Starting phenix.real_space_refine on Sun Mar 17 08:57:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5of4_3802/03_2024/5of4_3802_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5of4_3802/03_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_3802/03_2024/5of4_3802.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5of4_3802/03_2024/5of4_3802.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5of4_3802/03_2024/5of4_3802_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5of4_3802/03_2024/5of4_3802_updated.pdb" } 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 Residue "A PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 26": "NH1" <-> "NH2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 10.18, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.79 Conformation dependent library (CDL) restraints added in 2.5 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... running ksdssp... Secondary structure from input PDB file: 102 helices and 15 sheets defined 70.1% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'A' and resid 243 through 255 removed outlier: 4.019A pdb=" N UNK A 247 " --> pdb=" O UNK A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 287 Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 421 through 433 removed outlier: 3.550A pdb=" N ARG A 425 " --> pdb=" O TRP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 457 Processing helix chain 'A' and resid 480 through 484 removed outlier: 3.983A pdb=" N ILE A 484 " --> pdb=" O ASN A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 516 through 524 Processing helix chain 'A' and resid 529 through 535 Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 586 through 596 Processing helix chain 'A' and resid 633 through 643 Processing helix chain 'A' and resid 668 through 683 removed outlier: 3.953A pdb=" N LYS A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 718 Processing helix chain 'A' and resid 721 through 723 No H-bonds generated for 'chain 'A' and resid 721 through 723' Processing helix chain 'B' and resid 21 through 33 removed outlier: 4.347A pdb=" N ARG B 26 " --> pdb=" O PHE B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 60 Processing helix chain 'B' and resid 77 through 98 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 119 through 122 No H-bonds generated for 'chain 'B' and resid 119 through 122' Processing helix chain 'B' and resid 128 through 138 Processing helix chain 'B' and resid 156 through 166 Processing helix chain 'B' and resid 177 through 185 removed outlier: 3.531A pdb=" N LYS B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 200 Processing helix chain 'B' and resid 209 through 212 No H-bonds generated for 'chain 'B' and resid 209 through 212' Processing helix chain 'B' and resid 239 through 247 Processing helix chain 'B' and resid 253 through 272 Processing helix chain 'B' and resid 276 through 290 Processing helix chain 'B' and resid 300 through 303 No H-bonds generated for 'chain 'B' and resid 300 through 303' Processing helix chain 'B' and resid 325 through 347 Processing helix chain 'B' and resid 355 through 364 Processing helix chain 'B' and resid 375 through 384 Processing helix chain 'B' and resid 391 through 409 Proline residue: B 396 - end of helix Processing helix chain 'B' and resid 441 through 450 Proline residue: B 446 - end of helix Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 515 through 530 Processing helix chain 'B' and resid 542 through 554 Processing helix chain 'B' and resid 558 through 564 Processing helix chain 'B' and resid 575 through 588 Processing helix chain 'B' and resid 603 through 605 No H-bonds generated for 'chain 'B' and resid 603 through 605' Processing helix chain 'B' and resid 631 through 641 Processing helix chain 'B' and resid 647 through 666 removed outlier: 5.373A pdb=" N LEU B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ARG B 666 " --> pdb=" O GLN B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 690 Processing helix chain 'B' and resid 694 through 699 Processing helix chain 'B' and resid 710 through 725 Processing helix chain 'D' and resid 387 through 396 Processing helix chain 'D' and resid 416 through 427 Processing helix chain 'D' and resid 447 through 457 removed outlier: 4.596A pdb=" N LYS D 452 " --> pdb=" O SER D 449 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS D 456 " --> pdb=" O ARG D 453 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG D 457 " --> pdb=" O PHE D 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 80 through 98 Processing helix chain 'E' and resid 124 through 136 removed outlier: 4.896A pdb=" N ASP E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 157 Processing helix chain 'E' and resid 183 through 192 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 206 through 214 Processing helix chain 'E' and resid 225 through 236 Processing helix chain 'F' and resid 19 through 26 Processing helix chain 'F' and resid 34 through 51 Processing helix chain 'F' and resid 100 through 120 Processing helix chain 'F' and resid 130 through 150 Processing helix chain 'F' and resid 171 through 186 removed outlier: 3.864A pdb=" N TYR F 174 " --> pdb=" O ALA F 171 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N MET F 175 " --> pdb=" O LEU F 172 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN F 176 " --> pdb=" O GLN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 210 Processing helix chain 'F' and resid 220 through 236 Proline residue: F 233 - end of helix Processing helix chain 'G' and resid 14 through 26 Processing helix chain 'G' and resid 58 through 66 removed outlier: 5.530A pdb=" N GLN G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 59 Processing helix chain 'H' and resid 61 through 70 Processing helix chain 'H' and resid 76 through 87 Processing helix chain 'H' and resid 95 through 102 Processing helix chain 'H' and resid 108 through 167 Processing helix chain 'Z' and resid 103 through 117 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 179 Processing helix chain 'Z' and resid 210 through 222 Processing helix chain 'Z' and resid 251 through 266 Processing helix chain 'Z' and resid 282 through 292 Processing helix chain 'Z' and resid 402 through 420 Processing helix chain 'Z' and resid 432 through 453 Processing helix chain 'Z' and resid 466 through 486 Processing helix chain 'Z' and resid 503 through 518 Processing helix chain 'Z' and resid 534 through 537 No H-bonds generated for 'chain 'Z' and resid 534 through 537' Processing helix chain 'Z' and resid 553 through 558 Processing helix chain 'Z' and resid 572 through 582 Processing helix chain 'Y' and resid 37 through 48 Processing helix chain 'Y' and resid 62 through 73 Processing helix chain 'Y' and resid 107 through 116 Processing helix chain 'Y' and resid 122 through 129 Processing helix chain 'Y' and resid 133 through 145 Processing helix chain 'Y' and resid 237 through 249 Processing helix chain 'Y' and resid 262 through 270 Processing helix chain 'Y' and resid 305 through 319 Processing helix chain 'Y' and resid 375 through 382 Processing helix chain 'Y' and resid 501 through 510 Processing helix chain 'Y' and resid 602 through 611 Processing helix chain 'Y' and resid 646 through 648 No H-bonds generated for 'chain 'Y' and resid 646 through 648' Processing helix chain 'Y' and resid 663 through 669 Processing helix chain 'Y' and resid 688 through 697 Processing helix chain 'X' and resid 81 through 91 Processing helix chain 'X' and resid 136 through 143 Processing helix chain 'X' and resid 151 through 156 Processing helix chain 'X' and resid 738 through 750 Processing sheet with id= A, first strand: chain 'A' and resid 224 through 226 Processing sheet with id= B, first strand: chain 'A' and resid 234 through 237 removed outlier: 4.329A pdb=" N UNK A 234 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 336 through 338 Processing sheet with id= D, first strand: chain 'A' and resid 438 through 440 removed outlier: 6.798A pdb=" N LEU A 362 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 365 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 509 through 512 removed outlier: 6.787A pdb=" N VAL A 510 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER A 661 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS A 512 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 663 " --> pdb=" O CYS A 512 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE A 605 " --> pdb=" O VAL A 560 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 70 through 74 Processing sheet with id= G, first strand: chain 'B' and resid 230 through 233 removed outlier: 6.312A pdb=" N SER B 453 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE B 233 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE B 455 " --> pdb=" O PHE B 233 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, 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) Processing sheet with id= I, first strand: chain 'B' and resid 492 through 494 removed outlier: 6.872A pdb=" N MET B 677 " --> pdb=" O MET B 493 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL B 536 " --> pdb=" O ALA B 617 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU B 596 " --> pdb=" O ALA B 537 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE B 539 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N SER B 598 " --> pdb=" O PHE B 539 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 407 through 410 Processing sheet with id= K, first strand: chain 'E' and resid 60 through 66 removed outlier: 6.247A pdb=" N GLN E 103 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL E 63 " --> pdb=" O GLN E 103 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLY E 105 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL E 65 " --> pdb=" O GLY E 105 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE E 107 " --> pdb=" O VAL E 65 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 168 through 170 removed outlier: 6.827A pdb=" N SER E 197 " --> pdb=" O ILE E 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, 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: 6.476A pdb=" N LYS F 158 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL F 12 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ARG F 160 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N VAL F 14 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LEU F 162 " --> pdb=" O VAL F 14 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 8 through 11 Processing sheet with id= O, first strand: chain 'X' and resid 169 through 171 841 hydrogen bonds defined for protein. 2451 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: 5.26 Time building geometry restraints manager: 7.42 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: 75.24 - 87.52: 9 87.52 - 99.80: 40 99.80 - 112.09: 7518 112.09 - 124.37: 15245 124.37 - 136.65: 880 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: 86 2.55 - 3.14: 12814 3.14 - 3.72: 26409 3.72 - 4.31: 34522 4.31 - 4.90: 54755 Nonbonded interactions: 128586 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 2.440 nonbonded pdb=" NH2 ARG B 61 " pdb=" O PRO B 103 " model vdw 2.255 2.520 ... (remaining 128581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.400 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 49.690 Find NCS groups from input model: 0.590 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.980 ------------------------------------------------------------------------------- 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= 1.344 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 : 1.612 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: 0.3348 time to fit residues: 254.2474 Evaluate side-chains 349 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 343 time to evaluate : 1.676 ------------------------------------------------------------------------------- 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: 0.9990 chunk 183 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 219 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 433 GLN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN A 598 HIS ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 HIS ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN F 48 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17417 Z= 0.220 Angle : 0.740 10.439 23692 Z= 0.374 Chirality : 0.043 0.188 2879 Planarity : 0.005 0.077 3082 Dihedral : 6.573 39.589 2571 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.21 % Allowed : 4.36 % Favored : 95.43 % 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: -3.25 (0.18), residues: 1702 helix: -0.85 (0.17), residues: 765 sheet: -2.38 (0.31), residues: 236 loop : -3.60 (0.19), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 22 HIS 0.010 0.002 HIS B 37 PHE 0.024 0.002 PHE F 50 TYR 0.024 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 441 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 438 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 CYS cc_start: 0.9353 (m) cc_final: 0.9037 (t) REVERT: A 309 ASP cc_start: 0.6088 (m-30) cc_final: 0.4842 (m-30) REVERT: A 315 VAL cc_start: 0.8000 (t) cc_final: 0.7475 (p) REVERT: A 321 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8937 (tm-30) REVERT: A 322 LYS cc_start: 0.8826 (tttt) cc_final: 0.8436 (mmtm) REVERT: A 340 LEU cc_start: 0.8815 (mt) cc_final: 0.8409 (mt) REVERT: A 412 MET cc_start: 0.8698 (pmm) cc_final: 0.8380 (pmm) REVERT: A 452 ARG cc_start: 0.9379 (mtt180) cc_final: 0.9012 (tmm-80) REVERT: A 495 GLU cc_start: 0.9426 (mt-10) cc_final: 0.8650 (tp30) REVERT: A 501 TYR cc_start: 0.8977 (p90) cc_final: 0.8652 (p90) REVERT: A 511 TRP cc_start: 0.8114 (p-90) cc_final: 0.7793 (p-90) REVERT: A 536 MET cc_start: 0.9089 (mtp) cc_final: 0.8830 (mtp) REVERT: A 633 ARG cc_start: 0.8754 (mpp-170) cc_final: 0.8353 (mmm-85) REVERT: A 650 MET cc_start: 0.6361 (ttp) cc_final: 0.5990 (ttt) REVERT: A 674 THR cc_start: 0.9144 (m) cc_final: 0.8851 (p) REVERT: A 696 MET cc_start: 0.7589 (mtp) cc_final: 0.7298 (mtp) REVERT: B 156 ARG cc_start: 0.9491 (mpp80) cc_final: 0.9267 (ttp80) REVERT: B 174 ILE cc_start: 0.8902 (tt) cc_final: 0.8052 (tt) REVERT: B 227 ARG cc_start: 0.8617 (mtt180) cc_final: 0.8264 (mpp-170) REVERT: B 316 GLN cc_start: 0.8882 (mp-120) cc_final: 0.8532 (mm-40) REVERT: B 380 ARG cc_start: 0.9469 (tpt170) cc_final: 0.9200 (ppt170) REVERT: B 419 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8620 (tm-30) REVERT: B 526 GLU cc_start: 0.9430 (mt-10) cc_final: 0.8975 (mt-10) REVERT: B 535 ILE cc_start: 0.8728 (mt) cc_final: 0.8518 (mt) REVERT: B 634 LYS cc_start: 0.8900 (mttt) cc_final: 0.8647 (mttm) REVERT: B 641 ARG cc_start: 0.8933 (ttt180) cc_final: 0.8564 (tmm-80) REVERT: B 722 ARG cc_start: 0.8877 (ttm170) cc_final: 0.8592 (ttm-80) REVERT: D 404 THR cc_start: 0.9117 (m) cc_final: 0.8554 (p) REVERT: D 405 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7794 (tm-30) REVERT: D 426 ARG cc_start: 0.9085 (ttt180) cc_final: 0.8665 (tpm170) REVERT: E 57 MET cc_start: 0.6809 (ttm) cc_final: 0.6246 (ttp) REVERT: E 88 LEU cc_start: 0.9146 (mt) cc_final: 0.8900 (mt) REVERT: E 98 GLN cc_start: 0.9073 (mm110) cc_final: 0.8859 (tp40) REVERT: E 112 LYS cc_start: 0.8475 (mttt) cc_final: 0.8243 (tptm) REVERT: E 123 ASN cc_start: 0.9332 (m-40) cc_final: 0.8860 (p0) REVERT: E 137 MET cc_start: 0.8753 (ttm) cc_final: 0.8407 (ttm) REVERT: E 178 ASP cc_start: 0.8236 (p0) cc_final: 0.7618 (p0) REVERT: E 182 ILE cc_start: 0.8717 (tt) cc_final: 0.8467 (tt) REVERT: E 214 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8116 (tp30) REVERT: F 7 GLU cc_start: 0.8701 (tt0) cc_final: 0.8371 (mp0) REVERT: F 11 LEU cc_start: 0.9342 (tp) cc_final: 0.9094 (tp) REVERT: F 169 ASP cc_start: 0.6974 (t0) cc_final: 0.6458 (p0) REVERT: F 205 GLN cc_start: 0.9432 (mt0) cc_final: 0.9170 (mm-40) REVERT: F 215 LEU cc_start: 0.9320 (tp) cc_final: 0.9016 (tp) REVERT: G 9 LEU cc_start: 0.9025 (tp) cc_final: 0.8637 (tp) REVERT: G 11 GLU cc_start: 0.8862 (mp0) cc_final: 0.8465 (mp0) REVERT: G 36 GLN cc_start: 0.9082 (tt0) cc_final: 0.8651 (tm-30) REVERT: G 66 PHE cc_start: 0.8041 (m-10) cc_final: 0.7641 (m-10) outliers start: 3 outliers final: 0 residues processed: 440 average time/residue: 0.3079 time to fit residues: 196.2927 Evaluate side-chains 332 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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: 0.7980 chunk 68 optimal weight: 1.9990 chunk 182 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 218 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 HIS ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 ASN B 555 GLN B 643 GLN B 726 GLN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 HIS ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 ASN F 179 ASN ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17417 Z= 0.367 Angle : 0.864 12.904 23692 Z= 0.436 Chirality : 0.045 0.237 2879 Planarity : 0.006 0.075 3082 Dihedral : 6.697 44.612 2571 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 24.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 0.07 % Allowed : 5.70 % Favored : 94.23 % 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: -3.06 (0.18), residues: 1702 helix: -0.67 (0.17), residues: 760 sheet: -2.28 (0.31), residues: 233 loop : -3.50 (0.19), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 394 HIS 0.014 0.002 HIS B 700 PHE 0.027 0.003 PHE F 50 TYR 0.035 0.003 TYR E 183 ARG 0.012 0.001 ARG B 335 *********************** 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 373 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 372 time to evaluate : 1.723 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: A 284 CYS cc_start: 0.9417 (m) cc_final: 0.9186 (m) REVERT: A 315 VAL cc_start: 0.8089 (t) cc_final: 0.7599 (p) REVERT: A 321 GLU cc_start: 0.9212 (mt-10) cc_final: 0.9008 (tm-30) REVERT: A 322 LYS cc_start: 0.8983 (tttt) cc_final: 0.8667 (mptt) REVERT: A 372 GLU cc_start: 0.9760 (mp0) cc_final: 0.9560 (mp0) REVERT: A 412 MET cc_start: 0.9000 (pmm) cc_final: 0.8761 (pmm) REVERT: A 452 ARG cc_start: 0.9369 (mtt180) cc_final: 0.9017 (tmm-80) REVERT: A 495 GLU cc_start: 0.9448 (mt-10) cc_final: 0.8773 (tp30) REVERT: A 511 TRP cc_start: 0.8401 (p-90) cc_final: 0.8085 (p-90) REVERT: A 623 LEU cc_start: 0.9149 (tp) cc_final: 0.8908 (tt) REVERT: A 633 ARG cc_start: 0.8539 (mpp-170) cc_final: 0.8185 (mmm-85) REVERT: A 650 MET cc_start: 0.6988 (ttp) cc_final: 0.6736 (ttt) REVERT: A 696 MET cc_start: 0.7450 (mtp) cc_final: 0.7207 (mtp) REVERT: B 21 GLN cc_start: 0.8792 (mt0) cc_final: 0.8455 (pm20) REVERT: B 156 ARG cc_start: 0.9548 (mpp80) cc_final: 0.9328 (ttp80) REVERT: B 227 ARG cc_start: 0.8501 (mtt180) cc_final: 0.8255 (mpp-170) REVERT: B 352 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8441 (tm-30) REVERT: B 495 ILE cc_start: 0.9163 (mp) cc_final: 0.8928 (mt) REVERT: B 526 GLU cc_start: 0.9340 (mt-10) cc_final: 0.8784 (mt-10) REVERT: B 634 LYS cc_start: 0.8955 (mttt) cc_final: 0.8753 (mttm) REVERT: B 641 ARG cc_start: 0.9045 (ttt180) cc_final: 0.8803 (tmm160) REVERT: B 677 MET cc_start: 0.8876 (mtt) cc_final: 0.8605 (mmm) REVERT: B 722 ARG cc_start: 0.8730 (ttm170) cc_final: 0.8438 (ttm170) REVERT: D 405 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7874 (tp30) REVERT: D 426 ARG cc_start: 0.9094 (ttt180) cc_final: 0.8577 (tpm170) REVERT: D 438 LYS cc_start: 0.7978 (mtmt) cc_final: 0.7286 (tttt) REVERT: E 98 GLN cc_start: 0.8928 (mm110) cc_final: 0.8677 (tp-100) REVERT: E 112 LYS cc_start: 0.7668 (mttt) cc_final: 0.7416 (tptm) REVERT: E 123 ASN cc_start: 0.9514 (m-40) cc_final: 0.8992 (p0) REVERT: E 137 MET cc_start: 0.8914 (ttm) cc_final: 0.8516 (ttm) REVERT: E 214 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8230 (tp30) REVERT: F 7 GLU cc_start: 0.8651 (tt0) cc_final: 0.8438 (mp0) REVERT: F 11 LEU cc_start: 0.9485 (tp) cc_final: 0.9139 (tp) REVERT: F 158 LYS cc_start: 0.9045 (tptt) cc_final: 0.8819 (tptt) REVERT: F 169 ASP cc_start: 0.7662 (t0) cc_final: 0.6868 (p0) REVERT: F 179 ASN cc_start: 0.9767 (t0) cc_final: 0.9468 (t0) REVERT: F 215 LEU cc_start: 0.9253 (tp) cc_final: 0.8971 (tp) REVERT: G 9 LEU cc_start: 0.9192 (tp) cc_final: 0.8888 (tp) REVERT: G 36 GLN cc_start: 0.9188 (tt0) cc_final: 0.8825 (tp-100) REVERT: G 44 PHE cc_start: 0.9550 (m-10) cc_final: 0.9342 (m-80) REVERT: G 55 GLU cc_start: 0.8547 (mp0) cc_final: 0.8286 (mp0) outliers start: 1 outliers final: 1 residues processed: 373 average time/residue: 0.2971 time to fit residues: 163.2296 Evaluate side-chains 292 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 291 time to evaluate : 1.707 ------------------------------------------------------------------------------- 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: 10.0000 chunk 165 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 105 optimal weight: 0.0870 chunk 147 optimal weight: 6.9990 chunk 220 optimal weight: 8.9990 chunk 233 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 209 optimal weight: 10.0000 chunk 63 optimal weight: 0.0970 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 A 415 HIS ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN A 564 ASN ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN B 474 HIS ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4642 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= 0.175 Angle : 0.657 9.678 23692 Z= 0.332 Chirality : 0.041 0.214 2879 Planarity : 0.004 0.060 3082 Dihedral : 5.633 30.852 2571 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % 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: -2.42 (0.19), residues: 1702 helix: -0.11 (0.18), residues: 762 sheet: -1.64 (0.33), residues: 237 loop : -3.35 (0.20), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 22 HIS 0.011 0.001 HIS B 700 PHE 0.022 0.002 PHE B 157 TYR 0.028 0.002 TYR A 571 ARG 0.006 0.000 ARG D 402 *********************** 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 423 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 423 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 CYS cc_start: 0.9338 (m) cc_final: 0.9024 (t) REVERT: A 412 MET cc_start: 0.8881 (pmm) cc_final: 0.8345 (pmm) REVERT: A 452 ARG cc_start: 0.9397 (mtt180) cc_final: 0.9030 (tmm160) REVERT: A 494 MET cc_start: 0.9117 (ptt) cc_final: 0.8818 (ppp) REVERT: A 495 GLU cc_start: 0.9507 (mt-10) cc_final: 0.8726 (tp30) REVERT: A 510 VAL cc_start: 0.9497 (t) cc_final: 0.9160 (p) REVERT: A 511 TRP cc_start: 0.8513 (p-90) cc_final: 0.7758 (p-90) REVERT: A 581 TYR cc_start: 0.7936 (p90) cc_final: 0.7656 (t80) REVERT: A 650 MET cc_start: 0.6437 (ttp) cc_final: 0.6081 (ttt) REVERT: A 658 PHE cc_start: 0.9094 (m-80) cc_final: 0.8845 (m-80) REVERT: A 692 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8399 (mtmm) REVERT: A 693 LEU cc_start: 0.8215 (mp) cc_final: 0.7760 (mp) REVERT: A 696 MET cc_start: 0.7912 (mtp) cc_final: 0.7076 (ttt) REVERT: B 21 GLN cc_start: 0.8700 (mt0) cc_final: 0.8334 (pm20) REVERT: B 317 GLU cc_start: 0.9384 (mt-10) cc_final: 0.8952 (mm-30) REVERT: B 352 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8303 (tm-30) REVERT: B 526 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8158 (mt-10) REVERT: B 597 LEU cc_start: 0.6570 (pt) cc_final: 0.6360 (tt) REVERT: B 641 ARG cc_start: 0.8931 (ttt180) cc_final: 0.8541 (tmm-80) REVERT: B 684 PHE cc_start: 0.7923 (m-10) cc_final: 0.7692 (m-10) REVERT: B 722 ARG cc_start: 0.8730 (ttm170) cc_final: 0.8480 (ttm170) REVERT: D 405 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7913 (tp30) REVERT: D 426 ARG cc_start: 0.9152 (ttt180) cc_final: 0.8592 (tpm170) REVERT: E 98 GLN cc_start: 0.9090 (mm110) cc_final: 0.8512 (tp-100) REVERT: E 99 ASN cc_start: 0.8980 (m-40) cc_final: 0.7987 (m110) REVERT: E 123 ASN cc_start: 0.9443 (m-40) cc_final: 0.8997 (p0) REVERT: E 137 MET cc_start: 0.8888 (ttm) cc_final: 0.8620 (ttm) REVERT: E 178 ASP cc_start: 0.8015 (p0) cc_final: 0.7408 (p0) REVERT: E 214 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8117 (tp30) REVERT: F 179 ASN cc_start: 0.9752 (t0) cc_final: 0.9511 (t0) REVERT: F 215 LEU cc_start: 0.9303 (tp) cc_final: 0.9025 (tp) REVERT: G 9 LEU cc_start: 0.9070 (tp) cc_final: 0.8729 (tp) REVERT: G 36 GLN cc_start: 0.9201 (tt0) cc_final: 0.8869 (tp-100) REVERT: G 37 ASP cc_start: 0.9478 (t0) cc_final: 0.9175 (t0) REVERT: G 44 PHE cc_start: 0.9320 (m-10) cc_final: 0.9105 (m-80) REVERT: G 55 GLU cc_start: 0.8529 (mp0) cc_final: 0.8281 (mp0) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.2886 time to fit residues: 180.6127 Evaluate side-chains 318 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 1.642 ------------------------------------------------------------------------------- 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: 0.9980 chunk 3 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 96 optimal weight: 0.0070 chunk 199 optimal weight: 10.0000 chunk 161 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 119 optimal weight: 0.8980 chunk 209 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- 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 415 HIS ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 ASN ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN A 625 GLN ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS B 585 GLN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS ** 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: 0.7688 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17417 Z= 0.216 Angle : 0.692 9.057 23692 Z= 0.347 Chirality : 0.041 0.212 2879 Planarity : 0.005 0.074 3082 Dihedral : 5.557 35.740 2571 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % 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: -2.25 (0.19), residues: 1702 helix: 0.07 (0.18), residues: 763 sheet: -1.60 (0.32), residues: 245 loop : -3.31 (0.20), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 342 HIS 0.011 0.001 HIS B 700 PHE 0.023 0.002 PHE B 157 TYR 0.023 0.002 TYR B 719 ARG 0.005 0.001 ARG F 160 *********************** 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 389 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 1.778 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 284 CYS cc_start: 0.9261 (m) cc_final: 0.9059 (t) REVERT: A 332 ARG cc_start: 0.8145 (mtt180) cc_final: 0.7864 (mtp85) REVERT: A 362 LEU cc_start: 0.9155 (tp) cc_final: 0.8865 (mt) REVERT: A 380 MET cc_start: 0.9502 (mmp) cc_final: 0.9196 (ttm) REVERT: A 412 MET cc_start: 0.8960 (pmm) cc_final: 0.8377 (pmm) REVERT: A 452 ARG cc_start: 0.9338 (mtt180) cc_final: 0.8955 (tmm-80) REVERT: A 495 GLU cc_start: 0.9334 (mt-10) cc_final: 0.8574 (tp30) REVERT: A 511 TRP cc_start: 0.8487 (p-90) cc_final: 0.7909 (p-90) REVERT: A 625 GLN cc_start: 0.9507 (tp-100) cc_final: 0.9119 (tm-30) REVERT: A 650 MET cc_start: 0.6836 (ttp) cc_final: 0.6492 (ttt) REVERT: A 692 LYS cc_start: 0.8618 (mtmm) cc_final: 0.8399 (mtmm) REVERT: B 70 LEU cc_start: 0.8813 (tp) cc_final: 0.8368 (tt) REVERT: B 233 PHE cc_start: 0.8911 (m-80) cc_final: 0.8679 (m-80) REVERT: B 316 GLN cc_start: 0.9053 (mp-120) cc_final: 0.8739 (mm-40) REVERT: B 317 GLU cc_start: 0.9433 (mt-10) cc_final: 0.8971 (mm-30) REVERT: B 352 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8235 (tm-30) REVERT: B 357 PHE cc_start: 0.9210 (t80) cc_final: 0.8888 (t80) REVERT: B 526 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8746 (mt-10) REVERT: B 544 TYR cc_start: 0.8738 (t80) cc_final: 0.8259 (t80) REVERT: B 641 ARG cc_start: 0.8868 (ttt180) cc_final: 0.8455 (tmm-80) REVERT: B 677 MET cc_start: 0.8693 (mtp) cc_final: 0.8318 (mmm) REVERT: D 405 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7545 (tp30) REVERT: D 426 ARG cc_start: 0.8946 (ttt180) cc_final: 0.8434 (tpm170) REVERT: E 98 GLN cc_start: 0.9195 (mm110) cc_final: 0.8823 (tp40) REVERT: E 99 ASN cc_start: 0.9009 (m-40) cc_final: 0.8171 (m110) REVERT: E 123 ASN cc_start: 0.9458 (m-40) cc_final: 0.8952 (p0) REVERT: E 137 MET cc_start: 0.9011 (ttm) cc_final: 0.8696 (ttm) REVERT: E 204 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7600 (tm-30) REVERT: E 214 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8185 (tp30) REVERT: F 11 LEU cc_start: 0.9466 (tp) cc_final: 0.9110 (tp) REVERT: F 158 LYS cc_start: 0.9132 (tptt) cc_final: 0.8819 (tptp) REVERT: F 179 ASN cc_start: 0.9776 (t0) cc_final: 0.9525 (t0) REVERT: F 215 LEU cc_start: 0.9232 (tp) cc_final: 0.8933 (tp) REVERT: G 9 LEU cc_start: 0.9003 (tp) cc_final: 0.8738 (tp) REVERT: G 36 GLN cc_start: 0.9111 (tt0) cc_final: 0.8741 (tp-100) REVERT: G 37 ASP cc_start: 0.9402 (t0) cc_final: 0.9122 (t0) REVERT: G 55 GLU cc_start: 0.8457 (mp0) cc_final: 0.8248 (mp0) REVERT: G 66 PHE cc_start: 0.7868 (m-80) cc_final: 0.7562 (m-10) outliers start: 0 outliers final: 0 residues processed: 389 average time/residue: 0.3087 time to fit residues: 180.3590 Evaluate side-chains 283 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.655 ------------------------------------------------------------------------------- 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: 0.0770 chunk 210 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 137 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 chunk 234 optimal weight: 8.9990 chunk 194 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 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 474 HIS ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN D 390 GLN F 205 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17417 Z= 0.171 Angle : 0.663 10.767 23692 Z= 0.331 Chirality : 0.041 0.183 2879 Planarity : 0.004 0.070 3082 Dihedral : 5.271 38.955 2571 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: -2.05 (0.20), residues: 1702 helix: 0.15 (0.18), residues: 764 sheet: -1.31 (0.34), residues: 235 loop : -3.16 (0.20), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 22 HIS 0.007 0.001 HIS B 700 PHE 0.023 0.002 PHE B 157 TYR 0.022 0.002 TYR B 719 ARG 0.009 0.000 ARG B 335 *********************** 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 373 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 1.645 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 284 CYS cc_start: 0.9217 (m) cc_final: 0.9010 (t) REVERT: A 332 ARG cc_start: 0.7888 (mtt180) cc_final: 0.7615 (mtp85) REVERT: A 452 ARG cc_start: 0.9329 (mtt180) cc_final: 0.8956 (tmm160) REVERT: A 490 GLU cc_start: 0.7750 (pt0) cc_final: 0.7478 (pt0) REVERT: A 495 GLU cc_start: 0.9282 (mt-10) cc_final: 0.8566 (tp30) REVERT: A 511 TRP cc_start: 0.8541 (p-90) cc_final: 0.7901 (p-90) REVERT: A 514 MET cc_start: 0.8375 (ppp) cc_final: 0.7645 (ppp) REVERT: A 581 TYR cc_start: 0.8248 (p90) cc_final: 0.7932 (t80) REVERT: A 594 GLN cc_start: 0.9556 (mp-120) cc_final: 0.9321 (pm20) REVERT: A 625 GLN cc_start: 0.9551 (tp-100) cc_final: 0.9108 (tm-30) REVERT: A 650 MET cc_start: 0.7065 (ttp) cc_final: 0.6544 (ttt) REVERT: A 692 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8424 (mtmm) REVERT: B 21 GLN cc_start: 0.8654 (mt0) cc_final: 0.8300 (pm20) REVERT: B 317 GLU cc_start: 0.9432 (mt-10) cc_final: 0.9001 (mm-30) REVERT: B 352 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8157 (tm-30) REVERT: B 357 PHE cc_start: 0.9216 (t80) cc_final: 0.8897 (t80) REVERT: B 526 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8733 (mt-10) REVERT: B 544 TYR cc_start: 0.8628 (t80) cc_final: 0.8141 (t80) REVERT: B 641 ARG cc_start: 0.8832 (ttt180) cc_final: 0.8562 (tpp80) REVERT: B 677 MET cc_start: 0.8983 (mtt) cc_final: 0.8718 (mmm) REVERT: D 405 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7021 (tp30) REVERT: D 426 ARG cc_start: 0.9009 (ttt180) cc_final: 0.8446 (tpm170) REVERT: D 434 GLU cc_start: 0.8583 (tp30) cc_final: 0.8363 (pp20) REVERT: D 441 MET cc_start: 0.8096 (mmp) cc_final: 0.7626 (mmm) REVERT: E 98 GLN cc_start: 0.9163 (mm110) cc_final: 0.8771 (tp40) REVERT: E 99 ASN cc_start: 0.8819 (m-40) cc_final: 0.7909 (m110) REVERT: E 123 ASN cc_start: 0.9427 (m-40) cc_final: 0.8951 (p0) REVERT: E 137 MET cc_start: 0.8932 (ttm) cc_final: 0.8701 (ttm) REVERT: E 140 HIS cc_start: 0.8660 (t70) cc_final: 0.8319 (t-90) REVERT: E 166 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8242 (tp30) REVERT: E 178 ASP cc_start: 0.8144 (p0) cc_final: 0.7584 (p0) REVERT: F 215 LEU cc_start: 0.9402 (tp) cc_final: 0.9128 (tp) REVERT: G 37 ASP cc_start: 0.9348 (t0) cc_final: 0.9040 (t0) REVERT: G 55 GLU cc_start: 0.8439 (mp0) cc_final: 0.8194 (mp0) REVERT: G 66 PHE cc_start: 0.7897 (m-80) cc_final: 0.7538 (m-10) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.2755 time to fit residues: 154.3215 Evaluate side-chains 295 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.679 ------------------------------------------------------------------------------- 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: 0.8980 chunk 133 optimal weight: 0.5980 chunk 170 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 197 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 415 HIS ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 GLN F 185 GLN G 64 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17417 Z= 0.244 Angle : 0.713 12.637 23692 Z= 0.356 Chirality : 0.042 0.267 2879 Planarity : 0.005 0.102 3082 Dihedral : 5.426 38.791 2571 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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: -1.95 (0.20), residues: 1702 helix: 0.21 (0.19), residues: 755 sheet: -1.35 (0.34), residues: 235 loop : -3.01 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 394 HIS 0.006 0.001 HIS A 444 PHE 0.018 0.002 PHE F 50 TYR 0.020 0.002 TYR B 94 ARG 0.016 0.001 ARG B 343 *********************** 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 366 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 1.770 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 315 VAL cc_start: 0.7684 (t) cc_final: 0.7008 (p) REVERT: A 332 ARG cc_start: 0.8150 (mtt180) cc_final: 0.7803 (mtp85) REVERT: A 380 MET cc_start: 0.9484 (mmp) cc_final: 0.9111 (ttm) REVERT: A 412 MET cc_start: 0.8945 (pmm) cc_final: 0.8401 (pmm) REVERT: A 452 ARG cc_start: 0.9339 (mtt180) cc_final: 0.8983 (tmm160) REVERT: A 495 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8606 (tp30) REVERT: A 511 TRP cc_start: 0.8557 (p-90) cc_final: 0.7899 (p-90) REVERT: A 623 LEU cc_start: 0.8923 (tp) cc_final: 0.8561 (tt) REVERT: A 625 GLN cc_start: 0.9534 (tp-100) cc_final: 0.9050 (tm-30) REVERT: A 650 MET cc_start: 0.7188 (ttp) cc_final: 0.6626 (ttt) REVERT: A 658 PHE cc_start: 0.9107 (m-80) cc_final: 0.7830 (m-80) REVERT: A 692 LYS cc_start: 0.8676 (mtmm) cc_final: 0.8450 (mtmm) REVERT: A 696 MET cc_start: 0.7577 (mtp) cc_final: 0.6135 (tpt) REVERT: B 316 GLN cc_start: 0.9109 (mp-120) cc_final: 0.8861 (mm-40) REVERT: B 317 GLU cc_start: 0.9428 (mt-10) cc_final: 0.8999 (mm-30) REVERT: B 352 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8169 (tm-30) REVERT: B 357 PHE cc_start: 0.9222 (t80) cc_final: 0.8920 (t80) REVERT: B 526 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8604 (mt-10) REVERT: B 641 ARG cc_start: 0.8817 (ttt180) cc_final: 0.8584 (tpp80) REVERT: B 674 TYR cc_start: 0.9110 (m-80) cc_final: 0.8886 (m-80) REVERT: B 677 MET cc_start: 0.8901 (mtt) cc_final: 0.8645 (mmm) REVERT: D 405 GLU cc_start: 0.7686 (mt-10) cc_final: 0.6969 (tp30) REVERT: D 426 ARG cc_start: 0.9070 (ttt180) cc_final: 0.8506 (tpm170) REVERT: D 441 MET cc_start: 0.8140 (mmp) cc_final: 0.7817 (mmm) REVERT: E 72 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6717 (pt0) REVERT: E 98 GLN cc_start: 0.9164 (mm110) cc_final: 0.8764 (tp40) REVERT: E 99 ASN cc_start: 0.9005 (m-40) cc_final: 0.8051 (m110) REVERT: E 123 ASN cc_start: 0.9441 (m-40) cc_final: 0.8928 (p0) REVERT: E 137 MET cc_start: 0.8917 (ttm) cc_final: 0.8619 (ttm) REVERT: E 140 HIS cc_start: 0.8652 (t70) cc_final: 0.8351 (t-90) REVERT: F 143 TYR cc_start: 0.9068 (t80) cc_final: 0.8723 (t80) REVERT: F 215 LEU cc_start: 0.9275 (tp) cc_final: 0.9005 (tp) REVERT: G 37 ASP cc_start: 0.9387 (t0) cc_final: 0.9102 (t0) REVERT: G 55 GLU cc_start: 0.8463 (mp0) cc_final: 0.8237 (mp0) REVERT: G 66 PHE cc_start: 0.7895 (m-80) cc_final: 0.7511 (m-10) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.2790 time to fit residues: 154.4048 Evaluate side-chains 287 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 1.851 ------------------------------------------------------------------------------- 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: 0.0870 chunk 93 optimal weight: 0.7980 chunk 139 optimal weight: 0.0040 chunk 70 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 158 optimal weight: 0.0770 chunk 115 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 212 optimal weight: 8.9990 overall best weight: 0.7930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN B 474 HIS B 555 GLN D 390 GLN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17417 Z= 0.186 Angle : 0.675 11.752 23692 Z= 0.339 Chirality : 0.042 0.282 2879 Planarity : 0.004 0.072 3082 Dihedral : 5.159 37.326 2571 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: -1.95 (0.20), residues: 1702 helix: 0.20 (0.19), residues: 760 sheet: -1.30 (0.33), residues: 247 loop : -3.06 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 189 HIS 0.006 0.001 HIS B 37 PHE 0.022 0.002 PHE B 157 TYR 0.025 0.002 TYR A 571 ARG 0.011 0.001 ARG B 156 *********************** 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 367 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 1.881 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: A 315 VAL cc_start: 0.7573 (t) cc_final: 0.7029 (p) REVERT: A 380 MET cc_start: 0.9423 (mmp) cc_final: 0.9098 (ttm) REVERT: A 412 MET cc_start: 0.8871 (pmm) cc_final: 0.8382 (pmm) REVERT: A 452 ARG cc_start: 0.9397 (mtt180) cc_final: 0.8995 (tmm160) REVERT: A 490 GLU cc_start: 0.7696 (pt0) cc_final: 0.7458 (pt0) REVERT: A 495 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8631 (tp30) REVERT: A 511 TRP cc_start: 0.8612 (p-90) cc_final: 0.8011 (p-90) REVERT: A 514 MET cc_start: 0.8371 (ppp) cc_final: 0.7779 (ppp) REVERT: A 566 PHE cc_start: 0.9244 (m-80) cc_final: 0.8925 (m-80) REVERT: A 581 TYR cc_start: 0.8242 (p90) cc_final: 0.7914 (t80) REVERT: A 650 MET cc_start: 0.7332 (ttp) cc_final: 0.6843 (ttt) REVERT: A 655 TYR cc_start: 0.8279 (p90) cc_final: 0.7988 (p90) REVERT: A 696 MET cc_start: 0.7601 (mtp) cc_final: 0.6356 (tpt) REVERT: B 156 ARG cc_start: 0.9590 (ttp80) cc_final: 0.9326 (ptp90) REVERT: B 174 ILE cc_start: 0.8071 (tt) cc_final: 0.7690 (tt) REVERT: B 316 GLN cc_start: 0.9109 (mp-120) cc_final: 0.8866 (mp10) REVERT: B 317 GLU cc_start: 0.9411 (mt-10) cc_final: 0.9020 (mm-30) REVERT: B 352 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8168 (tm-30) REVERT: B 357 PHE cc_start: 0.9220 (t80) cc_final: 0.8904 (t80) REVERT: B 526 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8906 (mt-10) REVERT: B 545 MET cc_start: 0.8610 (mmm) cc_final: 0.8289 (tpp) REVERT: B 638 GLU cc_start: 0.9344 (mm-30) cc_final: 0.9096 (mt-10) REVERT: B 674 TYR cc_start: 0.9098 (m-80) cc_final: 0.8865 (m-80) REVERT: B 677 MET cc_start: 0.9024 (mtt) cc_final: 0.8787 (mmm) REVERT: D 405 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6868 (tp30) REVERT: D 426 ARG cc_start: 0.9094 (ttt180) cc_final: 0.8505 (tpm170) REVERT: E 72 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6581 (pt0) REVERT: E 123 ASN cc_start: 0.9435 (m-40) cc_final: 0.8962 (p0) REVERT: E 137 MET cc_start: 0.8885 (ttm) cc_final: 0.8593 (ttm) REVERT: E 140 HIS cc_start: 0.8623 (t70) cc_final: 0.8270 (t-90) REVERT: E 178 ASP cc_start: 0.8235 (p0) cc_final: 0.7492 (p0) REVERT: F 215 LEU cc_start: 0.9237 (tp) cc_final: 0.8970 (tp) REVERT: G 9 LEU cc_start: 0.9013 (tp) cc_final: 0.8787 (tp) REVERT: G 37 ASP cc_start: 0.9351 (t0) cc_final: 0.9074 (t0) REVERT: G 39 ASP cc_start: 0.8697 (t70) cc_final: 0.8367 (t70) REVERT: G 55 GLU cc_start: 0.8475 (mp0) cc_final: 0.8254 (mp0) REVERT: G 66 PHE cc_start: 0.7900 (m-80) cc_final: 0.7498 (m-10) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.2860 time to fit residues: 160.8373 Evaluate side-chains 292 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.668 ------------------------------------------------------------------------------- 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: 10.0000 chunk 217 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 170 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 205 optimal weight: 8.9990 chunk 216 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 GLN D 390 GLN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 GLN G 64 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 17417 Z= 0.416 Angle : 0.905 11.287 23692 Z= 0.454 Chirality : 0.048 0.267 2879 Planarity : 0.006 0.069 3082 Dihedral : 6.154 38.152 2571 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 27.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: -2.47 (0.19), residues: 1702 helix: -0.28 (0.18), residues: 744 sheet: -1.69 (0.33), residues: 246 loop : -3.14 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 435 HIS 0.017 0.002 HIS A 444 PHE 0.029 0.003 PHE B 93 TYR 0.025 0.003 TYR A 534 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 327 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 1.634 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: 0.8010 (t) cc_final: 0.7546 (p) REVERT: A 412 MET cc_start: 0.8998 (pmm) cc_final: 0.8519 (pmm) REVERT: A 452 ARG cc_start: 0.9427 (mtt180) cc_final: 0.9064 (tmm-80) REVERT: A 489 TYR cc_start: 0.8776 (t80) cc_final: 0.8575 (t80) REVERT: A 490 GLU cc_start: 0.8007 (pt0) cc_final: 0.7595 (pm20) REVERT: A 495 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8861 (tp30) REVERT: A 511 TRP cc_start: 0.8593 (p-90) cc_final: 0.8102 (p-90) REVERT: A 514 MET cc_start: 0.8332 (ppp) cc_final: 0.7619 (ppp) REVERT: A 623 LEU cc_start: 0.9076 (tp) cc_final: 0.8638 (tt) REVERT: A 625 GLN cc_start: 0.9373 (tp-100) cc_final: 0.9018 (tm-30) REVERT: A 650 MET cc_start: 0.6932 (ttp) cc_final: 0.6302 (ttt) REVERT: B 317 GLU cc_start: 0.9477 (mt-10) cc_final: 0.9030 (mm-30) REVERT: B 352 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8283 (tm-30) REVERT: B 526 GLU cc_start: 0.9332 (mt-10) cc_final: 0.8026 (mt-10) REVERT: B 634 LYS cc_start: 0.8781 (mttt) cc_final: 0.8165 (mttm) REVERT: B 674 TYR cc_start: 0.9159 (m-80) cc_final: 0.8764 (m-80) REVERT: D 405 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7120 (tp30) REVERT: D 426 ARG cc_start: 0.9081 (ttt180) cc_final: 0.8545 (tpm170) REVERT: E 72 GLU cc_start: 0.7568 (mt-10) cc_final: 0.6930 (pt0) REVERT: E 112 LYS cc_start: 0.6175 (tptt) cc_final: 0.5973 (tmtt) REVERT: E 137 MET cc_start: 0.8803 (ttm) cc_final: 0.8462 (ttm) REVERT: F 147 MET cc_start: 0.8956 (mmp) cc_final: 0.8619 (mmp) REVERT: F 173 GLN cc_start: 0.9510 (mt0) cc_final: 0.9011 (pt0) REVERT: G 36 GLN cc_start: 0.8110 (tp-100) cc_final: 0.7894 (tp-100) REVERT: G 37 ASP cc_start: 0.9368 (t0) cc_final: 0.9085 (t0) REVERT: G 55 GLU cc_start: 0.8483 (mp0) cc_final: 0.8280 (mp0) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.2703 time to fit residues: 134.6106 Evaluate side-chains 246 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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: 3.9990 chunk 109 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 241 optimal weight: 7.9990 chunk 221 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 GLN D 390 GLN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.6079 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= 0.281 Angle : 0.775 12.070 23692 Z= 0.391 Chirality : 0.045 0.235 2879 Planarity : 0.005 0.104 3082 Dihedral : 5.791 37.230 2571 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 22.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % 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 : 0.12 % 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: -2.41 (0.19), residues: 1702 helix: -0.26 (0.18), residues: 757 sheet: -1.60 (0.33), residues: 242 loop : -3.13 (0.20), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 394 HIS 0.011 0.002 HIS A 444 PHE 0.027 0.003 PHE B 451 TYR 0.016 0.002 TYR B 410 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 332 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 1.625 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: A 315 VAL cc_start: 0.7997 (t) cc_final: 0.7650 (p) REVERT: A 412 MET cc_start: 0.8946 (pmm) cc_final: 0.8490 (pmm) REVERT: A 442 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8907 (mm-30) REVERT: A 452 ARG cc_start: 0.9396 (mtt180) cc_final: 0.9054 (tmm-80) REVERT: A 495 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8870 (tp30) REVERT: A 511 TRP cc_start: 0.8708 (p-90) cc_final: 0.8200 (p-90) REVERT: A 514 MET cc_start: 0.8386 (ppp) cc_final: 0.7777 (ppp) REVERT: A 581 TYR cc_start: 0.8274 (p90) cc_final: 0.7889 (t80) REVERT: A 625 GLN cc_start: 0.9402 (tp-100) cc_final: 0.8991 (tm-30) REVERT: A 650 MET cc_start: 0.6906 (ttp) cc_final: 0.6319 (ttt) REVERT: A 696 MET cc_start: 0.7171 (mtp) cc_final: 0.6934 (mtp) REVERT: B 25 MET cc_start: 0.8701 (ttp) cc_final: 0.8470 (ttt) REVERT: B 316 GLN cc_start: 0.9296 (mp10) cc_final: 0.8989 (mp10) REVERT: B 317 GLU cc_start: 0.9428 (mt-10) cc_final: 0.9029 (mm-30) REVERT: B 352 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8215 (tm-30) REVERT: B 357 PHE cc_start: 0.9173 (t80) cc_final: 0.8836 (t80) REVERT: B 418 ILE cc_start: 0.9207 (mt) cc_final: 0.8859 (pt) REVERT: B 577 THR cc_start: 0.8622 (m) cc_final: 0.8255 (p) REVERT: B 634 LYS cc_start: 0.8730 (mttt) cc_final: 0.8137 (mttm) REVERT: B 674 TYR cc_start: 0.9182 (m-80) cc_final: 0.8899 (m-80) REVERT: D 405 GLU cc_start: 0.7540 (mt-10) cc_final: 0.6890 (tp30) REVERT: D 426 ARG cc_start: 0.9087 (ttt180) cc_final: 0.8533 (tpm170) REVERT: E 72 GLU cc_start: 0.7597 (mt-10) cc_final: 0.6896 (pt0) REVERT: E 112 LYS cc_start: 0.6207 (tptt) cc_final: 0.5935 (tmtt) REVERT: E 123 ASN cc_start: 0.9562 (m-40) cc_final: 0.9124 (p0) REVERT: E 137 MET cc_start: 0.8761 (ttm) cc_final: 0.8420 (ttm) REVERT: E 178 ASP cc_start: 0.8120 (p0) cc_final: 0.7271 (p0) REVERT: F 178 MET cc_start: 0.9218 (ptp) cc_final: 0.8997 (pmm) REVERT: G 39 ASP cc_start: 0.9011 (t70) cc_final: 0.8755 (p0) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.2623 time to fit residues: 134.6242 Evaluate side-chains 253 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 1.840 ------------------------------------------------------------------------------- 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: 0.8980 chunk 177 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 192 optimal weight: 10.0000 chunk 80 optimal weight: 0.0980 chunk 197 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 GLN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.092993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.078285 restraints weight = 83615.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.079850 restraints weight = 60665.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.080977 restraints weight = 47217.750| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17417 Z= 0.184 Angle : 0.683 10.529 23692 Z= 0.344 Chirality : 0.042 0.226 2879 Planarity : 0.005 0.098 3082 Dihedral : 5.254 36.193 2571 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % 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 : 0.12 % 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: -2.04 (0.20), residues: 1702 helix: 0.12 (0.18), residues: 746 sheet: -1.52 (0.33), residues: 247 loop : -2.97 (0.21), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 511 HIS 0.006 0.001 HIS B 37 PHE 0.021 0.002 PHE B 157 TYR 0.028 0.002 TYR A 489 ARG 0.016 0.001 ARG D 392 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3643.23 seconds wall clock time: 66 minutes 14.96 seconds (3974.96 seconds total)