Starting phenix.real_space_refine (version: dev) on Sat Feb 25 02:36:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmi_0452/02_2023/6nmi_0452_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmi_0452/02_2023/6nmi_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_0452/02_2023/6nmi_0452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmi_0452/02_2023/6nmi_0452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmi_0452/02_2023/6nmi_0452_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmi_0452/02_2023/6nmi_0452_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 13.59, per 1000 atoms: 0.56 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: 10.18 Conformation dependent library (CDL) restraints added in 3.6 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: 2.63 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: 7.76 Time building geometry restraints manager: 10.81 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 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. 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: 0.750 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: 0.010 Extract box with map and model: 6.130 Check model and map are aligned: 0.380 Process input model: 70.020 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.240 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 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= 0.610 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 % 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 *********************** 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 : 3.214 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 outliers start: 4 outliers final: 2 residues processed: 778 average time/residue: 0.4688 time to fit residues: 537.0486 Evaluate side-chains 400 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 398 time to evaluate : 2.862 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.2481 time to fit residues: 4.8060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 249 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 328 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 613 HIS B 715 GLN B 726 GLN C 228 HIS C 346 GLN C 384 HIS C 398 GLN C 474 HIS 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** 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 134 GLN ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 24844 Z= 0.229 Angle : 0.710 10.229 33693 Z= 0.364 Chirality : 0.043 0.214 3863 Planarity : 0.005 0.086 4354 Dihedral : 6.537 73.777 3433 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.26 % Favored : 91.67 % Rotamer Outliers : 3.14 % 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: -2.82 (0.14), residues: 2870 helix: -0.88 (0.13), residues: 1376 sheet: -2.11 (0.27), residues: 334 loop : -2.99 (0.16), residues: 1160 *********************** 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 555 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 477 time to evaluate : 2.997 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 outliers start: 78 outliers final: 40 residues processed: 526 average time/residue: 0.3986 time to fit residues: 323.0757 Evaluate side-chains 405 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 365 time to evaluate : 2.982 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. outliers start: 40 outliers final: 1 residues processed: 40 average time/residue: 0.2437 time to fit residues: 21.9354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 138 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 170 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 250 optimal weight: 8.9990 chunk 270 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 200 optimal weight: 0.8980 overall best weight: 4.5786 ------------------------------------------------------------------------------- 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 ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 HIS ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN C 384 HIS C 398 GLN C 474 HIS ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN F 185 GLN 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.128 24844 Z= 0.446 Angle : 0.829 12.684 33693 Z= 0.424 Chirality : 0.048 0.284 3863 Planarity : 0.006 0.087 4354 Dihedral : 6.660 70.132 3433 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.84 % Favored : 89.02 % Rotamer Outliers : 3.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 2.52 % Twisted General : 0.25 % 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: -2.54 (0.15), residues: 2870 helix: -0.52 (0.13), residues: 1387 sheet: -2.38 (0.28), residues: 309 loop : -2.91 (0.17), residues: 1174 *********************** 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 490 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 391 time to evaluate : 2.948 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: symmetry clash outliers start: 99 outliers final: 52 residues processed: 461 average time/residue: 0.3729 time to fit residues: 267.6301 Evaluate side-chains 399 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 347 time to evaluate : 3.184 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. outliers start: 52 outliers final: 1 residues processed: 52 average time/residue: 0.2270 time to fit residues: 26.7150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 247 optimal weight: 0.0870 chunk 188 optimal weight: 20.0000 chunk 129 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 251 optimal weight: 8.9990 chunk 265 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 237 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 HIS C 226 GLN C 384 HIS C 398 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 98 GLN ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 GLN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 24844 Z= 0.240 Angle : 0.678 10.647 33693 Z= 0.344 Chirality : 0.043 0.266 3863 Planarity : 0.005 0.078 4354 Dihedral : 6.008 63.112 3433 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.15 % Favored : 91.81 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 2.52 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.15), residues: 2870 helix: 0.09 (0.14), residues: 1380 sheet: -2.06 (0.28), residues: 324 loop : -2.79 (0.17), residues: 1166 *********************** 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 461 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 399 time to evaluate : 3.132 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 outliers start: 62 outliers final: 27 residues processed: 438 average time/residue: 0.3753 time to fit residues: 255.7037 Evaluate side-chains 376 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 349 time to evaluate : 3.018 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. outliers start: 27 outliers final: 2 residues processed: 27 average time/residue: 0.2457 time to fit residues: 15.8031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 221 optimal weight: 0.0980 chunk 150 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 506 GLN A 551 HIS A 677 GLN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 GLN C 226 GLN C 375 ASN C 384 HIS C 398 GLN C 474 HIS ** 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** ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 HIS ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.105 24844 Z= 0.333 Angle : 0.728 10.748 33693 Z= 0.370 Chirality : 0.045 0.291 3863 Planarity : 0.005 0.081 4354 Dihedral : 6.020 57.330 3433 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.49 % Favored : 89.44 % Rotamer Outliers : 2.57 % 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: -1.85 (0.15), residues: 2870 helix: 0.21 (0.14), residues: 1363 sheet: -2.21 (0.27), residues: 350 loop : -2.69 (0.17), residues: 1157 *********************** 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 430 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 366 time to evaluate : 2.987 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 outliers start: 64 outliers final: 41 residues processed: 409 average time/residue: 0.3758 time to fit residues: 241.9600 Evaluate side-chains 381 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 340 time to evaluate : 3.403 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. outliers start: 41 outliers final: 2 residues processed: 41 average time/residue: 0.2335 time to fit residues: 22.2126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 89 optimal weight: 0.6980 chunk 239 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 266 optimal weight: 0.9990 chunk 220 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS C 226 GLN C 384 HIS ** 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 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 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** F 46 ASN F 108 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 24844 Z= 0.176 Angle : 0.636 9.669 33693 Z= 0.322 Chirality : 0.042 0.280 3863 Planarity : 0.004 0.072 4354 Dihedral : 5.479 56.895 3433 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.39 % Favored : 92.58 % Rotamer Outliers : 1.45 % 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: -1.41 (0.16), residues: 2870 helix: 0.64 (0.14), residues: 1361 sheet: -1.96 (0.28), residues: 341 loop : -2.55 (0.17), residues: 1168 *********************** 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 444 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 408 time to evaluate : 3.073 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 outliers start: 36 outliers final: 16 residues processed: 429 average time/residue: 0.3705 time to fit residues: 251.8367 Evaluate side-chains 370 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 354 time to evaluate : 3.168 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. outliers start: 16 outliers final: 2 residues processed: 16 average time/residue: 0.2304 time to fit residues: 11.1919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 256 optimal weight: 50.0000 chunk 29 optimal weight: 0.0980 chunk 151 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 223 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 265 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 GLN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN B 715 GLN B 733 GLN C 226 GLN C 346 GLN C 375 ASN 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** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 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** H 136 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 24844 Z= 0.168 Angle : 0.629 10.265 33693 Z= 0.317 Chirality : 0.042 0.288 3863 Planarity : 0.004 0.073 4354 Dihedral : 5.215 53.818 3433 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.84 % Favored : 92.13 % Rotamer Outliers : 1.29 % 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: -1.21 (0.16), residues: 2870 helix: 0.79 (0.14), residues: 1373 sheet: -1.91 (0.27), residues: 355 loop : -2.47 (0.17), residues: 1142 *********************** 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 432 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 400 time to evaluate : 2.921 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 32 outliers final: 13 residues processed: 416 average time/residue: 0.3594 time to fit residues: 235.5269 Evaluate side-chains 372 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 359 time to evaluate : 2.765 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. outliers start: 13 outliers final: 2 residues processed: 13 average time/residue: 0.2742 time to fit residues: 9.7683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 163 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 158 optimal weight: 0.0870 chunk 79 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 168 optimal weight: 9.9990 chunk 180 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 208 optimal weight: 8.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN B 135 HIS C 226 GLN 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** ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 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** F 108 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 24844 Z= 0.180 Angle : 0.642 12.769 33693 Z= 0.322 Chirality : 0.042 0.271 3863 Planarity : 0.004 0.070 4354 Dihedral : 5.109 54.191 3433 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.53 % Favored : 92.44 % Rotamer Outliers : 1.05 % 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: -1.04 (0.16), residues: 2870 helix: 0.89 (0.14), residues: 1379 sheet: -1.78 (0.28), residues: 335 loop : -2.35 (0.17), residues: 1156 *********************** 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 405 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 379 time to evaluate : 3.028 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 outliers start: 26 outliers final: 19 residues processed: 391 average time/residue: 0.3720 time to fit residues: 231.6928 Evaluate side-chains 369 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 350 time to evaluate : 2.925 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. outliers start: 19 outliers final: 2 residues processed: 19 average time/residue: 0.2303 time to fit residues: 12.2974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 241 optimal weight: 0.9990 chunk 253 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 246 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 193 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 chunk 233 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 551 HIS ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 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** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** 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 148 ASN ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN H 136 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 24844 Z= 0.244 Angle : 0.674 11.117 33693 Z= 0.339 Chirality : 0.043 0.266 3863 Planarity : 0.004 0.074 4354 Dihedral : 5.197 52.614 3433 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.68 % Favored : 91.29 % Rotamer Outliers : 0.72 % 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: -1.08 (0.16), residues: 2870 helix: 0.87 (0.14), residues: 1368 sheet: -1.84 (0.27), residues: 354 loop : -2.35 (0.17), residues: 1148 *********************** 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 378 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 360 time to evaluate : 2.931 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 outliers start: 18 outliers final: 11 residues processed: 368 average time/residue: 0.3676 time to fit residues: 215.6030 Evaluate side-chains 354 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 343 time to evaluate : 3.232 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.2565 time to fit residues: 9.4609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 261 optimal weight: 0.9980 chunk 159 optimal weight: 0.0770 chunk 123 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 chunk 252 optimal weight: 0.9980 chunk 218 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 173 optimal weight: 0.6980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN C 226 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 ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 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: 0.7672 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 24844 Z= 0.173 Angle : 0.640 11.335 33693 Z= 0.321 Chirality : 0.042 0.300 3863 Planarity : 0.004 0.067 4354 Dihedral : 4.982 50.567 3433 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.93 % Favored : 93.03 % Rotamer Outliers : 0.40 % 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: -0.91 (0.16), residues: 2870 helix: 0.98 (0.14), residues: 1378 sheet: -1.75 (0.27), residues: 354 loop : -2.24 (0.18), residues: 1138 ********************** 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 399 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 389 time to evaluate : 2.864 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 outliers start: 10 outliers final: 8 residues processed: 392 average time/residue: 0.3626 time to fit residues: 226.2599 Evaluate side-chains 355 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 347 time to evaluate : 2.683 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 0.2489 time to fit residues: 7.5678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 218 optimal weight: 0.3980 chunk 91 optimal weight: 0.9980 chunk 224 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN C 474 HIS ** 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 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 147 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** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.151631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.126723 restraints weight = 44949.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.126839 restraints weight = 32225.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.127944 restraints weight = 25768.334| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4007 r_free = 0.4007 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4003 r_free = 0.4003 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4984 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= 0.199 Angle : 0.646 11.050 33693 Z= 0.323 Chirality : 0.042 0.287 3863 Planarity : 0.004 0.071 4354 Dihedral : 4.988 50.294 3433 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.63 % Favored : 92.33 % Rotamer Outliers : 0.32 % 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: -0.86 (0.16), residues: 2870 helix: 0.98 (0.14), residues: 1386 sheet: -1.69 (0.27), residues: 354 loop : -2.19 (0.18), residues: 1130 =============================================================================== Job complete usr+sys time: 5278.13 seconds wall clock time: 97 minutes 10.67 seconds (5830.67 seconds total)