Starting phenix.real_space_refine on Fri Sep 27 23:52:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5of4_3802/09_2024/5of4_3802.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5of4_3802/09_2024/5of4_3802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5of4_3802/09_2024/5of4_3802.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5of4_3802/09_2024/5of4_3802.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5of4_3802/09_2024/5of4_3802.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5of4_3802/09_2024/5of4_3802.cif" } resolution = 4.4 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: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 81 5.16 5 C 10827 2.51 5 N 3081 2.21 5 O 3207 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17200 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3887 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 15, 'TRANS': 483} Chain breaks: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'UNK:plan-1': 36, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 5671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5671 Classifications: {'peptide': 724} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 691} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 116 Chain: "D" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1451 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 9, 'TRANS': 174} Chain: "F" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1498 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 62 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: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 620 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'TRANS': 123} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 124 Planarities with less than four sites: {'UNK:plan-1': 124} Unresolved non-hydrogen planarities: 124 Chain: "Z" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1350 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 270} Link IDs: {'TRANS': 269} Chain breaks: 15 Unresolved non-hydrogen bonds: 540 Unresolved non-hydrogen angles: 810 Unresolved non-hydrogen dihedrals: 270 Planarities with less than four sites: {'UNK:plan-1': 270} Unresolved non-hydrogen planarities: 270 Chain: "Y" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1160 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 232} Link IDs: {'TRANS': 231} Chain breaks: 18 Unresolved non-hydrogen bonds: 464 Unresolved non-hydrogen angles: 696 Unresolved non-hydrogen dihedrals: 232 Planarities with less than four sites: {'UNK:plan-1': 232} Unresolved non-hydrogen planarities: 232 Chain: "X" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 390 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'CIS': 1, 'TRANS': 76} Chain breaks: 6 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'UNK:plan-1': 78} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4744 SG CYS B 116 30.474 85.833 90.763 1.00110.23 S ATOM 5001 SG CYS B 155 26.916 88.074 96.067 1.00314.68 S ATOM 4884 SG CYS B 134 30.325 91.193 92.387 1.00147.22 S ATOM 5290 SG CYS B 190 32.215 86.707 97.680 1.00100.13 S Time building chain proxies: 9.75, per 1000 atoms: 0.57 Number of scatterers: 17200 At special positions: 0 Unit cell: (163.68, 158.4, 129.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 81 16.00 O 3207 8.00 N 3081 7.00 C 10827 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 4.62 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " Number of angles added : 12 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4766 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 12 sheets defined 79.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 242 through 256 removed outlier: 4.008A pdb=" N UNK A 246 " --> pdb=" O UNK A 242 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N UNK A 247 " --> pdb=" O UNK A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 Processing helix chain 'A' and resid 317 through 329 removed outlier: 3.550A pdb=" N GLU A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 358 removed outlier: 3.577A pdb=" N ARG A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 420 through 434 removed outlier: 3.605A pdb=" N GLU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 425 " --> pdb=" O TRP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 492 through 498 Processing helix chain 'A' and resid 515 through 525 removed outlier: 3.914A pdb=" N TYR A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 536 Processing helix chain 'A' and resid 537 through 554 Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 585 through 598 Processing helix chain 'A' and resid 632 through 644 Processing helix chain 'A' and resid 667 through 684 removed outlier: 3.953A pdb=" N LYS A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 699 Processing helix chain 'A' and resid 705 through 719 removed outlier: 3.579A pdb=" N GLN A 709 " --> pdb=" O THR A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 724 removed outlier: 3.876A pdb=" N ASP A 723 " --> pdb=" O THR A 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 34 removed outlier: 4.347A pdb=" N ARG B 26 " --> pdb=" O PHE B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 61 Processing helix chain 'B' and resid 76 through 99 removed outlier: 3.872A pdb=" N GLU B 81 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 140 Processing helix chain 'B' and resid 155 through 167 removed outlier: 3.771A pdb=" N GLU B 159 " --> pdb=" O CYS B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.808A pdb=" N LEU B 180 " --> pdb=" O ASN B 176 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 200 Processing helix chain 'B' and resid 209 through 213 removed outlier: 3.511A pdb=" N LEU B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 209 through 213' Processing helix chain 'B' and resid 238 through 248 Processing helix chain 'B' and resid 253 through 272 Processing helix chain 'B' and resid 275 through 291 Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 324 through 347 removed outlier: 3.840A pdb=" N HIS B 328 " --> pdb=" O ARG B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 365 removed outlier: 4.400A pdb=" N LEU B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 385 removed outlier: 5.689A pdb=" N ALA B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 410 Proline residue: B 396 - end of helix Processing helix chain 'B' and resid 440 through 451 Proline residue: B 446 - end of helix removed outlier: 3.824A pdb=" N PHE B 451 " --> pdb=" O VAL B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 470 removed outlier: 3.793A pdb=" N LYS B 469 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 531 Processing helix chain 'B' and resid 541 through 555 Processing helix chain 'B' and resid 558 through 565 Processing helix chain 'B' and resid 574 through 589 Processing helix chain 'B' and resid 604 through 609 removed outlier: 4.360A pdb=" N ILE B 608 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASP B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 604 through 609' Processing helix chain 'B' and resid 630 through 642 Processing helix chain 'B' and resid 646 through 665 removed outlier: 4.043A pdb=" N ASP B 650 " --> pdb=" O ILE B 646 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 700 Processing helix chain 'B' and resid 709 through 726 Processing helix chain 'D' and resid 386 through 397 Processing helix chain 'D' and resid 415 through 428 Processing helix chain 'D' and resid 447 through 458 removed outlier: 4.482A pdb=" N ARG D 453 " --> pdb=" O SER D 449 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN D 458 " --> pdb=" O PHE D 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 79 through 99 removed outlier: 3.708A pdb=" N CYS E 83 " --> pdb=" O ASN E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 134 removed outlier: 3.883A pdb=" N HIS E 127 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 137 No H-bonds generated for 'chain 'E' and resid 135 through 137' Processing helix chain 'E' and resid 144 through 158 removed outlier: 3.930A pdb=" N SER E 148 " --> pdb=" O SER E 144 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N HIS E 158 " --> pdb=" O GLN E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 193 removed outlier: 3.741A pdb=" N LYS E 190 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 215 Processing helix chain 'E' and resid 224 through 237 removed outlier: 3.943A pdb=" N SER E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 25 Processing helix chain 'F' and resid 33 through 52 removed outlier: 4.034A pdb=" N ASN F 52 " --> pdb=" O HIS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 121 Processing helix chain 'F' and resid 130 through 151 removed outlier: 3.776A pdb=" N VAL F 151 " --> pdb=" O MET F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 172 No H-bonds generated for 'chain 'F' and resid 170 through 172' Processing helix chain 'F' and resid 173 through 186 removed outlier: 3.544A pdb=" N PHE F 177 " --> pdb=" O GLN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 211 removed outlier: 3.768A pdb=" N GLN F 204 " --> pdb=" O SER F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 232 Processing helix chain 'G' and resid 13 through 25 Processing helix chain 'G' and resid 57 through 67 removed outlier: 5.530A pdb=" N GLN G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 60 removed outlier: 3.757A pdb=" N UNK H 51 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N UNK H 60 " --> pdb=" O UNK H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 71 removed outlier: 3.703A pdb=" N UNK H 71 " --> pdb=" O UNK H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 88 Processing helix chain 'H' and resid 94 through 103 Processing helix chain 'H' and resid 107 through 168 Processing helix chain 'Z' and resid 103 through 118 removed outlier: 3.615A pdb=" N UNK Z 116 " --> pdb=" O UNK Z 112 " (cutoff:3.500A) Processing helix chain 'Z' and resid 172 through 180 Processing helix chain 'Z' and resid 209 through 223 Processing helix chain 'Z' and resid 251 through 267 Processing helix chain 'Z' and resid 282 through 293 Processing helix chain 'Z' and resid 402 through 421 Processing helix chain 'Z' and resid 431 through 454 Processing helix chain 'Z' and resid 466 through 487 Processing helix chain 'Z' and resid 502 through 519 Processing helix chain 'Z' and resid 533 through 538 Processing helix chain 'Z' and resid 552 through 559 Processing helix chain 'Z' and resid 572 through 583 Processing helix chain 'Y' and resid 37 through 49 Processing helix chain 'Y' and resid 62 through 74 Processing helix chain 'Y' and resid 105 through 105 No H-bonds generated for 'chain 'Y' and resid 105 through 105' Processing helix chain 'Y' and resid 108 through 117 Processing helix chain 'Y' and resid 122 through 130 removed outlier: 4.434A pdb=" N UNK Y 130 " --> pdb=" O UNK Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 132 through 146 Processing helix chain 'Y' and resid 237 through 249 Processing helix chain 'Y' and resid 262 through 271 Processing helix chain 'Y' and resid 304 through 320 Processing helix chain 'Y' and resid 374 through 383 Processing helix chain 'Y' and resid 500 through 511 Processing helix chain 'Y' and resid 602 through 612 removed outlier: 3.822A pdb=" N UNK Y 612 " --> pdb=" O UNK Y 608 " (cutoff:3.500A) Processing helix chain 'Y' and resid 645 through 649 removed outlier: 4.190A pdb=" N UNK Y 649 " --> pdb=" O UNK Y 646 " (cutoff:3.500A) Processing helix chain 'Y' and resid 663 through 670 Processing helix chain 'Y' and resid 688 through 698 Processing helix chain 'X' and resid 81 through 92 Processing helix chain 'X' and resid 135 through 144 Processing helix chain 'X' and resid 150 through 157 removed outlier: 3.809A pdb=" N UNK X 157 " --> pdb=" O UNK X 153 " (cutoff:3.500A) Processing helix chain 'X' and resid 738 through 750 Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 226 removed outlier: 6.756A pdb=" N UNK A 224 " --> pdb=" O ALA A 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 338 removed outlier: 5.661A pdb=" N MET A 438 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 466 " --> pdb=" O MET A 438 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LEU A 440 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS A 361 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N SER A 408 " --> pdb=" O CYS A 361 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL A 363 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 505 through 512 removed outlier: 7.258A pdb=" N GLN A 506 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N SER A 661 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA A 508 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL A 663 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 510 " --> pdb=" O VAL A 663 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A 623 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU A 662 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLN A 625 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N SER A 664 " --> pdb=" O GLN A 625 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL A 560 " --> pdb=" O ILE A 607 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 204 through 208 Processing sheet with id=AA6, first strand: chain 'B' and resid 249 through 252 removed outlier: 3.662A pdb=" N SER B 436 " --> pdb=" O THR B 415 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN B 351 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 492 through 494 removed outlier: 6.636A pdb=" N MET B 493 " --> pdb=" O PHE B 679 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL B 618 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ALA B 680 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N MET B 620 " --> pdb=" O ALA B 680 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL B 536 " --> pdb=" O ALA B 617 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N VAL B 599 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 402 through 405 Processing sheet with id=AA9, first strand: chain 'D' and resid 407 through 409 removed outlier: 6.067A pdb=" N VAL D 442 " --> pdb=" O VAL D 432 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 114 through 116 removed outlier: 6.795A pdb=" N LEU E 61 " --> pdb=" O GLY E 105 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE E 107 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL E 63 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N THR E 109 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL E 65 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE E 169 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL E 198 " --> pdb=" O HIS E 220 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 68 through 70 removed outlier: 4.097A pdb=" N ARG F 68 " --> pdb=" O ALA F 61 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA F 61 " --> pdb=" O ARG F 68 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASN F 9 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ALA F 58 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU F 11 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILE F 60 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE F 13 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU F 10 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU F 162 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL F 12 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE F 164 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL F 14 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'X' and resid 162 through 163 973 hydrogen bonds defined for protein. 2859 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: 5.37 Time building geometry restraints manager: 5.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.30: 2977 1.30 - 1.55: 13125 1.55 - 1.80: 1220 1.80 - 2.04: 83 2.04 - 2.29: 12 Bond restraints: 17417 Sorted by residual: bond pdb=" C TYR A 489 " pdb=" O TYR A 489 " ideal model delta sigma weight residual 1.236 1.051 0.185 1.20e-02 6.94e+03 2.38e+02 bond pdb=" N PHE B 539 " pdb=" CA PHE B 539 " ideal model delta sigma weight residual 1.455 1.315 0.140 1.36e-02 5.41e+03 1.05e+02 bond pdb=" C PHE A 270 " pdb=" O PHE A 270 " ideal model delta sigma weight residual 1.236 1.340 -0.104 1.14e-02 7.69e+03 8.26e+01 bond pdb=" C UNK Y 245 " pdb=" O UNK Y 245 " ideal model delta sigma weight residual 1.232 1.409 -0.177 2.00e-02 2.50e+03 7.82e+01 bond pdb=" C LEU A 464 " pdb=" O LEU A 464 " ideal model delta sigma weight residual 1.235 1.130 0.106 1.24e-02 6.50e+03 7.25e+01 ... (remaining 17412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.23: 23291 6.23 - 12.47: 370 12.47 - 18.70: 27 18.70 - 24.93: 1 24.93 - 31.16: 3 Bond angle restraints: 23692 Sorted by residual: angle pdb="FE1 SF4 B1000 " pdb=" S2 SF4 B1000 " pdb="FE4 SF4 B1000 " ideal model delta sigma weight residual 73.70 104.86 -31.16 1.50e+00 4.44e-01 4.32e+02 angle pdb=" S2 SF4 B1000 " pdb="FE4 SF4 B1000 " pdb=" S3 SF4 B1000 " ideal model delta sigma weight residual 104.10 75.24 28.86 1.50e+00 4.44e-01 3.70e+02 angle pdb=" S2 SF4 B1000 " pdb="FE1 SF4 B1000 " pdb=" S3 SF4 B1000 " ideal model delta sigma weight residual 104.10 76.60 27.50 1.50e+00 4.44e-01 3.36e+02 angle pdb="FE1 SF4 B1000 " pdb=" S3 SF4 B1000 " pdb="FE4 SF4 B1000 " ideal model delta sigma weight residual 73.70 98.08 -24.38 1.50e+00 4.44e-01 2.64e+02 angle pdb="FE2 SF4 B1000 " pdb=" S1 SF4 B1000 " pdb="FE3 SF4 B1000 " ideal model delta sigma weight residual 73.70 89.57 -15.87 1.50e+00 4.44e-01 1.12e+02 ... (remaining 23687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.35: 9396 14.35 - 28.70: 902 28.70 - 43.06: 192 43.06 - 57.41: 31 57.41 - 71.76: 4 Dihedral angle restraints: 10525 sinusoidal: 3287 harmonic: 7238 Sorted by residual: dihedral pdb=" CA PRO B 727 " pdb=" C PRO B 727 " pdb=" N PHE B 728 " pdb=" CA PHE B 728 " ideal model delta harmonic sigma weight residual 180.00 121.18 58.82 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CA UNK D 378 " pdb=" C UNK D 378 " pdb=" N UNK D 379 " pdb=" CA UNK D 379 " ideal model delta harmonic sigma weight residual -180.00 -130.23 -49.77 0 5.00e+00 4.00e-02 9.91e+01 dihedral pdb=" CA UNK Z 88 " pdb=" C UNK Z 88 " pdb=" N UNK Z 89 " pdb=" CA UNK Z 89 " ideal model delta harmonic sigma weight residual -180.00 -130.78 -49.22 0 5.00e+00 4.00e-02 9.69e+01 ... (remaining 10522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.305: 2823 0.305 - 0.610: 51 0.610 - 0.915: 3 0.915 - 1.220: 1 1.220 - 1.525: 1 Chirality restraints: 2879 Sorted by residual: chirality pdb="FE1 SF4 B1000 " pdb=" S2 SF4 B1000 " pdb=" S3 SF4 B1000 " pdb=" S4 SF4 B1000 " both_signs ideal model delta sigma weight residual False -10.55 -9.03 -1.53 2.00e-01 2.50e+01 5.82e+01 chirality pdb="FE4 SF4 B1000 " pdb=" S1 SF4 B1000 " pdb=" S2 SF4 B1000 " pdb=" S3 SF4 B1000 " both_signs ideal model delta sigma weight residual False 10.55 9.39 1.16 2.00e-01 2.50e+01 3.36e+01 chirality pdb=" CA UNK Y 512 " pdb=" N UNK Y 512 " pdb=" C UNK Y 512 " pdb=" CB UNK Y 512 " both_signs ideal model delta sigma weight residual False 2.52 1.80 0.72 2.00e-01 2.50e+01 1.30e+01 ... (remaining 2876 not shown) Planarity restraints: 3082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 394 " 0.091 2.00e-02 2.50e+03 5.55e-02 7.71e+01 pdb=" CG TRP D 394 " -0.084 2.00e-02 2.50e+03 pdb=" CD1 TRP D 394 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP D 394 " -0.078 2.00e-02 2.50e+03 pdb=" NE1 TRP D 394 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TRP D 394 " -0.020 2.00e-02 2.50e+03 pdb=" CE3 TRP D 394 " -0.054 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 394 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 394 " 0.053 2.00e-02 2.50e+03 pdb=" CH2 TRP D 394 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 319 " -0.056 2.00e-02 2.50e+03 5.12e-02 5.24e+01 pdb=" CG TYR A 319 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 TYR A 319 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR A 319 " 0.089 2.00e-02 2.50e+03 pdb=" CE1 TYR A 319 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR A 319 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR A 319 " -0.083 2.00e-02 2.50e+03 pdb=" OH TYR A 319 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 482 " 0.079 2.00e-02 2.50e+03 4.91e-02 4.21e+01 pdb=" CG PHE A 482 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 482 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 PHE A 482 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE A 482 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 PHE A 482 " 0.022 2.00e-02 2.50e+03 pdb=" CZ PHE A 482 " 0.025 2.00e-02 2.50e+03 ... (remaining 3079 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 84 2.55 - 3.14: 12717 3.14 - 3.72: 26282 3.72 - 4.31: 34269 4.31 - 4.90: 54706 Nonbonded interactions: 128058 Sorted by model distance: nonbonded pdb=" O UNK Y 698 " pdb=" O UNK Y 699 " model vdw 1.962 3.040 nonbonded pdb=" O UNK X 752 " pdb=" CB UNK X 752 " model vdw 2.185 2.752 nonbonded pdb=" OE1 GLN A 668 " pdb=" O ASN G 64 " model vdw 2.243 3.040 nonbonded pdb=" O ILE A 531 " pdb=" OG1 THR A 535 " model vdw 2.248 3.040 nonbonded pdb=" NH2 ARG B 61 " pdb=" O PRO B 103 " model vdw 2.255 3.120 ... (remaining 128053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'Y' selection = (chain 'Z' and resid 110 through 584) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.010 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: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 42.490 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 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 : 0.022 0.208 17417 Z= 1.334 Angle : 2.150 31.164 23692 Z= 1.227 Chirality : 0.124 1.525 2879 Planarity : 0.011 0.116 3082 Dihedral : 12.454 71.759 5759 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.71 % Allowed : 11.46 % Favored : 87.84 % Rotamer: Outliers : 1.90 % Allowed : 4.29 % Favored : 93.81 % Cbeta Deviations : 0.80 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.97 % 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: -4.34 (0.16), residues: 1702 helix: -2.08 (0.15), residues: 767 sheet: -2.69 (0.30), residues: 232 loop : -3.82 (0.19), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.019 TRP D 394 HIS 0.031 0.007 HIS F 145 PHE 0.079 0.013 PHE A 482 TYR 0.089 0.015 TYR A 319 ARG 0.041 0.004 ARG D 400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 521 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 CYS cc_start: 0.9409 (m) cc_final: 0.9096 (t) REVERT: A 294 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8499 (tm-30) REVERT: A 309 ASP cc_start: 0.5806 (m-30) cc_final: 0.4747 (m-30) REVERT: A 315 VAL cc_start: 0.8340 (t) cc_final: 0.8090 (p) REVERT: A 322 LYS cc_start: 0.8720 (tttt) cc_final: 0.8355 (mmtm) REVERT: A 340 LEU cc_start: 0.8885 (mt) cc_final: 0.8430 (mt) REVERT: A 452 ARG cc_start: 0.9317 (mtt180) cc_final: 0.9031 (tmm-80) REVERT: A 464 LEU cc_start: 0.9638 (tp) cc_final: 0.9394 (tp) REVERT: A 495 GLU cc_start: 0.9409 (mt-10) cc_final: 0.8830 (tp30) REVERT: A 501 TYR cc_start: 0.9281 (p90) cc_final: 0.9002 (p90) REVERT: A 536 MET cc_start: 0.9069 (mtp) cc_final: 0.8773 (mtp) REVERT: A 553 ARG cc_start: 0.8577 (mmt90) cc_final: 0.8265 (mmt-90) REVERT: A 605 ILE cc_start: 0.9392 (tt) cc_final: 0.8966 (mt) REVERT: A 633 ARG cc_start: 0.8888 (mpp-170) cc_final: 0.8612 (mmm-85) REVERT: A 650 MET cc_start: 0.6299 (ttp) cc_final: 0.5897 (ttt) REVERT: A 674 THR cc_start: 0.9061 (m) cc_final: 0.8773 (p) REVERT: A 698 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8802 (pt0) REVERT: B 57 MET cc_start: 0.9562 (mtp) cc_final: 0.9199 (tpp) REVERT: B 88 ARG cc_start: 0.9180 (mmm160) cc_final: 0.8753 (mtp85) REVERT: B 105 LEU cc_start: 0.9331 (tp) cc_final: 0.8958 (tp) REVERT: B 174 ILE cc_start: 0.8984 (tt) cc_final: 0.8402 (tt) REVERT: B 227 ARG cc_start: 0.8769 (mtt180) cc_final: 0.8396 (mtm-85) REVERT: B 233 PHE cc_start: 0.9312 (m-80) cc_final: 0.9026 (m-80) REVERT: B 368 GLN cc_start: 0.9258 (mt0) cc_final: 0.9023 (pm20) REVERT: B 380 ARG cc_start: 0.9499 (tpt170) cc_final: 0.9242 (ppt170) REVERT: B 393 ASP cc_start: 0.9654 (m-30) cc_final: 0.9331 (t0) REVERT: B 419 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8815 (tm-30) REVERT: B 454 VAL cc_start: 0.9097 (m) cc_final: 0.8749 (p) REVERT: B 493 MET cc_start: 0.9310 (ttp) cc_final: 0.9046 (tmm) REVERT: B 504 ILE cc_start: 0.8477 (mt) cc_final: 0.8186 (tt) REVERT: B 526 GLU cc_start: 0.9508 (mt-10) cc_final: 0.8231 (mt-10) REVERT: B 618 VAL cc_start: 0.7744 (t) cc_final: 0.7514 (t) REVERT: B 641 ARG cc_start: 0.9198 (tmt90) cc_final: 0.8928 (tmm-80) REVERT: D 404 THR cc_start: 0.9098 (m) cc_final: 0.8763 (p) REVERT: D 405 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8096 (tp30) REVERT: D 426 ARG cc_start: 0.9012 (ttt180) cc_final: 0.8795 (ptm160) REVERT: D 433 PHE cc_start: 0.9239 (t80) cc_final: 0.8763 (t80) REVERT: D 434 GLU cc_start: 0.9062 (pp20) cc_final: 0.8690 (tp30) REVERT: E 63 VAL cc_start: 0.9396 (t) cc_final: 0.9196 (m) REVERT: E 79 ASN cc_start: 0.8806 (m-40) cc_final: 0.8492 (m-40) REVERT: E 94 GLU cc_start: 0.9366 (tt0) cc_final: 0.9058 (tp30) REVERT: E 98 GLN cc_start: 0.9032 (mm110) cc_final: 0.8783 (tp40) REVERT: E 103 GLN cc_start: 0.9417 (pt0) cc_final: 0.9012 (pt0) REVERT: E 112 LYS cc_start: 0.7740 (mttt) cc_final: 0.7326 (tttm) REVERT: E 123 ASN cc_start: 0.9535 (m-40) cc_final: 0.8995 (p0) REVERT: E 137 MET cc_start: 0.8820 (ttm) cc_final: 0.8386 (ttm) REVERT: E 166 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8436 (mm-30) REVERT: E 167 VAL cc_start: 0.9245 (t) cc_final: 0.9017 (p) REVERT: E 171 PHE cc_start: 0.8785 (t80) cc_final: 0.8369 (t80) REVERT: E 178 ASP cc_start: 0.8353 (p0) cc_final: 0.7804 (p0) REVERT: E 204 GLU cc_start: 0.8390 (tt0) cc_final: 0.7979 (tm-30) REVERT: E 214 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8300 (tp30) REVERT: E 221 VAL cc_start: 0.9297 (t) cc_final: 0.8962 (p) REVERT: F 7 GLU cc_start: 0.8743 (tt0) cc_final: 0.8368 (mp0) REVERT: F 15 VAL cc_start: 0.9315 (t) cc_final: 0.9058 (p) REVERT: F 139 LYS cc_start: 0.7737 (mmtt) cc_final: 0.7441 (tptt) REVERT: F 143 TYR cc_start: 0.9026 (t80) cc_final: 0.8809 (t80) REVERT: F 147 MET cc_start: 0.9342 (mmm) cc_final: 0.8803 (mmm) REVERT: F 160 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7780 (ttm110) REVERT: F 169 ASP cc_start: 0.8187 (t0) cc_final: 0.7859 (p0) REVERT: G 36 GLN cc_start: 0.9266 (tt0) cc_final: 0.8658 (tm-30) REVERT: G 56 ARG cc_start: 0.8128 (ttm170) cc_final: 0.7837 (mmm160) outliers start: 27 outliers final: 6 residues processed: 540 average time/residue: 0.3337 time to fit residues: 253.8865 Evaluate side-chains 349 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 343 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 219 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 GLN A 598 HIS ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 114 ASN B 164 HIS B 237 HIS ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS E 154 GLN F 48 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17417 Z= 0.223 Angle : 0.774 10.602 23692 Z= 0.394 Chirality : 0.044 0.199 2879 Planarity : 0.005 0.076 3082 Dihedral : 6.691 41.023 2571 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 0.21 % Allowed : 4.85 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.18), residues: 1702 helix: -0.70 (0.17), residues: 781 sheet: -2.42 (0.31), residues: 244 loop : -3.57 (0.19), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 394 HIS 0.010 0.002 HIS B 37 PHE 0.026 0.002 PHE F 50 TYR 0.026 0.002 TYR B 14 ARG 0.006 0.001 ARG A 574 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 452 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 CYS cc_start: 0.9368 (m) cc_final: 0.9084 (t) REVERT: A 309 ASP cc_start: 0.6111 (m-30) cc_final: 0.4834 (m-30) REVERT: A 315 VAL cc_start: 0.7889 (t) cc_final: 0.7326 (p) REVERT: A 322 LYS cc_start: 0.8918 (tttt) cc_final: 0.8443 (mmtm) REVERT: A 340 LEU cc_start: 0.8813 (mt) cc_final: 0.8435 (mt) REVERT: A 412 MET cc_start: 0.8627 (pmm) cc_final: 0.8320 (pmm) REVERT: A 452 ARG cc_start: 0.9388 (mtt180) cc_final: 0.9023 (tmm-80) REVERT: A 495 GLU cc_start: 0.9374 (mt-10) cc_final: 0.8748 (tp30) REVERT: A 501 TYR cc_start: 0.8969 (p90) cc_final: 0.8654 (p90) REVERT: A 511 TRP cc_start: 0.8179 (p-90) cc_final: 0.7816 (p-90) REVERT: A 536 MET cc_start: 0.9005 (mtp) cc_final: 0.8791 (mtp) REVERT: A 568 LEU cc_start: 0.9101 (tp) cc_final: 0.8892 (tp) REVERT: A 636 GLU cc_start: 0.9404 (mt-10) cc_final: 0.9179 (mt-10) REVERT: A 650 MET cc_start: 0.6418 (ttp) cc_final: 0.5985 (ttt) REVERT: B 156 ARG cc_start: 0.9487 (mpp80) cc_final: 0.9259 (ttp80) REVERT: B 174 ILE cc_start: 0.8920 (tt) cc_final: 0.8040 (tt) REVERT: B 227 ARG cc_start: 0.8621 (mtt180) cc_final: 0.8257 (mpp-170) REVERT: B 233 PHE cc_start: 0.9032 (m-80) cc_final: 0.8716 (m-80) REVERT: B 284 GLU cc_start: 0.9387 (mt-10) cc_final: 0.9183 (pp20) REVERT: B 316 GLN cc_start: 0.8853 (mp-120) cc_final: 0.8498 (mm-40) REVERT: B 368 GLN cc_start: 0.9236 (mt0) cc_final: 0.8858 (pm20) REVERT: B 380 ARG cc_start: 0.9456 (tpt170) cc_final: 0.9194 (ppt170) REVERT: B 419 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8573 (tm-30) REVERT: B 449 GLU cc_start: 0.9650 (mm-30) cc_final: 0.9348 (pp20) REVERT: B 526 GLU cc_start: 0.9392 (mt-10) cc_final: 0.8858 (mt-10) REVERT: B 634 LYS cc_start: 0.8689 (mttt) cc_final: 0.8369 (mttm) REVERT: B 641 ARG cc_start: 0.8985 (ttt180) cc_final: 0.8620 (tmm-80) REVERT: B 657 MET cc_start: 0.7993 (mmp) cc_final: 0.7683 (mmp) REVERT: B 681 ASP cc_start: 0.6907 (t0) cc_final: 0.6614 (t0) REVERT: B 684 PHE cc_start: 0.8296 (m-10) cc_final: 0.7206 (m-80) REVERT: B 722 ARG cc_start: 0.9051 (ttm170) cc_final: 0.8743 (ttm-80) REVERT: D 404 THR cc_start: 0.9162 (m) cc_final: 0.8712 (p) REVERT: D 405 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7849 (tp30) REVERT: D 426 ARG cc_start: 0.9071 (ttt180) cc_final: 0.8595 (tpm170) REVERT: E 57 MET cc_start: 0.6620 (ttm) cc_final: 0.6003 (ttp) REVERT: E 94 GLU cc_start: 0.9346 (tt0) cc_final: 0.9108 (pp20) REVERT: E 98 GLN cc_start: 0.9056 (mm110) cc_final: 0.8839 (tp40) REVERT: E 123 ASN cc_start: 0.9321 (m-40) cc_final: 0.8845 (p0) REVERT: E 137 MET cc_start: 0.8687 (ttm) cc_final: 0.8322 (ttm) REVERT: E 171 PHE cc_start: 0.8744 (t80) cc_final: 0.8294 (t80) REVERT: E 178 ASP cc_start: 0.8052 (p0) cc_final: 0.7319 (p0) REVERT: E 214 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8371 (tp30) REVERT: E 221 VAL cc_start: 0.9136 (t) cc_final: 0.8652 (p) REVERT: F 7 GLU cc_start: 0.8702 (tt0) cc_final: 0.8352 (mp0) REVERT: F 11 LEU cc_start: 0.9490 (tp) cc_final: 0.9160 (tp) REVERT: F 147 MET cc_start: 0.9273 (mmm) cc_final: 0.8953 (mmp) REVERT: F 169 ASP cc_start: 0.6876 (t0) cc_final: 0.6342 (p0) REVERT: F 205 GLN cc_start: 0.9399 (mt0) cc_final: 0.9119 (tp40) REVERT: F 215 LEU cc_start: 0.9349 (tp) cc_final: 0.9058 (tp) REVERT: G 9 LEU cc_start: 0.9109 (tp) cc_final: 0.8754 (tp) REVERT: G 36 GLN cc_start: 0.9079 (tt0) cc_final: 0.8592 (tm-30) REVERT: G 37 ASP cc_start: 0.9475 (t0) cc_final: 0.9267 (t0) REVERT: G 39 ASP cc_start: 0.9116 (t70) cc_final: 0.8764 (p0) REVERT: G 54 GLN cc_start: 0.8640 (mt0) cc_final: 0.8429 (mm110) REVERT: G 60 LEU cc_start: 0.9092 (tt) cc_final: 0.8826 (mt) REVERT: G 66 PHE cc_start: 0.7846 (m-10) cc_final: 0.7612 (m-10) outliers start: 3 outliers final: 0 residues processed: 454 average time/residue: 0.3176 time to fit residues: 208.2389 Evaluate side-chains 339 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 182 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 chunk 60 optimal weight: 0.5980 chunk 220 optimal weight: 9.9990 chunk 237 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 218 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 176 optimal weight: 8.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 GLN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 HIS A 621 ASN ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN B 241 ASN ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 HIS ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 ASN F 179 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17417 Z= 0.391 Angle : 0.935 16.097 23692 Z= 0.471 Chirality : 0.048 0.238 2879 Planarity : 0.006 0.081 3082 Dihedral : 6.989 46.285 2571 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 0.21 % Allowed : 5.98 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.18), residues: 1702 helix: -0.67 (0.17), residues: 783 sheet: -2.57 (0.30), residues: 246 loop : -3.57 (0.20), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 394 HIS 0.014 0.003 HIS B 700 PHE 0.037 0.003 PHE A 328 TYR 0.041 0.003 TYR E 183 ARG 0.010 0.001 ARG B 343 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 367 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLN cc_start: 0.9069 (tp-100) cc_final: 0.8867 (tp-100) REVERT: A 284 CYS cc_start: 0.9423 (m) cc_final: 0.9192 (m) REVERT: A 322 LYS cc_start: 0.9059 (tttt) cc_final: 0.8827 (mmtm) REVERT: A 327 MET cc_start: 0.9404 (tpp) cc_final: 0.8962 (tpp) REVERT: A 452 ARG cc_start: 0.9381 (mtt180) cc_final: 0.9016 (tmm-80) REVERT: A 495 GLU cc_start: 0.9379 (mt-10) cc_final: 0.8911 (tp30) REVERT: A 511 TRP cc_start: 0.8374 (p-90) cc_final: 0.8072 (p-90) REVERT: A 536 MET cc_start: 0.9118 (mtp) cc_final: 0.8853 (mtp) REVERT: A 623 LEU cc_start: 0.9326 (tp) cc_final: 0.8983 (tt) REVERT: A 650 MET cc_start: 0.6981 (ttp) cc_final: 0.6693 (ttt) REVERT: B 156 ARG cc_start: 0.9600 (mpp80) cc_final: 0.9357 (ttp80) REVERT: B 227 ARG cc_start: 0.8613 (mtt180) cc_final: 0.8266 (mpp-170) REVERT: B 317 GLU cc_start: 0.9407 (mt-10) cc_final: 0.8937 (tp30) REVERT: B 418 ILE cc_start: 0.8780 (mm) cc_final: 0.8172 (pt) REVERT: B 419 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8518 (tm-30) REVERT: B 526 GLU cc_start: 0.9393 (mt-10) cc_final: 0.9093 (mt-10) REVERT: B 620 MET cc_start: 0.8173 (ttm) cc_final: 0.7803 (ttm) REVERT: B 634 LYS cc_start: 0.8840 (mttt) cc_final: 0.8563 (mttm) REVERT: B 641 ARG cc_start: 0.8895 (ttt180) cc_final: 0.8581 (tmm160) REVERT: B 674 TYR cc_start: 0.9056 (m-80) cc_final: 0.8773 (m-80) REVERT: B 707 ASN cc_start: 0.9091 (m-40) cc_final: 0.7712 (p0) REVERT: D 404 THR cc_start: 0.9294 (m) cc_final: 0.8986 (p) REVERT: D 405 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7952 (tp30) REVERT: D 426 ARG cc_start: 0.9143 (ttt180) cc_final: 0.8542 (tpm170) REVERT: D 433 PHE cc_start: 0.9173 (t80) cc_final: 0.8956 (t80) REVERT: D 438 LYS cc_start: 0.7932 (mtmt) cc_final: 0.7204 (tttt) REVERT: D 457 ARG cc_start: 0.7473 (mtm180) cc_final: 0.7262 (mtm-85) REVERT: E 98 GLN cc_start: 0.9119 (mm110) cc_final: 0.8440 (tp40) REVERT: E 99 ASN cc_start: 0.9077 (m-40) cc_final: 0.7631 (m110) REVERT: E 112 LYS cc_start: 0.8996 (tppt) cc_final: 0.8425 (tptm) REVERT: E 123 ASN cc_start: 0.9562 (m-40) cc_final: 0.9102 (p0) REVERT: E 137 MET cc_start: 0.8750 (ttm) cc_final: 0.8319 (ttm) REVERT: E 171 PHE cc_start: 0.8604 (t80) cc_final: 0.8046 (t80) REVERT: E 214 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8479 (tp30) REVERT: F 7 GLU cc_start: 0.8606 (tt0) cc_final: 0.8374 (mp0) REVERT: F 8 LEU cc_start: 0.8228 (mt) cc_final: 0.7945 (mt) REVERT: F 14 VAL cc_start: 0.9405 (t) cc_final: 0.9177 (p) REVERT: F 156 GLU cc_start: 0.7870 (pt0) cc_final: 0.7267 (tm-30) REVERT: F 179 ASN cc_start: 0.9586 (t0) cc_final: 0.9216 (t0) REVERT: F 205 GLN cc_start: 0.9445 (mt0) cc_final: 0.9188 (tp40) REVERT: F 215 LEU cc_start: 0.9228 (tp) cc_final: 0.8924 (tp) REVERT: G 9 LEU cc_start: 0.9260 (tp) cc_final: 0.8983 (tp) REVERT: G 36 GLN cc_start: 0.9231 (tt0) cc_final: 0.8864 (tp-100) REVERT: G 37 ASP cc_start: 0.9451 (t0) cc_final: 0.9059 (t0) REVERT: G 39 ASP cc_start: 0.9029 (t70) cc_final: 0.8762 (p0) REVERT: G 55 GLU cc_start: 0.8576 (mp0) cc_final: 0.8282 (mp0) REVERT: G 60 LEU cc_start: 0.9259 (tt) cc_final: 0.9009 (mp) REVERT: G 61 MET cc_start: 0.9013 (ppp) cc_final: 0.8777 (ppp) outliers start: 3 outliers final: 2 residues processed: 370 average time/residue: 0.3194 time to fit residues: 176.0122 Evaluate side-chains 299 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 297 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 217 optimal weight: 7.9990 chunk 165 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 220 optimal weight: 8.9990 chunk 233 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 209 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 GLN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 HIS ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17417 Z= 0.308 Angle : 0.812 12.639 23692 Z= 0.413 Chirality : 0.045 0.185 2879 Planarity : 0.005 0.081 3082 Dihedral : 6.458 38.831 2571 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 0.14 % Allowed : 4.15 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.75 (0.19), residues: 1702 helix: -0.34 (0.18), residues: 785 sheet: -2.43 (0.31), residues: 232 loop : -3.42 (0.20), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 394 HIS 0.013 0.002 HIS B 700 PHE 0.032 0.003 PHE B 539 TYR 0.025 0.002 TYR B 639 ARG 0.008 0.001 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 366 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 CYS cc_start: 0.9382 (m) cc_final: 0.9147 (t) REVERT: A 327 MET cc_start: 0.9450 (tpp) cc_final: 0.9006 (tpp) REVERT: A 412 MET cc_start: 0.8834 (pmm) cc_final: 0.8305 (pmm) REVERT: A 450 MET cc_start: 0.9203 (mpp) cc_final: 0.8863 (mmm) REVERT: A 452 ARG cc_start: 0.9397 (mtt180) cc_final: 0.9054 (tmm160) REVERT: A 489 TYR cc_start: 0.8749 (t80) cc_final: 0.8478 (t80) REVERT: A 490 GLU cc_start: 0.8237 (pt0) cc_final: 0.7970 (pm20) REVERT: A 495 GLU cc_start: 0.9239 (mt-10) cc_final: 0.9026 (tp30) REVERT: A 650 MET cc_start: 0.6895 (ttp) cc_final: 0.6605 (ttt) REVERT: A 692 LYS cc_start: 0.8723 (mtmm) cc_final: 0.8464 (mtmm) REVERT: A 696 MET cc_start: 0.7012 (mtp) cc_final: 0.6714 (mtp) REVERT: B 105 LEU cc_start: 0.9419 (tp) cc_final: 0.9187 (tp) REVERT: B 186 ARG cc_start: 0.8941 (ttp80) cc_final: 0.8537 (ttp-170) REVERT: B 284 GLU cc_start: 0.9435 (mt-10) cc_final: 0.9215 (pp20) REVERT: B 317 GLU cc_start: 0.9412 (mt-10) cc_final: 0.9010 (mm-30) REVERT: B 418 ILE cc_start: 0.8766 (mm) cc_final: 0.8200 (pt) REVERT: B 419 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8438 (tm-30) REVERT: B 447 VAL cc_start: 0.9485 (t) cc_final: 0.9211 (t) REVERT: B 526 GLU cc_start: 0.9383 (mt-10) cc_final: 0.8904 (mt-10) REVERT: B 544 TYR cc_start: 0.8850 (t80) cc_final: 0.8452 (t80) REVERT: B 634 LYS cc_start: 0.8790 (mttt) cc_final: 0.8489 (mttm) REVERT: B 641 ARG cc_start: 0.8790 (ttt180) cc_final: 0.8418 (tmm-80) REVERT: B 674 TYR cc_start: 0.9027 (m-80) cc_final: 0.8818 (m-80) REVERT: D 405 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7743 (tp30) REVERT: D 426 ARG cc_start: 0.9186 (ttt180) cc_final: 0.8637 (tpm170) REVERT: D 457 ARG cc_start: 0.7471 (mtm180) cc_final: 0.7118 (mtm110) REVERT: E 98 GLN cc_start: 0.9231 (mm110) cc_final: 0.8898 (tp-100) REVERT: E 123 ASN cc_start: 0.9542 (m-40) cc_final: 0.9095 (p0) REVERT: E 137 MET cc_start: 0.8643 (ttm) cc_final: 0.8257 (ttm) REVERT: E 140 HIS cc_start: 0.8686 (t70) cc_final: 0.8455 (t70) REVERT: E 171 PHE cc_start: 0.8679 (t80) cc_final: 0.8172 (t80) REVERT: E 176 THR cc_start: 0.8657 (m) cc_final: 0.8236 (p) REVERT: E 214 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8552 (tp30) REVERT: F 169 ASP cc_start: 0.7438 (t0) cc_final: 0.6788 (p0) REVERT: F 179 ASN cc_start: 0.9517 (t0) cc_final: 0.9139 (t0) REVERT: F 205 GLN cc_start: 0.9454 (mt0) cc_final: 0.9176 (tp40) REVERT: G 32 LYS cc_start: 0.9012 (tttt) cc_final: 0.8799 (tmtt) REVERT: G 36 GLN cc_start: 0.9350 (tt0) cc_final: 0.8992 (tp-100) REVERT: G 37 ASP cc_start: 0.9397 (t0) cc_final: 0.8981 (t0) REVERT: G 39 ASP cc_start: 0.9087 (t70) cc_final: 0.8782 (p0) REVERT: G 55 GLU cc_start: 0.8502 (mp0) cc_final: 0.7988 (mp0) REVERT: G 56 ARG cc_start: 0.8115 (ttm170) cc_final: 0.7866 (mtp85) REVERT: G 61 MET cc_start: 0.8956 (ppp) cc_final: 0.8742 (ppp) outliers start: 2 outliers final: 0 residues processed: 367 average time/residue: 0.3090 time to fit residues: 166.9736 Evaluate side-chains 288 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 194 optimal weight: 20.0000 chunk 132 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 174 optimal weight: 9.9990 chunk 96 optimal weight: 0.0770 chunk 199 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 209 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 overall best weight: 2.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN A 594 GLN A 595 ASN A 598 HIS ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN B 519 ASN B 555 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17417 Z= 0.260 Angle : 0.761 10.945 23692 Z= 0.386 Chirality : 0.043 0.201 2879 Planarity : 0.005 0.072 3082 Dihedral : 6.069 37.540 2571 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.40 (0.19), residues: 1702 helix: -0.05 (0.18), residues: 793 sheet: -2.23 (0.32), residues: 228 loop : -3.28 (0.20), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 394 HIS 0.008 0.002 HIS B 135 PHE 0.030 0.002 PHE B 539 TYR 0.031 0.003 TYR A 571 ARG 0.008 0.001 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 367 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 ASN cc_start: 0.8820 (t0) cc_final: 0.8593 (m110) REVERT: A 322 LYS cc_start: 0.8956 (tttt) cc_final: 0.8637 (mtmm) REVERT: A 327 MET cc_start: 0.9434 (tpp) cc_final: 0.9218 (tpp) REVERT: A 372 GLU cc_start: 0.9703 (mp0) cc_final: 0.9479 (mp0) REVERT: A 412 MET cc_start: 0.8998 (pmm) cc_final: 0.8486 (pmm) REVERT: A 450 MET cc_start: 0.9242 (mpp) cc_final: 0.8994 (mmm) REVERT: A 452 ARG cc_start: 0.9332 (mtt180) cc_final: 0.8987 (tmm160) REVERT: A 489 TYR cc_start: 0.8663 (t80) cc_final: 0.8449 (t80) REVERT: A 490 GLU cc_start: 0.8219 (pt0) cc_final: 0.7927 (pm20) REVERT: A 511 TRP cc_start: 0.8272 (p-90) cc_final: 0.7849 (p-90) REVERT: A 650 MET cc_start: 0.6878 (ttp) cc_final: 0.6604 (ttt) REVERT: A 692 LYS cc_start: 0.8712 (mtmm) cc_final: 0.8454 (mtmm) REVERT: B 186 ARG cc_start: 0.8991 (ttp80) cc_final: 0.8620 (ttp-170) REVERT: B 317 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9004 (mm-30) REVERT: B 418 ILE cc_start: 0.8655 (mm) cc_final: 0.8104 (pt) REVERT: B 419 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8193 (tm-30) REVERT: B 526 GLU cc_start: 0.9436 (mt-10) cc_final: 0.9030 (mt-10) REVERT: B 634 LYS cc_start: 0.8565 (mttt) cc_final: 0.8271 (mttm) REVERT: B 641 ARG cc_start: 0.8814 (ttt180) cc_final: 0.8407 (tmm-80) REVERT: B 677 MET cc_start: 0.8840 (mtt) cc_final: 0.8545 (mmm) REVERT: B 723 GLN cc_start: 0.9046 (mt0) cc_final: 0.8835 (mt0) REVERT: D 404 THR cc_start: 0.9215 (m) cc_final: 0.8993 (p) REVERT: D 405 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7756 (tp30) REVERT: D 426 ARG cc_start: 0.9105 (ttt180) cc_final: 0.8564 (tpm170) REVERT: D 450 ASP cc_start: 0.7152 (t0) cc_final: 0.6780 (p0) REVERT: E 98 GLN cc_start: 0.9264 (mm110) cc_final: 0.8988 (tp40) REVERT: E 123 ASN cc_start: 0.9504 (m-40) cc_final: 0.9037 (p0) REVERT: E 137 MET cc_start: 0.8657 (ttm) cc_final: 0.8269 (ttm) REVERT: E 140 HIS cc_start: 0.8633 (t70) cc_final: 0.8384 (t70) REVERT: E 171 PHE cc_start: 0.8695 (t80) cc_final: 0.8118 (t80) REVERT: E 214 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8389 (tp30) REVERT: F 169 ASP cc_start: 0.7353 (t0) cc_final: 0.6672 (p0) REVERT: F 179 ASN cc_start: 0.9515 (t0) cc_final: 0.9105 (t0) REVERT: F 205 GLN cc_start: 0.9468 (mt0) cc_final: 0.9116 (mm-40) REVERT: G 36 GLN cc_start: 0.9206 (tt0) cc_final: 0.8935 (tp-100) REVERT: G 37 ASP cc_start: 0.9421 (t0) cc_final: 0.9026 (t0) REVERT: G 39 ASP cc_start: 0.9104 (t70) cc_final: 0.8765 (p0) REVERT: G 55 GLU cc_start: 0.8381 (mp0) cc_final: 0.7900 (mp0) outliers start: 1 outliers final: 0 residues processed: 367 average time/residue: 0.3053 time to fit residues: 164.6029 Evaluate side-chains 285 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 78 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 chunk 46 optimal weight: 0.4980 chunk 137 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 234 optimal weight: 8.9990 chunk 194 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 HIS ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS D 390 GLN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 140 HIS F 185 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17417 Z= 0.242 Angle : 0.748 10.475 23692 Z= 0.378 Chirality : 0.043 0.297 2879 Planarity : 0.005 0.105 3082 Dihedral : 5.907 39.598 2571 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 0.07 % Allowed : 3.23 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.16 (0.19), residues: 1702 helix: 0.17 (0.18), residues: 787 sheet: -1.98 (0.32), residues: 243 loop : -3.25 (0.20), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 189 HIS 0.007 0.001 HIS B 135 PHE 0.031 0.002 PHE B 539 TYR 0.028 0.002 TYR B 639 ARG 0.014 0.001 ARG B 343 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 360 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8996 (pmm) cc_final: 0.8036 (pmm) REVERT: A 450 MET cc_start: 0.9098 (mpp) cc_final: 0.8851 (tpt) REVERT: A 452 ARG cc_start: 0.9375 (mtt180) cc_final: 0.8996 (tmm160) REVERT: A 490 GLU cc_start: 0.8200 (pt0) cc_final: 0.7943 (pm20) REVERT: A 511 TRP cc_start: 0.8227 (p-90) cc_final: 0.7788 (p-90) REVERT: A 536 MET cc_start: 0.8569 (ttm) cc_final: 0.8096 (ttm) REVERT: A 650 MET cc_start: 0.6740 (ttp) cc_final: 0.6421 (ttt) REVERT: A 692 LYS cc_start: 0.8733 (mtmm) cc_final: 0.8482 (mtmm) REVERT: B 186 ARG cc_start: 0.9045 (ttp80) cc_final: 0.8719 (ptt180) REVERT: B 317 GLU cc_start: 0.9426 (mt-10) cc_final: 0.9014 (mm-30) REVERT: B 357 PHE cc_start: 0.9114 (t80) cc_final: 0.8649 (t80) REVERT: B 418 ILE cc_start: 0.8425 (mm) cc_final: 0.7899 (pt) REVERT: B 419 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7938 (tm-30) REVERT: B 493 MET cc_start: 0.9151 (tmm) cc_final: 0.8791 (tmm) REVERT: B 526 GLU cc_start: 0.9403 (mt-10) cc_final: 0.9044 (mt-10) REVERT: B 634 LYS cc_start: 0.8558 (mttt) cc_final: 0.8194 (mttm) REVERT: B 641 ARG cc_start: 0.8841 (ttt180) cc_final: 0.8424 (tmm-80) REVERT: B 677 MET cc_start: 0.8927 (mtt) cc_final: 0.8646 (mmm) REVERT: D 392 ARG cc_start: 0.9609 (ttm110) cc_final: 0.9107 (tpm170) REVERT: D 405 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7613 (tp30) REVERT: D 426 ARG cc_start: 0.9101 (ttt180) cc_final: 0.8540 (tpm170) REVERT: D 433 PHE cc_start: 0.8793 (t80) cc_final: 0.8470 (t80) REVERT: D 450 ASP cc_start: 0.7106 (t0) cc_final: 0.6751 (p0) REVERT: E 123 ASN cc_start: 0.9499 (m-40) cc_final: 0.9043 (p0) REVERT: E 137 MET cc_start: 0.8604 (ttm) cc_final: 0.8232 (ttm) REVERT: E 171 PHE cc_start: 0.8724 (t80) cc_final: 0.8483 (t80) REVERT: E 214 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8382 (tp30) REVERT: F 169 ASP cc_start: 0.7360 (t0) cc_final: 0.6687 (p0) REVERT: F 179 ASN cc_start: 0.9487 (t0) cc_final: 0.9111 (t0) REVERT: F 205 GLN cc_start: 0.9443 (mt0) cc_final: 0.9068 (mm-40) REVERT: F 215 LEU cc_start: 0.9214 (tp) cc_final: 0.8904 (tp) REVERT: G 9 LEU cc_start: 0.9092 (tp) cc_final: 0.8725 (tp) REVERT: G 36 GLN cc_start: 0.9197 (tt0) cc_final: 0.8928 (tp-100) REVERT: G 37 ASP cc_start: 0.9419 (t0) cc_final: 0.9001 (t0) REVERT: G 55 GLU cc_start: 0.8494 (mp0) cc_final: 0.7968 (mp0) outliers start: 1 outliers final: 0 residues processed: 361 average time/residue: 0.2630 time to fit residues: 144.9272 Evaluate side-chains 280 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 225 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 197 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 233 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 GLN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS D 390 GLN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS F 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17417 Z= 0.201 Angle : 0.709 9.458 23692 Z= 0.363 Chirality : 0.043 0.265 2879 Planarity : 0.005 0.068 3082 Dihedral : 5.609 37.357 2571 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 0.07 % Allowed : 1.55 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.89 (0.20), residues: 1702 helix: 0.41 (0.18), residues: 781 sheet: -1.67 (0.33), residues: 238 loop : -3.17 (0.20), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 189 HIS 0.007 0.001 HIS B 135 PHE 0.027 0.002 PHE B 157 TYR 0.030 0.002 TYR B 639 ARG 0.007 0.001 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 369 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.9740 (mp0) cc_final: 0.9504 (mp0) REVERT: A 407 ILE cc_start: 0.9701 (mm) cc_final: 0.9429 (pt) REVERT: A 412 MET cc_start: 0.8840 (pmm) cc_final: 0.7931 (pmm) REVERT: A 452 ARG cc_start: 0.9375 (mtt180) cc_final: 0.9013 (tmm160) REVERT: A 489 TYR cc_start: 0.8491 (t80) cc_final: 0.8018 (t80) REVERT: A 490 GLU cc_start: 0.8110 (pt0) cc_final: 0.7742 (pm20) REVERT: A 511 TRP cc_start: 0.8179 (p-90) cc_final: 0.7724 (p-90) REVERT: A 536 MET cc_start: 0.8556 (ttm) cc_final: 0.8237 (ttm) REVERT: A 581 TYR cc_start: 0.8273 (p90) cc_final: 0.8065 (t80) REVERT: A 650 MET cc_start: 0.6618 (ttp) cc_final: 0.6223 (ttt) REVERT: A 692 LYS cc_start: 0.8762 (mtmm) cc_final: 0.8503 (mtmm) REVERT: B 74 SER cc_start: 0.9542 (m) cc_final: 0.8826 (p) REVERT: B 105 LEU cc_start: 0.9389 (tp) cc_final: 0.9184 (tp) REVERT: B 186 ARG cc_start: 0.8991 (ttp80) cc_final: 0.8640 (ptt180) REVERT: B 284 GLU cc_start: 0.9388 (mt-10) cc_final: 0.9176 (pp20) REVERT: B 317 GLU cc_start: 0.9439 (mt-10) cc_final: 0.9037 (mm-30) REVERT: B 357 PHE cc_start: 0.9106 (t80) cc_final: 0.8690 (t80) REVERT: B 419 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7736 (tm-30) REVERT: B 447 VAL cc_start: 0.9588 (t) cc_final: 0.9357 (t) REVERT: B 526 GLU cc_start: 0.9331 (mt-10) cc_final: 0.8191 (mt-10) REVERT: B 634 LYS cc_start: 0.8531 (mttt) cc_final: 0.8132 (mttm) REVERT: B 641 ARG cc_start: 0.8755 (ttt180) cc_final: 0.8350 (tmm-80) REVERT: B 657 MET cc_start: 0.8557 (mmp) cc_final: 0.8217 (mmm) REVERT: D 405 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7216 (tp30) REVERT: D 426 ARG cc_start: 0.9098 (ttt180) cc_final: 0.8513 (tpm170) REVERT: E 63 VAL cc_start: 0.9180 (t) cc_final: 0.8961 (m) REVERT: E 72 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6792 (pt0) REVERT: E 123 ASN cc_start: 0.9487 (m-40) cc_final: 0.9058 (p0) REVERT: E 137 MET cc_start: 0.8637 (ttm) cc_final: 0.8264 (ttm) REVERT: E 171 PHE cc_start: 0.8650 (t80) cc_final: 0.8413 (t80) REVERT: E 176 THR cc_start: 0.8459 (m) cc_final: 0.8250 (p) REVERT: F 150 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8782 (mt-10) REVERT: F 169 ASP cc_start: 0.7282 (t0) cc_final: 0.6439 (p0) REVERT: F 179 ASN cc_start: 0.9473 (t0) cc_final: 0.9086 (t0) REVERT: F 215 LEU cc_start: 0.9196 (tp) cc_final: 0.8932 (tp) REVERT: F 217 VAL cc_start: 0.8035 (t) cc_final: 0.7821 (t) REVERT: G 9 LEU cc_start: 0.8859 (tp) cc_final: 0.8594 (tp) REVERT: G 36 GLN cc_start: 0.9306 (tt0) cc_final: 0.8917 (tp-100) REVERT: G 37 ASP cc_start: 0.9397 (t0) cc_final: 0.8992 (t0) REVERT: G 55 GLU cc_start: 0.8506 (mp0) cc_final: 0.8055 (mp0) outliers start: 1 outliers final: 0 residues processed: 369 average time/residue: 0.2801 time to fit residues: 156.9107 Evaluate side-chains 292 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 144 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 139 optimal weight: 0.0170 chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 148 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 212 optimal weight: 8.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN A 598 HIS ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 60 GLN ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS D 390 GLN F 55 ASN ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17417 Z= 0.180 Angle : 0.689 9.542 23692 Z= 0.352 Chirality : 0.042 0.224 2879 Planarity : 0.005 0.064 3082 Dihedral : 5.319 36.814 2571 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.70 (0.20), residues: 1702 helix: 0.55 (0.19), residues: 790 sheet: -1.51 (0.34), residues: 239 loop : -3.12 (0.21), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 189 HIS 0.007 0.001 HIS A 598 PHE 0.028 0.002 PHE B 157 TYR 0.031 0.002 TYR B 639 ARG 0.010 0.001 ARG B 616 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ASP cc_start: 0.5068 (m-30) cc_final: 0.3728 (m-30) REVERT: A 332 ARG cc_start: 0.8072 (mtt180) cc_final: 0.7756 (mmm160) REVERT: A 372 GLU cc_start: 0.9695 (mp0) cc_final: 0.9472 (mp0) REVERT: A 407 ILE cc_start: 0.9668 (mm) cc_final: 0.9429 (pt) REVERT: A 412 MET cc_start: 0.8947 (pmm) cc_final: 0.8513 (pmm) REVERT: A 452 ARG cc_start: 0.9397 (mtt180) cc_final: 0.9025 (tmm160) REVERT: A 511 TRP cc_start: 0.8247 (p-90) cc_final: 0.7765 (p-90) REVERT: A 536 MET cc_start: 0.8534 (ttm) cc_final: 0.8107 (ttm) REVERT: A 549 LYS cc_start: 0.9252 (mttt) cc_final: 0.8843 (pttm) REVERT: A 594 GLN cc_start: 0.9730 (mm-40) cc_final: 0.9522 (pt0) REVERT: A 650 MET cc_start: 0.6655 (ttp) cc_final: 0.6296 (ttt) REVERT: A 692 LYS cc_start: 0.8708 (mtmm) cc_final: 0.8450 (mtmm) REVERT: B 174 ILE cc_start: 0.8306 (tt) cc_final: 0.7921 (tt) REVERT: B 247 MET cc_start: 0.7890 (tmm) cc_final: 0.7633 (tmm) REVERT: B 317 GLU cc_start: 0.9447 (mt-10) cc_final: 0.9056 (mm-30) REVERT: B 352 GLU cc_start: 0.9364 (mp0) cc_final: 0.8680 (tm-30) REVERT: B 357 PHE cc_start: 0.9109 (t80) cc_final: 0.8636 (t80) REVERT: B 361 LEU cc_start: 0.9300 (tp) cc_final: 0.8736 (pp) REVERT: B 526 GLU cc_start: 0.9370 (mt-10) cc_final: 0.8352 (mt-10) REVERT: B 634 LYS cc_start: 0.8208 (mttt) cc_final: 0.7826 (mttm) REVERT: B 641 ARG cc_start: 0.8627 (ttt180) cc_final: 0.8252 (tmm160) REVERT: B 657 MET cc_start: 0.8490 (mmp) cc_final: 0.8208 (mmm) REVERT: D 391 ILE cc_start: 0.9218 (pt) cc_final: 0.8934 (pt) REVERT: D 404 THR cc_start: 0.8995 (m) cc_final: 0.8743 (p) REVERT: D 405 GLU cc_start: 0.7553 (mt-10) cc_final: 0.6992 (tp30) REVERT: D 426 ARG cc_start: 0.9102 (ttt180) cc_final: 0.8516 (tpm170) REVERT: E 63 VAL cc_start: 0.9137 (t) cc_final: 0.8901 (m) REVERT: E 72 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6752 (pt0) REVERT: E 99 ASN cc_start: 0.7943 (m-40) cc_final: 0.7674 (t0) REVERT: E 123 ASN cc_start: 0.9441 (m-40) cc_final: 0.8987 (p0) REVERT: E 137 MET cc_start: 0.8577 (ttm) cc_final: 0.8232 (ttm) REVERT: E 171 PHE cc_start: 0.8584 (t80) cc_final: 0.8304 (t80) REVERT: E 178 ASP cc_start: 0.7780 (p0) cc_final: 0.7059 (p0) REVERT: E 186 ILE cc_start: 0.9095 (mt) cc_final: 0.8881 (mt) REVERT: F 150 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8981 (mp0) REVERT: F 169 ASP cc_start: 0.6975 (t0) cc_final: 0.6167 (p0) REVERT: F 179 ASN cc_start: 0.9443 (t0) cc_final: 0.9058 (t0) REVERT: F 215 LEU cc_start: 0.9132 (tp) cc_final: 0.8862 (tp) REVERT: F 220 MET cc_start: 0.8280 (mpp) cc_final: 0.8069 (mmm) REVERT: G 6 LYS cc_start: 0.8377 (pttm) cc_final: 0.7546 (tppt) REVERT: G 9 LEU cc_start: 0.9016 (tp) cc_final: 0.8699 (tp) REVERT: G 36 GLN cc_start: 0.9285 (tt0) cc_final: 0.8926 (tp-100) REVERT: G 37 ASP cc_start: 0.9440 (t0) cc_final: 0.9055 (t0) REVERT: G 55 GLU cc_start: 0.8433 (mp0) cc_final: 0.7969 (mp0) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.2718 time to fit residues: 154.6779 Evaluate side-chains 293 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 223 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 217 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 205 optimal weight: 7.9990 chunk 216 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 HIS ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 GLN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN F 55 ASN ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.6075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 17417 Z= 0.407 Angle : 0.936 13.361 23692 Z= 0.475 Chirality : 0.049 0.356 2879 Planarity : 0.007 0.067 3082 Dihedral : 6.396 38.899 2571 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 24.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.35 (0.19), residues: 1702 helix: -0.12 (0.18), residues: 789 sheet: -1.84 (0.33), residues: 235 loop : -3.25 (0.21), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 493 HIS 0.010 0.002 HIS A 598 PHE 0.028 0.003 PHE B 451 TYR 0.033 0.003 TYR B 59 ARG 0.015 0.001 ARG D 392 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 CYS cc_start: 0.9249 (t) cc_final: 0.8877 (m) REVERT: A 372 GLU cc_start: 0.9681 (mp0) cc_final: 0.9459 (mp0) REVERT: A 412 MET cc_start: 0.8983 (pmm) cc_final: 0.8161 (pmm) REVERT: A 442 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8880 (mm-30) REVERT: A 452 ARG cc_start: 0.9442 (mtt180) cc_final: 0.9116 (tmm160) REVERT: A 489 TYR cc_start: 0.8296 (t80) cc_final: 0.8004 (t80) REVERT: A 490 GLU cc_start: 0.8298 (pt0) cc_final: 0.7912 (pm20) REVERT: A 511 TRP cc_start: 0.8479 (p-90) cc_final: 0.8169 (p-90) REVERT: A 536 MET cc_start: 0.9025 (ttm) cc_final: 0.8644 (ttm) REVERT: A 581 TYR cc_start: 0.8385 (p90) cc_final: 0.8016 (t80) REVERT: A 650 MET cc_start: 0.6556 (ttp) cc_final: 0.6031 (ttt) REVERT: B 94 TYR cc_start: 0.8252 (p90) cc_final: 0.8013 (p90) REVERT: B 105 LEU cc_start: 0.9542 (tp) cc_final: 0.9306 (tp) REVERT: B 317 GLU cc_start: 0.9496 (mt-10) cc_final: 0.9086 (mm-30) REVERT: B 357 PHE cc_start: 0.9220 (t80) cc_final: 0.8956 (t80) REVERT: B 419 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7878 (tm-30) REVERT: B 526 GLU cc_start: 0.9366 (mt-10) cc_final: 0.8986 (mt-10) REVERT: B 634 LYS cc_start: 0.8453 (mttt) cc_final: 0.8117 (mttm) REVERT: B 641 ARG cc_start: 0.8690 (ttt180) cc_final: 0.8370 (tmm-80) REVERT: D 404 THR cc_start: 0.9233 (m) cc_final: 0.8978 (p) REVERT: D 405 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7315 (tp30) REVERT: D 426 ARG cc_start: 0.9063 (ttt180) cc_final: 0.8538 (tpm170) REVERT: D 457 ARG cc_start: 0.7693 (mtm180) cc_final: 0.7405 (mtm180) REVERT: E 72 GLU cc_start: 0.7612 (mt-10) cc_final: 0.6960 (pt0) REVERT: E 137 MET cc_start: 0.8579 (ttm) cc_final: 0.8122 (ttm) REVERT: F 143 TYR cc_start: 0.9358 (t80) cc_final: 0.9140 (t80) REVERT: F 158 LYS cc_start: 0.9173 (tmtt) cc_final: 0.8875 (tptp) REVERT: F 169 ASP cc_start: 0.7382 (t0) cc_final: 0.6837 (p0) REVERT: F 175 MET cc_start: 0.6721 (mmt) cc_final: 0.6467 (mmt) REVERT: G 9 LEU cc_start: 0.9150 (tp) cc_final: 0.8884 (tp) REVERT: G 55 GLU cc_start: 0.8467 (mp0) cc_final: 0.7983 (mp0) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.2750 time to fit residues: 133.6649 Evaluate side-chains 257 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 229 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 241 optimal weight: 7.9990 chunk 221 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 HIS ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS D 390 GLN E 99 ASN ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.6256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17417 Z= 0.213 Angle : 0.763 10.964 23692 Z= 0.386 Chirality : 0.044 0.250 2879 Planarity : 0.005 0.063 3082 Dihedral : 5.639 37.092 2571 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.99 (0.20), residues: 1702 helix: 0.16 (0.18), residues: 800 sheet: -1.71 (0.33), residues: 243 loop : -3.09 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 189 HIS 0.017 0.002 HIS A 286 PHE 0.028 0.002 PHE B 157 TYR 0.023 0.002 TYR A 534 ARG 0.015 0.001 ARG D 392 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 VAL cc_start: 0.7692 (t) cc_final: 0.7295 (p) REVERT: A 372 GLU cc_start: 0.9716 (mp0) cc_final: 0.9471 (mp0) REVERT: A 407 ILE cc_start: 0.9703 (mm) cc_final: 0.9464 (pt) REVERT: A 442 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8812 (mm-30) REVERT: A 452 ARG cc_start: 0.9490 (mtt180) cc_final: 0.9111 (tmm160) REVERT: A 489 TYR cc_start: 0.7657 (t80) cc_final: 0.7332 (t80) REVERT: A 511 TRP cc_start: 0.8291 (p-90) cc_final: 0.7867 (p-90) REVERT: A 514 MET cc_start: 0.8315 (ppp) cc_final: 0.7643 (ppp) REVERT: A 546 PHE cc_start: 0.8947 (t80) cc_final: 0.8577 (t80) REVERT: A 549 LYS cc_start: 0.9175 (mttt) cc_final: 0.8710 (pttm) REVERT: A 568 LEU cc_start: 0.9138 (tp) cc_final: 0.8875 (tp) REVERT: A 581 TYR cc_start: 0.8163 (p90) cc_final: 0.7912 (t80) REVERT: B 94 TYR cc_start: 0.8497 (p90) cc_final: 0.8282 (p90) REVERT: B 156 ARG cc_start: 0.9290 (tmm160) cc_final: 0.8954 (ptp90) REVERT: B 174 ILE cc_start: 0.8296 (tt) cc_final: 0.7946 (tt) REVERT: B 247 MET cc_start: 0.7727 (tmm) cc_final: 0.7457 (tmm) REVERT: B 284 GLU cc_start: 0.9396 (mt-10) cc_final: 0.9163 (pp20) REVERT: B 317 GLU cc_start: 0.9441 (mt-10) cc_final: 0.9054 (mm-30) REVERT: B 357 PHE cc_start: 0.9036 (t80) cc_final: 0.8636 (t80) REVERT: B 419 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7518 (tm-30) REVERT: B 526 GLU cc_start: 0.9418 (mt-10) cc_final: 0.9023 (mt-10) REVERT: B 634 LYS cc_start: 0.8225 (mttt) cc_final: 0.7818 (mttm) REVERT: B 641 ARG cc_start: 0.8663 (ttt180) cc_final: 0.8248 (tmm-80) REVERT: B 657 MET cc_start: 0.8561 (mmp) cc_final: 0.8024 (mmm) REVERT: B 688 ASP cc_start: 0.8487 (t0) cc_final: 0.7793 (t0) REVERT: D 405 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7141 (tp30) REVERT: D 426 ARG cc_start: 0.9051 (ttt180) cc_final: 0.8519 (tpm170) REVERT: D 457 ARG cc_start: 0.7804 (mtm180) cc_final: 0.7554 (mtm-85) REVERT: E 58 MET cc_start: 0.8200 (mpp) cc_final: 0.7709 (tpt) REVERT: E 72 GLU cc_start: 0.7549 (mt-10) cc_final: 0.6866 (pt0) REVERT: E 123 ASN cc_start: 0.9537 (m-40) cc_final: 0.9144 (p0) REVERT: E 137 MET cc_start: 0.8489 (ttm) cc_final: 0.8150 (ttm) REVERT: E 178 ASP cc_start: 0.8003 (p0) cc_final: 0.7255 (p0) REVERT: F 158 LYS cc_start: 0.9151 (tmtt) cc_final: 0.8850 (tptp) REVERT: F 169 ASP cc_start: 0.7143 (t0) cc_final: 0.6543 (p0) REVERT: F 179 ASN cc_start: 0.9497 (t0) cc_final: 0.9152 (t0) REVERT: G 6 LYS cc_start: 0.8253 (pttm) cc_final: 0.7465 (tppt) REVERT: G 36 GLN cc_start: 0.9256 (tt0) cc_final: 0.8967 (tp-100) REVERT: G 37 ASP cc_start: 0.9128 (t70) cc_final: 0.8895 (t0) REVERT: G 55 GLU cc_start: 0.8462 (mp0) cc_final: 0.8052 (mp0) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.2758 time to fit residues: 143.1451 Evaluate side-chains 276 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 192 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 197 optimal weight: 8.9990 chunk 24 optimal weight: 0.3980 chunk 35 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 ASN A 459 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 HIS B 262 ASN B 474 HIS D 390 GLN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.092083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.078380 restraints weight = 88739.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.079839 restraints weight = 65032.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.080911 restraints weight = 50749.997| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.6454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17417 Z= 0.213 Angle : 0.756 10.795 23692 Z= 0.383 Chirality : 0.044 0.222 2879 Planarity : 0.005 0.063 3082 Dihedral : 5.512 36.700 2571 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.87 (0.20), residues: 1702 helix: 0.35 (0.18), residues: 788 sheet: -1.76 (0.32), residues: 243 loop : -3.04 (0.21), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 189 HIS 0.012 0.002 HIS B 164 PHE 0.027 0.002 PHE B 157 TYR 0.034 0.002 TYR F 174 ARG 0.015 0.001 ARG D 392 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3637.40 seconds wall clock time: 65 minutes 33.72 seconds (3933.72 seconds total)