: 0.5950 (tmt170) REVERT: A 495 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6731 (tm-30) REVERT: A 529 LYS cc_start: 0.8129 (tttt) cc_final: 0.7713 (mttp) REVERT: A 564 ASN cc_start: 0.8157 (t0) cc_final: 0.7574 (t0) REVERT: A 581 TYR cc_start: 0.5897 (p90) cc_final: 0.5691 (p90) REVERT: B 1 MET cc_start: 0.7174 (ttm) cc_final: 0.6863 (ttm) REVERT: B 25 MET cc_start: 0.7548 (mmm) cc_final: 0.7171 (mmt) REVERT: B 211 TYR cc_start: 0.8350 (t80) cc_final: 0.7467 (t80) REVERT: B 274 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7761 (tptp) REVERT: B 329 PHE cc_start: 0.7920 (t80) cc_final: 0.7526 (t80) REVERT: B 338 GLU cc_start: 0.6772 (mm-30) cc_final: 0.6348 (mm-30) REVERT: B 344 LEU cc_start: 0.9147 (tp) cc_final: 0.8902 (tt) REVERT: B 421 PHE cc_start: 0.7617 (p90) cc_final: 0.7331 (p90) REVERT: B 478 MET cc_start: 0.8175 (tpp) cc_final: 0.7808 (ttp) REVERT: B 542 TYR cc_start: 0.7497 (m-80) cc_final: 0.7209 (m-80) REVERT: B 629 GLN cc_start: 0.6446 (tp-100) cc_final: 0.5314 (tt0) REVERT: C 313 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.6658 (mmt) REVERT: C 346 GLN cc_start: 0.4970 (mt0) cc_final: 0.4433 (pm20) REVERT: C 405 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7906 (mp10) REVERT: D 37 HIS cc_start: 0.7363 (OUTLIER) cc_final: 0.6728 (t-90) REVERT: D 54 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8108 (t160) REVERT: D 115 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6628 (ttm170) REVERT: D 127 LYS cc_start: 0.7632 (pttm) cc_final: 0.7345 (mtmm) REVERT: D 188 THR cc_start: 0.6914 (OUTLIER) cc_final: 0.6615 (t) REVERT: D 247 LYS cc_start: 0.6935 (mttt) cc_final: 0.6291 (ptmm) REVERT: D 268 PHE cc_start: 0.8286 (m-10) cc_final: 0.7859 (m-80) REVERT: E 66 ASP cc_start: 0.8666 (m-30) cc_final: 0.8396 (m-30) REVERT: E 249 LEU cc_start: 0.8811 (tp) cc_final: 0.8275 (mp) REVERT: E 331 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.6717 (m-10) REVERT: F 147 MET cc_start: 0.7772 (mmt) cc_final: 0.7236 (mmm) REVERT: F 160 ARG cc_start: 0.8456 (ptt90) cc_final: 0.8091 (ptt90) REVERT: F 213 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7377 (tt) REVERT: H 71 GLU cc_start: 0.8035 (tt0) cc_final: 0.7752 (tt0) REVERT: H 108 ASN cc_start: 0.7599 (m-40) cc_final: 0.7037 (m110) REVERT: H 154 GLU cc_start: 0.8038 (tt0) cc_final: 0.7361 (tp30) REVERT: H 155 ARG cc_start: 0.7249 (mtt180) cc_final: 0.6630 (ttp80) outliers start: 107 outliers final: 67 residues processed: 486 average time/residue: 0.3549 time to fit residues: 269.3490 Evaluate side-chains 453 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 375 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain C residue 212 PRO Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 474 HIS Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 299 CYS Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain H residue 186 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 89 optimal weight: 0.9990 chunk 239 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 266 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 HIS ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS D 181 GLN ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 ASN ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24844 Z= 0.176 Angle : 0.612 9.575 33693 Z= 0.310 Chirality : 0.042 0.262 3863 Planarity : 0.004 0.071 4354 Dihedral : 5.241 57.855 3434 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.42 % Favored : 92.54 % Rotamer: Outliers : 3.58 % Allowed : 16.40 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.16), residues: 2870 helix: 0.79 (0.14), residues: 1386 sheet: -1.94 (0.28), residues: 335 loop : -2.39 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 511 HIS 0.018 0.001 HIS C 474 PHE 0.032 0.002 PHE A 615 TYR 0.033 0.001 TYR A 581 ARG 0.007 0.000 ARG B 518 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 426 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7865 (ttmm) REVERT: A 54 ASP cc_start: 0.7899 (m-30) cc_final: 0.7222 (t0) REVERT: A 167 LYS cc_start: 0.8560 (mttt) cc_final: 0.8249 (mttm) REVERT: A 399 LYS cc_start: 0.7442 (mmmm) cc_final: 0.7203 (mmtm) REVERT: A 425 ARG cc_start: 0.6886 (ttt180) cc_final: 0.5958 (tmt170) REVERT: A 427 MET cc_start: 0.7764 (mmt) cc_final: 0.7359 (mmt) REVERT: A 495 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6644 (tm-30) REVERT: A 529 LYS cc_start: 0.8128 (tttt) cc_final: 0.7782 (mttp) REVERT: A 564 ASN cc_start: 0.8089 (t0) cc_final: 0.7541 (t0) REVERT: A 621 ASN cc_start: 0.7755 (m110) cc_final: 0.7439 (t0) REVERT: B 1 MET cc_start: 0.7039 (ttm) cc_final: 0.6650 (ttm) REVERT: B 16 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.7286 (m-80) REVERT: B 25 MET cc_start: 0.7456 (mmm) cc_final: 0.7149 (mmt) REVERT: B 211 TYR cc_start: 0.8289 (t80) cc_final: 0.7420 (t80) REVERT: B 274 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7731 (tptp) REVERT: B 329 PHE cc_start: 0.7933 (t80) cc_final: 0.7689 (t80) REVERT: B 338 GLU cc_start: 0.6686 (mm-30) cc_final: 0.6345 (mm-30) REVERT: B 344 LEU cc_start: 0.9106 (tp) cc_final: 0.8864 (tt) REVERT: B 371 PRO cc_start: 0.8825 (Cg_endo) cc_final: 0.8617 (Cg_exo) REVERT: B 421 PHE cc_start: 0.7576 (p90) cc_final: 0.7030 (p90) REVERT: B 478 MET cc_start: 0.8170 (tpp) cc_final: 0.7776 (ttp) REVERT: B 527 MET cc_start: 0.8568 (tpp) cc_final: 0.8074 (tpp) REVERT: B 542 TYR cc_start: 0.7433 (m-80) cc_final: 0.7207 (m-80) REVERT: B 629 GLN cc_start: 0.6198 (tp-100) cc_final: 0.5179 (tt0) REVERT: C 346 GLN cc_start: 0.4934 (mt0) cc_final: 0.4427 (pm20) REVERT: C 405 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7921 (mp10) REVERT: D 57 MET cc_start: 0.8343 (tpp) cc_final: 0.7675 (mpp) REVERT: D 115 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6604 (ttm170) REVERT: D 127 LYS cc_start: 0.7637 (pttm) cc_final: 0.7344 (mtmm) REVERT: D 188 THR cc_start: 0.7122 (OUTLIER) cc_final: 0.6870 (t) REVERT: D 247 LYS cc_start: 0.6962 (mttt) cc_final: 0.6312 (ptmm) REVERT: D 268 PHE cc_start: 0.8209 (m-10) cc_final: 0.7841 (m-80) REVERT: E 66 ASP cc_start: 0.8613 (m-30) cc_final: 0.8297 (m-30) REVERT: E 185 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8247 (tp) REVERT: E 249 LEU cc_start: 0.8767 (tp) cc_final: 0.8277 (mp) REVERT: E 331 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.6784 (m-10) REVERT: F 147 MET cc_start: 0.7761 (mmt) cc_final: 0.7241 (mmm) REVERT: F 160 ARG cc_start: 0.8422 (ptt90) cc_final: 0.8025 (ptt90) REVERT: F 213 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7285 (tt) REVERT: H 71 GLU cc_start: 0.7979 (tt0) cc_final: 0.7691 (tt0) REVERT: H 108 ASN cc_start: 0.7561 (m-40) cc_final: 0.7029 (m110) REVERT: H 154 GLU cc_start: 0.7990 (tt0) cc_final: 0.7550 (tp30) REVERT: H 155 ARG cc_start: 0.7357 (mtt180) cc_final: 0.6721 (ttp80) outliers start: 89 outliers final: 62 residues processed: 496 average time/residue: 0.3502 time to fit residues: 271.8309 Evaluate side-chains 450 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 378 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 16 TYR Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain C residue 212 PRO Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain H residue 186 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 256 optimal weight: 40.0000 chunk 29 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 265 optimal weight: 7.9990 chunk 165 optimal weight: 20.0000 chunk 161 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS A 594 GLN A 677 GLN B 135 HIS ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS C 474 HIS ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 GLN ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 24844 Z= 0.398 Angle : 0.758 10.700 33693 Z= 0.386 Chirality : 0.047 0.245 3863 Planarity : 0.005 0.077 4354 Dihedral : 5.802 57.869 3434 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.73 % Favored : 89.23 % Rotamer: Outliers : 4.74 % Allowed : 16.72 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.15), residues: 2870 helix: 0.46 (0.14), residues: 1363 sheet: -2.10 (0.27), residues: 356 loop : -2.46 (0.17), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 129 HIS 0.009 0.002 HIS C 474 PHE 0.028 0.002 PHE D 331 TYR 0.024 0.002 TYR B 520 ARG 0.007 0.001 ARG B 518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 375 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8131 (ttmm) REVERT: A 54 ASP cc_start: 0.7967 (m-30) cc_final: 0.7482 (t0) REVERT: A 146 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8417 (p) REVERT: A 167 LYS cc_start: 0.8597 (mttt) cc_final: 0.8386 (mttm) REVERT: A 399 LYS cc_start: 0.7563 (mmmm) cc_final: 0.7339 (mmtm) REVERT: A 425 ARG cc_start: 0.6953 (ttt180) cc_final: 0.6018 (tmt170) REVERT: A 511 TRP cc_start: 0.7205 (m-10) cc_final: 0.6718 (m-90) REVERT: A 529 LYS cc_start: 0.8191 (tttt) cc_final: 0.7848 (mttp) REVERT: B 1 MET cc_start: 0.7267 (ttm) cc_final: 0.6985 (ttm) REVERT: B 16 TYR cc_start: 0.7664 (OUTLIER) cc_final: 0.7460 (m-80) REVERT: B 274 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7811 (tptp) REVERT: B 338 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6545 (mm-30) REVERT: B 421 PHE cc_start: 0.7587 (p90) cc_final: 0.7020 (p90) REVERT: B 478 MET cc_start: 0.8212 (tpp) cc_final: 0.7468 (ttp) REVERT: B 526 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7159 (mt-10) REVERT: B 629 GLN cc_start: 0.6284 (tp-100) cc_final: 0.5478 (tt0) REVERT: B 708 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8090 (mp) REVERT: C 346 GLN cc_start: 0.4930 (mt0) cc_final: 0.4344 (pm20) REVERT: C 383 TYR cc_start: 0.7763 (m-10) cc_final: 0.7285 (m-80) REVERT: C 405 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7920 (mp10) REVERT: D 37 HIS cc_start: 0.7308 (OUTLIER) cc_final: 0.6840 (t-90) REVERT: D 54 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8182 (t160) REVERT: D 115 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.6753 (ttm170) REVERT: D 127 LYS cc_start: 0.7708 (pttm) cc_final: 0.7368 (mtmm) REVERT: D 181 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7065 (mp10) REVERT: D 188 THR cc_start: 0.6939 (OUTLIER) cc_final: 0.6610 (t) REVERT: D 247 LYS cc_start: 0.6803 (mttt) cc_final: 0.6205 (ptmm) REVERT: D 268 PHE cc_start: 0.8347 (m-10) cc_final: 0.7920 (m-80) REVERT: D 341 MET cc_start: 0.7928 (ptm) cc_final: 0.7115 (ptp) REVERT: E 66 ASP cc_start: 0.8740 (m-30) cc_final: 0.8475 (m-30) REVERT: E 249 LEU cc_start: 0.8818 (tp) cc_final: 0.8513 (mt) REVERT: E 370 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7676 (p0) REVERT: F 147 MET cc_start: 0.7781 (mmt) cc_final: 0.7290 (mmm) REVERT: F 213 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7537 (tt) REVERT: F 261 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8807 (mt) REVERT: G 5 LEU cc_start: 0.4412 (OUTLIER) cc_final: 0.4076 (tt) REVERT: H 71 GLU cc_start: 0.8050 (tt0) cc_final: 0.7788 (tt0) REVERT: H 108 ASN cc_start: 0.7882 (m-40) cc_final: 0.7282 (m110) REVERT: H 155 ARG cc_start: 0.7571 (mtt180) cc_final: 0.6771 (ttp80) outliers start: 118 outliers final: 81 residues processed: 468 average time/residue: 0.3353 time to fit residues: 248.9865 Evaluate side-chains 446 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 349 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 16 TYR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain C residue 212 PRO Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 474 HIS Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 455 TRP Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 122 MET Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 186 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 163 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 158 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 208 optimal weight: 0.9980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS D 181 GLN ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24844 Z= 0.238 Angle : 0.663 11.376 33693 Z= 0.335 Chirality : 0.043 0.264 3863 Planarity : 0.004 0.071 4354 Dihedral : 5.479 56.822 3434 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.26 % Favored : 91.71 % Rotamer: Outliers : 3.86 % Allowed : 18.09 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.16), residues: 2870 helix: 0.65 (0.14), residues: 1387 sheet: -1.90 (0.27), residues: 357 loop : -2.41 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 129 HIS 0.021 0.001 HIS C 474 PHE 0.030 0.002 PHE A 615 TYR 0.029 0.002 TYR A 522 ARG 0.006 0.001 ARG A 678 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 373 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8051 (m-30) cc_final: 0.7672 (t0) REVERT: A 153 MET cc_start: 0.8449 (mmt) cc_final: 0.7951 (mmt) REVERT: A 167 LYS cc_start: 0.8567 (mttt) cc_final: 0.8363 (mttm) REVERT: A 399 LYS cc_start: 0.7451 (mmmm) cc_final: 0.7208 (mmtm) REVERT: A 425 ARG cc_start: 0.6943 (ttt180) cc_final: 0.5946 (tmt170) REVERT: A 495 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6836 (tm-30) REVERT: A 529 LYS cc_start: 0.8147 (tttt) cc_final: 0.7797 (mttp) REVERT: A 650 MET cc_start: 0.6168 (mtt) cc_final: 0.5896 (ttm) REVERT: B 25 MET cc_start: 0.7421 (mmm) cc_final: 0.6997 (mmt) REVERT: B 220 LEU cc_start: 0.4872 (OUTLIER) cc_final: 0.4649 (pp) REVERT: B 274 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7823 (tptp) REVERT: B 338 GLU cc_start: 0.6687 (mm-30) cc_final: 0.6247 (mm-30) REVERT: B 421 PHE cc_start: 0.7477 (p90) cc_final: 0.6989 (p90) REVERT: B 478 MET cc_start: 0.8169 (tpp) cc_final: 0.7385 (ttp) REVERT: B 526 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: B 542 TYR cc_start: 0.7617 (m-80) cc_final: 0.7321 (m-80) REVERT: B 629 GLN cc_start: 0.6155 (tp-100) cc_final: 0.5233 (tt0) REVERT: C 346 GLN cc_start: 0.4843 (mt0) cc_final: 0.4360 (pm20) REVERT: C 383 TYR cc_start: 0.7714 (m-10) cc_final: 0.7194 (m-80) REVERT: C 405 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7915 (mp10) REVERT: D 54 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8121 (t160) REVERT: D 57 MET cc_start: 0.8350 (tpp) cc_final: 0.7566 (mpp) REVERT: D 115 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6858 (ttm170) REVERT: D 127 LYS cc_start: 0.7696 (pttm) cc_final: 0.7318 (mtmm) REVERT: D 181 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6788 (mp10) REVERT: D 188 THR cc_start: 0.6828 (OUTLIER) cc_final: 0.6551 (t) REVERT: D 247 LYS cc_start: 0.6812 (mttt) cc_final: 0.6260 (ptmm) REVERT: D 268 PHE cc_start: 0.8273 (m-10) cc_final: 0.7898 (m-80) REVERT: D 341 MET cc_start: 0.7904 (ptm) cc_final: 0.7222 (ptp) REVERT: E 66 ASP cc_start: 0.8702 (m-30) cc_final: 0.8400 (m-30) REVERT: E 249 LEU cc_start: 0.8825 (tp) cc_final: 0.8300 (mp) REVERT: F 147 MET cc_start: 0.7776 (mmt) cc_final: 0.7273 (mmm) REVERT: F 213 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7384 (tt) REVERT: F 261 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8768 (mt) REVERT: H 71 GLU cc_start: 0.7999 (tt0) cc_final: 0.7713 (tt0) REVERT: H 108 ASN cc_start: 0.7621 (m-40) cc_final: 0.7070 (m110) REVERT: H 155 ARG cc_start: 0.7596 (mtt180) cc_final: 0.6828 (ttp80) outliers start: 96 outliers final: 67 residues processed: 449 average time/residue: 0.3525 time to fit residues: 247.9245 Evaluate side-chains 436 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 358 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain C residue 212 PRO Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 186 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 241 optimal weight: 3.9990 chunk 253 optimal weight: 1.9990 chunk 231 optimal weight: 0.0270 chunk 246 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 193 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 223 optimal weight: 0.9980 chunk 233 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS C 474 HIS D 181 GLN ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 ASN ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24844 Z= 0.195 Angle : 0.640 10.992 33693 Z= 0.322 Chirality : 0.042 0.269 3863 Planarity : 0.004 0.070 4354 Dihedral : 5.266 55.732 3434 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.71 % Favored : 91.25 % Rotamer: Outliers : 3.30 % Allowed : 18.69 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.16), residues: 2870 helix: 0.84 (0.14), residues: 1386 sheet: -1.87 (0.27), residues: 354 loop : -2.31 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 493 HIS 0.011 0.001 HIS C 474 PHE 0.030 0.002 PHE A 615 TYR 0.027 0.001 TYR B 339 ARG 0.007 0.000 ARG D 371 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 379 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8017 (m-30) cc_final: 0.7674 (t0) REVERT: A 167 LYS cc_start: 0.8537 (mttt) cc_final: 0.8298 (mttm) REVERT: A 378 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8365 (t80) REVERT: A 399 LYS cc_start: 0.7375 (mmmm) cc_final: 0.7146 (mmtm) REVERT: A 425 ARG cc_start: 0.6975 (ttt180) cc_final: 0.6014 (tmt170) REVERT: A 495 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6623 (tm-30) REVERT: A 529 LYS cc_start: 0.8155 (tttt) cc_final: 0.7731 (mttp) REVERT: A 564 ASN cc_start: 0.8199 (t0) cc_final: 0.7966 (t0) REVERT: A 650 MET cc_start: 0.6123 (mtt) cc_final: 0.5909 (ttm) REVERT: B 25 MET cc_start: 0.7411 (mmm) cc_final: 0.7039 (mmt) REVERT: B 220 LEU cc_start: 0.4719 (OUTLIER) cc_final: 0.4501 (pp) REVERT: B 274 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7787 (tptp) REVERT: B 338 GLU cc_start: 0.6603 (mm-30) cc_final: 0.6178 (mm-30) REVERT: B 421 PHE cc_start: 0.7577 (p90) cc_final: 0.7259 (p90) REVERT: B 478 MET cc_start: 0.8174 (tpp) cc_final: 0.7350 (ttp) REVERT: B 629 GLN cc_start: 0.6094 (tp-100) cc_final: 0.5252 (tt0) REVERT: C 346 GLN cc_start: 0.4809 (mt0) cc_final: 0.4345 (pm20) REVERT: C 405 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7872 (mp10) REVERT: D 54 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8122 (t160) REVERT: D 57 MET cc_start: 0.8283 (tpp) cc_final: 0.7636 (mpp) REVERT: D 115 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6837 (ttm170) REVERT: D 127 LYS cc_start: 0.7719 (pttm) cc_final: 0.7342 (mtmm) REVERT: D 247 LYS cc_start: 0.6801 (mttt) cc_final: 0.6217 (ptmm) REVERT: D 268 PHE cc_start: 0.8227 (m-10) cc_final: 0.7837 (m-80) REVERT: D 341 MET cc_start: 0.8057 (ptm) cc_final: 0.7473 (ptp) REVERT: E 66 ASP cc_start: 0.8685 (m-30) cc_final: 0.8344 (m-30) REVERT: E 249 LEU cc_start: 0.8824 (tp) cc_final: 0.8377 (mp) REVERT: E 331 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.6583 (m-10) REVERT: F 147 MET cc_start: 0.7760 (mmt) cc_final: 0.7270 (mmm) REVERT: F 213 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7320 (tt) REVERT: H 71 GLU cc_start: 0.7995 (tt0) cc_final: 0.7671 (tt0) REVERT: H 108 ASN cc_start: 0.7568 (m-40) cc_final: 0.7033 (m110) REVERT: H 155 ARG cc_start: 0.7465 (mtt180) cc_final: 0.6767 (ttp80) outliers start: 82 outliers final: 58 residues processed: 444 average time/residue: 0.3565 time to fit residues: 249.3437 Evaluate side-chains 429 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 362 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain C residue 212 PRO Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 474 HIS Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 186 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 261 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 181 optimal weight: 5.9990 chunk 273 optimal weight: 6.9990 chunk 252 optimal weight: 5.9990 chunk 218 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 168 optimal weight: 10.0000 chunk 133 optimal weight: 0.5980 chunk 173 optimal weight: 0.0170 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS C 474 HIS D 181 GLN ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 ASN F 108 ASN F 205 GLN ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24844 Z= 0.174 Angle : 0.630 10.747 33693 Z= 0.316 Chirality : 0.042 0.270 3863 Planarity : 0.004 0.068 4354 Dihedral : 5.057 54.264 3434 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.07 % Favored : 92.89 % Rotamer: Outliers : 2.69 % Allowed : 18.97 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.16), residues: 2870 helix: 1.01 (0.14), residues: 1376 sheet: -1.75 (0.28), residues: 357 loop : -2.14 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 189 HIS 0.019 0.001 HIS C 474 PHE 0.030 0.002 PHE A 615 TYR 0.022 0.001 TYR B 339 ARG 0.006 0.000 ARG D 371 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 396 time to evaluate : 3.003 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7962 (m-30) cc_final: 0.7634 (t0) REVERT: A 167 LYS cc_start: 0.8522 (mttt) cc_final: 0.8253 (mttm) REVERT: A 378 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8344 (t80) REVERT: A 380 MET cc_start: 0.7373 (tpp) cc_final: 0.6872 (tpp) REVERT: A 425 ARG cc_start: 0.6857 (ttt180) cc_final: 0.5975 (tmt170) REVERT: A 495 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6612 (tm-30) REVERT: A 529 LYS cc_start: 0.8157 (tttt) cc_final: 0.7799 (mttp) REVERT: A 564 ASN cc_start: 0.8202 (t0) cc_final: 0.7978 (t0) REVERT: A 650 MET cc_start: 0.6063 (mtt) cc_final: 0.5849 (ttm) REVERT: B 25 MET cc_start: 0.7314 (mmm) cc_final: 0.7034 (mmt) REVERT: B 274 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7764 (tptp) REVERT: B 338 GLU cc_start: 0.6488 (mm-30) cc_final: 0.6257 (mm-30) REVERT: B 421 PHE cc_start: 0.7372 (p90) cc_final: 0.7059 (p90) REVERT: B 478 MET cc_start: 0.8180 (tpp) cc_final: 0.7317 (ttp) REVERT: B 629 GLN cc_start: 0.5906 (tp-100) cc_final: 0.5127 (tt0) REVERT: C 346 GLN cc_start: 0.4810 (mt0) cc_final: 0.4399 (pm20) REVERT: C 405 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7815 (mp10) REVERT: D 54 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8081 (t160) REVERT: D 57 MET cc_start: 0.8248 (tpp) cc_final: 0.7706 (mpp) REVERT: D 100 LEU cc_start: 0.6507 (tp) cc_final: 0.6294 (tp) REVERT: D 115 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.6792 (ttm170) REVERT: D 127 LYS cc_start: 0.7626 (pttm) cc_final: 0.7244 (mtmm) REVERT: D 181 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.6512 (mp10) REVERT: D 247 LYS cc_start: 0.6886 (mttt) cc_final: 0.6118 (ptmm) REVERT: D 268 PHE cc_start: 0.8237 (m-10) cc_final: 0.7879 (m-80) REVERT: D 341 MET cc_start: 0.7922 (ptm) cc_final: 0.7262 (ptp) REVERT: E 66 ASP cc_start: 0.8670 (m-30) cc_final: 0.8312 (m-30) REVERT: E 170 ILE cc_start: 0.8910 (mt) cc_final: 0.8548 (mt) REVERT: E 249 LEU cc_start: 0.8752 (tp) cc_final: 0.8347 (mp) REVERT: E 331 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.6579 (m-10) REVERT: F 147 MET cc_start: 0.7801 (mmt) cc_final: 0.7364 (mmm) REVERT: F 150 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7923 (mt-10) REVERT: F 213 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7345 (tt) REVERT: H 71 GLU cc_start: 0.7999 (tt0) cc_final: 0.7680 (tt0) REVERT: H 108 ASN cc_start: 0.7561 (m-40) cc_final: 0.7036 (m110) REVERT: H 155 ARG cc_start: 0.7338 (mtt180) cc_final: 0.6752 (ttp80) outliers start: 67 outliers final: 47 residues processed: 445 average time/residue: 0.3584 time to fit residues: 250.0694 Evaluate side-chains 416 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 360 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain C residue 212 PRO Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 474 HIS Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 144 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 201 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 224 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN C 384 HIS D 181 GLN ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 ASN ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.149437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.123248 restraints weight = 45129.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.125184 restraints weight = 30813.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.126417 restraints weight = 22391.465| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 24844 Z= 0.276 Angle : 0.817 58.880 33693 Z= 0.451 Chirality : 0.050 1.699 3863 Planarity : 0.005 0.196 4354 Dihedral : 5.064 54.257 3434 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.07 % Favored : 92.89 % Rotamer: Outliers : 2.49 % Allowed : 19.29 % Favored : 78.22 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.16), residues: 2870 helix: 1.00 (0.14), residues: 1382 sheet: -1.71 (0.28), residues: 358 loop : -2.16 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP B 189 HIS 0.317 0.003 HIS C 474 PHE 0.071 0.002 PHE D 418 TYR 0.062 0.002 TYR A 655 ARG 0.079 0.001 ARG B 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5561.77 seconds wall clock time: 100 minutes 40.79 seconds (6040.79 seconds total)