Starting phenix.real_space_refine on Sun Apr 7 18:35:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wiv_21685/04_2024/6wiv_21685_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wiv_21685/04_2024/6wiv_21685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wiv_21685/04_2024/6wiv_21685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wiv_21685/04_2024/6wiv_21685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wiv_21685/04_2024/6wiv_21685_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wiv_21685/04_2024/6wiv_21685_updated.pdb" } resolution = 3.3 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= 0.017 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 2 5.49 5 S 61 5.16 5 C 7361 2.51 5 N 1791 2.21 5 O 1990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 91": "OD1" <-> "OD2" Residue "A ASP 207": "OD1" <-> "OD2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 441": "OD1" <-> "OD2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 533": "OD1" <-> "OD2" Residue "A PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 604": "OD1" <-> "OD2" Residue "A PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 223": "OD1" <-> "OD2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B ASP 235": "OD1" <-> "OD2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 256": "OD1" <-> "OD2" Residue "B PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 318": "OD1" <-> "OD2" Residue "B PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 540": "OD1" <-> "OD2" Residue "B PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 631": "OE1" <-> "OE2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 715": "OD1" <-> "OD2" Residue "B PHE 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11206 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 5427 Classifications: {'peptide': 681} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 652} Chain breaks: 2 Chain: "B" Number of atoms: 5333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5333 Classifications: {'peptide': 671} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 643} Chain breaks: 3 Chain: "A" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 208 Unusual residues: {' CA': 1, 'CLR': 4, 'NAG': 3, 'U3G': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 238 Unusual residues: {'CLR': 6, 'NAG': 1, 'U3D': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.58, per 1000 atoms: 0.59 Number of scatterers: 11206 At special positions: 0 Unit cell: (86.9, 97.9, 162.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 61 16.00 P 2 15.00 O 1990 8.00 N 1791 7.00 C 7361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 103 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 293 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.04 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 648 " distance=2.03 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 Links applied NAG-ASN " NAG A 901 " - " ASN A 365 " " NAG A 902 " - " ASN A 385 " " NAG A 903 " - " ASN A 397 " " NAG B 901 " - " ASN B 404 " Time building additional restraints: 4.09 Conformation dependent library (CDL) restraints added in 2.0 seconds 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2530 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 10 sheets defined 52.5% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 67 through 84 removed outlier: 4.860A pdb=" N GLN A 72 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Proline residue: A 73 - end of helix removed outlier: 3.925A pdb=" N MET A 77 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU A 79 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN A 83 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER A 84 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 removed outlier: 4.292A pdb=" N LYS A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR A 111 " --> pdb=" O GLN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 142 removed outlier: 4.769A pdb=" N ARG A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N MET A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 173 through 187 Proline residue: A 178 - end of helix removed outlier: 3.993A pdb=" N VAL A 181 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 215 removed outlier: 3.722A pdb=" N GLU A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.555A pdb=" N LYS A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 295 through 302 Processing helix chain 'A' and resid 326 through 336 Processing helix chain 'A' and resid 350 through 367 Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'A' and resid 472 through 498 Processing helix chain 'A' and resid 503 through 507 Processing helix chain 'A' and resid 510 through 531 removed outlier: 4.049A pdb=" N VAL A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Proline residue: A 529 - end of helix Processing helix chain 'A' and resid 534 through 537 No H-bonds generated for 'chain 'A' and resid 534 through 537' Processing helix chain 'A' and resid 541 through 575 removed outlier: 3.543A pdb=" N LEU A 552 " --> pdb=" O ARG A 549 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 553 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 555 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 559 " --> pdb=" O GLY A 556 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 561 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER A 563 " --> pdb=" O GLY A 560 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 565 " --> pdb=" O GLY A 562 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR A 573 " --> pdb=" O TRP A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 614 removed outlier: 3.863A pdb=" N VAL A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 673 removed outlier: 3.603A pdb=" N ILE A 655 " --> pdb=" O THR A 651 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 656 " --> pdb=" O TRP A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 708 removed outlier: 3.732A pdb=" N TYR A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN A 694 " --> pdb=" O MET A 690 " (cutoff:3.500A) Proline residue: A 704 - end of helix removed outlier: 3.918A pdb=" N MET A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 746 Proline residue: A 738 - end of helix Processing helix chain 'B' and resid 69 through 76 removed outlier: 3.897A pdb=" N SER B 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG B 75 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 110 through 123 Processing helix chain 'B' and resid 136 through 148 removed outlier: 3.647A pdb=" N SER B 145 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN B 147 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLY B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 164 Processing helix chain 'B' and resid 179 through 193 removed outlier: 3.693A pdb=" N VAL B 182 " --> pdb=" O ASP B 179 " (cutoff:3.500A) Proline residue: B 184 - end of helix removed outlier: 4.034A pdb=" N LEU B 187 " --> pdb=" O PRO B 184 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR B 193 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 219 removed outlier: 3.940A pdb=" N VAL B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 246 removed outlier: 3.698A pdb=" N ASN B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 269 removed outlier: 3.760A pdb=" N ALA B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 335 through 345 Processing helix chain 'B' and resid 355 through 375 removed outlier: 3.720A pdb=" N GLY B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 404 Processing helix chain 'B' and resid 479 through 505 Processing helix chain 'B' and resid 510 through 514 Processing helix chain 'B' and resid 517 through 538 removed outlier: 4.329A pdb=" N GLY B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 583 removed outlier: 3.516A pdb=" N ALA B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET B 571 " --> pdb=" O ALA B 567 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR B 575 " --> pdb=" O MET B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 618 Processing helix chain 'B' and resid 653 through 678 removed outlier: 3.667A pdb=" N LEU B 667 " --> pdb=" O TYR B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 713 removed outlier: 3.587A pdb=" N THR B 713 " --> pdb=" O VAL B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 747 Proline residue: B 742 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 92 through 100 removed outlier: 5.974A pdb=" N ARG A 51 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LYS A 95 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL A 53 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE A 97 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE A 55 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N HIS A 99 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA A 57 " --> pdb=" O HIS A 99 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N GLY A 56 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 125 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU A 58 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 147 through 149 Processing sheet with id= C, first strand: chain 'A' and resid 223 through 226 removed outlier: 8.941A pdb=" N GLN A 224 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR A 194 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N PHE A 226 " --> pdb=" O THR A 194 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLN A 196 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE A 244 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE A 195 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL A 246 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLN A 197 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU A 248 " --> pdb=" O GLN A 197 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A 272 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLY A 247 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE A 274 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 306 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN A 424 " --> pdb=" O LYS A 432 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LYS A 432 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLN A 426 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N TYR A 430 " --> pdb=" O GLN A 426 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 400 through 403 Processing sheet with id= E, first strand: chain 'A' and resid 464 through 468 Processing sheet with id= F, first strand: chain 'B' and resid 98 through 104 removed outlier: 6.414A pdb=" N MET B 129 " --> pdb=" O MET B 59 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU B 61 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE B 131 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 153 through 155 Processing sheet with id= H, first strand: chain 'B' and resid 229 through 232 removed outlier: 8.744A pdb=" N GLU B 230 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR B 200 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N PHE B 232 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR B 202 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE B 250 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LEU B 201 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N GLN B 203 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLN B 254 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLN B 278 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLY B 253 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE B 280 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE B 315 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLN B 430 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LYS B 438 " --> pdb=" O GLN B 430 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLN B 432 " --> pdb=" O GLU B 436 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLU B 436 " --> pdb=" O GLN B 432 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 407 through 410 Processing sheet with id= J, first strand: chain 'B' and resid 622 through 627 removed outlier: 3.553A pdb=" N ARG B 622 " --> pdb=" O GLU B 649 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1407 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: 3.25 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1719 1.30 - 1.43: 2982 1.43 - 1.56: 6631 1.56 - 1.68: 58 1.68 - 1.81: 97 Bond restraints: 11487 Sorted by residual: bond pdb=" C38 U3D B 902 " pdb=" O37 U3D B 902 " ideal model delta sigma weight residual 1.330 1.449 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" C20 U3D B 902 " pdb=" O22 U3D B 902 " ideal model delta sigma weight residual 1.330 1.431 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C40 U3D B 902 " pdb=" C41 U3D B 902 " ideal model delta sigma weight residual 1.527 1.615 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C24 U3G A 905 " pdb=" O23 U3G A 905 " ideal model delta sigma weight residual 1.337 1.424 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C18 U3G A 905 " pdb=" O20 U3G A 905 " ideal model delta sigma weight residual 1.334 1.419 -0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 11482 not shown) Histogram of bond angle deviations from ideal: 98.40 - 105.53: 255 105.53 - 112.66: 6345 112.66 - 119.78: 3576 119.78 - 126.91: 5290 126.91 - 134.03: 150 Bond angle restraints: 15616 Sorted by residual: angle pdb=" O28 U3D B 902 " pdb=" P27 U3D B 902 " pdb=" O29 U3D B 902 " ideal model delta sigma weight residual 122.96 110.19 12.77 3.00e+00 1.11e-01 1.81e+01 angle pdb=" C22 U3G A 905 " pdb=" O23 U3G A 905 " pdb=" C24 U3G A 905 " ideal model delta sigma weight residual 124.44 111.98 12.46 3.00e+00 1.11e-01 1.72e+01 angle pdb=" O46 U3G A 905 " pdb=" P47 U3G A 905 " pdb=" O50 U3G A 905 " ideal model delta sigma weight residual 97.04 109.31 -12.27 3.00e+00 1.11e-01 1.67e+01 angle pdb=" O48 U3G A 905 " pdb=" P47 U3G A 905 " pdb=" O49 U3G A 905 " ideal model delta sigma weight residual 121.54 110.01 11.53 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C GLN A 541 " pdb=" N PHE A 542 " pdb=" CA PHE A 542 " ideal model delta sigma weight residual 120.58 124.84 -4.26 1.32e+00 5.74e-01 1.04e+01 ... (remaining 15611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.02: 6930 23.02 - 46.04: 379 46.04 - 69.06: 54 69.06 - 92.07: 14 92.07 - 115.09: 1 Dihedral angle restraints: 7378 sinusoidal: 3448 harmonic: 3930 Sorted by residual: dihedral pdb=" CA GLN B 432 " pdb=" C GLN B 432 " pdb=" N ASP B 433 " pdb=" CA ASP B 433 " ideal model delta harmonic sigma weight residual 180.00 155.97 24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA PHE B 388 " pdb=" C PHE B 388 " pdb=" N ASN B 389 " pdb=" CA ASN B 389 " ideal model delta harmonic sigma weight residual 180.00 157.65 22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA SER B 434 " pdb=" C SER B 434 " pdb=" N ARG B 435 " pdb=" CA ARG B 435 " ideal model delta harmonic sigma weight residual -180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 7375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1555 0.063 - 0.127: 204 0.127 - 0.190: 15 0.190 - 0.254: 10 0.254 - 0.317: 8 Chirality restraints: 1792 Sorted by residual: chirality pdb=" C14 CLR A 906 " pdb=" C13 CLR A 906 " pdb=" C15 CLR A 906 " pdb=" C8 CLR A 906 " both_signs ideal model delta sigma weight residual False -2.32 -2.63 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" C14 CLR B 907 " pdb=" C13 CLR B 907 " pdb=" C15 CLR B 907 " pdb=" C8 CLR B 907 " both_signs ideal model delta sigma weight residual False -2.32 -2.63 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" C14 CLR B 906 " pdb=" C13 CLR B 906 " pdb=" C15 CLR B 906 " pdb=" C8 CLR B 906 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 1789 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 432 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" C GLN B 432 " -0.053 2.00e-02 2.50e+03 pdb=" O GLN B 432 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP B 433 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 695 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.09e+00 pdb=" C VAL A 695 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL A 695 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA A 696 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 696 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.68e+00 pdb=" C ALA A 696 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA A 696 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL A 697 " 0.014 2.00e-02 2.50e+03 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 112 2.61 - 3.19: 10491 3.19 - 3.76: 16641 3.76 - 4.33: 23763 4.33 - 4.90: 38936 Nonbonded interactions: 89943 Sorted by model distance: nonbonded pdb=" OD2 ASP A 81 " pdb=" OH TYR A 354 " model vdw 2.042 2.440 nonbonded pdb=" OH TYR A 92 " pdb=" OE1 GLU A 379 " model vdw 2.113 2.440 nonbonded pdb=" O VAL B 364 " pdb=" OG1 THR B 368 " model vdw 2.115 2.440 nonbonded pdb=" OG SER A 508 " pdb=" OD1 ASP A 684 " model vdw 2.135 2.440 nonbonded pdb=" OE1 GLN B 87 " pdb=" OH TYR B 359 " model vdw 2.138 2.440 ... (remaining 89938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.850 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: 4.070 Check model and map are aligned: 0.170 Set scattering table: 0.090 Process input model: 32.200 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.006 0.119 11487 Z= 0.390 Angle : 0.787 12.766 15616 Z= 0.411 Chirality : 0.049 0.317 1792 Planarity : 0.004 0.046 1884 Dihedral : 13.856 115.092 4827 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.08 % Allowed : 3.82 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.94 (0.21), residues: 1338 helix: -0.58 (0.17), residues: 721 sheet: -1.84 (0.33), residues: 219 loop : -1.97 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 676 HIS 0.005 0.001 HIS A 170 PHE 0.018 0.001 PHE B 537 TYR 0.020 0.001 TYR A 535 ARG 0.003 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 615 ASP cc_start: 0.7895 (t0) cc_final: 0.7235 (t0) REVERT: A 619 ARG cc_start: 0.7863 (ttt180) cc_final: 0.7620 (ttt180) REVERT: B 206 GLN cc_start: 0.7874 (tp40) cc_final: 0.7464 (tp-100) REVERT: B 272 MET cc_start: 0.7511 (mtp) cc_final: 0.7145 (mtp) REVERT: B 423 MET cc_start: 0.6209 (mmm) cc_final: 0.5990 (mmm) REVERT: B 734 ILE cc_start: 0.8561 (tt) cc_final: 0.8166 (tp) outliers start: 1 outliers final: 1 residues processed: 128 average time/residue: 0.3237 time to fit residues: 54.8169 Evaluate side-chains 96 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.1980 chunk 69 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 64 optimal weight: 0.1980 chunk 78 optimal weight: 0.8980 chunk 122 optimal weight: 0.3980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 170 HIS A 196 GLN A 236 ASN A 391 GLN A 511 ASN A 513 ASN A 514 ASN B 206 GLN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 ASN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN B 616 GLN B 687 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11487 Z= 0.157 Angle : 0.558 8.455 15616 Z= 0.284 Chirality : 0.042 0.208 1792 Planarity : 0.004 0.069 1884 Dihedral : 8.898 101.653 2288 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.27 % Allowed : 8.40 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.22), residues: 1338 helix: 0.86 (0.19), residues: 723 sheet: -1.45 (0.33), residues: 209 loop : -1.32 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 676 HIS 0.003 0.001 HIS A 305 PHE 0.017 0.001 PHE A 258 TYR 0.015 0.001 TYR B 697 ARG 0.004 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 ASP cc_start: 0.7927 (t0) cc_final: 0.7510 (t0) REVERT: B 206 GLN cc_start: 0.7886 (tp-100) cc_final: 0.7645 (tp-100) REVERT: B 272 MET cc_start: 0.7329 (mtp) cc_final: 0.7009 (mtp) REVERT: B 433 ASP cc_start: 0.7603 (p0) cc_final: 0.7402 (p0) REVERT: B 494 ILE cc_start: 0.8278 (tp) cc_final: 0.8039 (tt) REVERT: B 687 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8648 (t0) REVERT: B 734 ILE cc_start: 0.8659 (tt) cc_final: 0.8220 (tp) outliers start: 15 outliers final: 8 residues processed: 112 average time/residue: 0.2647 time to fit residues: 42.0965 Evaluate side-chains 101 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 730 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 132 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11487 Z= 0.160 Angle : 0.527 7.821 15616 Z= 0.267 Chirality : 0.041 0.225 1792 Planarity : 0.004 0.051 1884 Dihedral : 8.233 80.644 2288 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.04 % Allowed : 10.02 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.23), residues: 1338 helix: 1.33 (0.19), residues: 724 sheet: -1.07 (0.34), residues: 207 loop : -1.07 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 676 HIS 0.002 0.001 HIS A 305 PHE 0.018 0.001 PHE A 222 TYR 0.021 0.001 TYR B 697 ARG 0.008 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7702 (mt-10) REVERT: A 615 ASP cc_start: 0.7958 (t0) cc_final: 0.7562 (t0) REVERT: B 206 GLN cc_start: 0.7869 (tp-100) cc_final: 0.7610 (tp-100) REVERT: B 272 MET cc_start: 0.7366 (mtp) cc_final: 0.7050 (mtp) REVERT: B 328 LYS cc_start: 0.7885 (mmmt) cc_final: 0.7542 (mmmt) outliers start: 24 outliers final: 10 residues processed: 108 average time/residue: 0.2587 time to fit residues: 40.1864 Evaluate side-chains 103 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 668 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11487 Z= 0.237 Angle : 0.551 7.121 15616 Z= 0.279 Chirality : 0.042 0.227 1792 Planarity : 0.004 0.046 1884 Dihedral : 8.076 70.640 2287 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.12 % Allowed : 12.99 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.23), residues: 1338 helix: 1.45 (0.19), residues: 726 sheet: -0.92 (0.35), residues: 207 loop : -1.00 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 676 HIS 0.002 0.001 HIS B 355 PHE 0.018 0.001 PHE A 258 TYR 0.020 0.001 TYR B 697 ARG 0.004 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7715 (mt-10) REVERT: A 615 ASP cc_start: 0.7990 (t0) cc_final: 0.7642 (t0) REVERT: B 110 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.8147 (m-40) REVERT: B 206 GLN cc_start: 0.7917 (tp-100) cc_final: 0.7634 (tp-100) REVERT: B 272 MET cc_start: 0.7431 (mtp) cc_final: 0.7118 (mtp) REVERT: B 667 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8176 (mt) outliers start: 25 outliers final: 16 residues processed: 114 average time/residue: 0.2448 time to fit residues: 40.6076 Evaluate side-chains 106 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 730 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 97 optimal weight: 0.0170 chunk 53 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 117 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.0620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11487 Z= 0.187 Angle : 0.536 10.355 15616 Z= 0.270 Chirality : 0.041 0.224 1792 Planarity : 0.003 0.048 1884 Dihedral : 7.749 66.674 2287 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.78 % Allowed : 14.86 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.23), residues: 1338 helix: 1.60 (0.19), residues: 724 sheet: -0.79 (0.35), residues: 206 loop : -0.98 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 676 HIS 0.002 0.001 HIS A 305 PHE 0.018 0.001 PHE A 222 TYR 0.021 0.001 TYR B 697 ARG 0.004 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7687 (mt-10) REVERT: A 615 ASP cc_start: 0.8018 (t0) cc_final: 0.7687 (t0) REVERT: B 206 GLN cc_start: 0.7854 (tp-100) cc_final: 0.7580 (tp-100) REVERT: B 272 MET cc_start: 0.7451 (mtp) cc_final: 0.7132 (mtp) REVERT: B 667 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8342 (mt) outliers start: 21 outliers final: 12 residues processed: 104 average time/residue: 0.2535 time to fit residues: 38.1151 Evaluate side-chains 103 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 535 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 730 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11487 Z= 0.194 Angle : 0.529 9.510 15616 Z= 0.266 Chirality : 0.041 0.223 1792 Planarity : 0.003 0.047 1884 Dihedral : 7.504 64.940 2287 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.04 % Allowed : 14.94 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.23), residues: 1338 helix: 1.67 (0.19), residues: 724 sheet: -0.69 (0.35), residues: 204 loop : -0.93 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 676 HIS 0.002 0.001 HIS A 305 PHE 0.017 0.001 PHE A 258 TYR 0.013 0.001 TYR B 628 ARG 0.004 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7706 (mt-10) REVERT: A 615 ASP cc_start: 0.8018 (t0) cc_final: 0.7674 (t0) REVERT: B 206 GLN cc_start: 0.7838 (tp-100) cc_final: 0.7502 (tp-100) REVERT: B 272 MET cc_start: 0.7447 (mtp) cc_final: 0.7141 (mtp) outliers start: 24 outliers final: 14 residues processed: 110 average time/residue: 0.2325 time to fit residues: 37.6045 Evaluate side-chains 101 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 535 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 730 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 81 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11487 Z= 0.192 Angle : 0.538 9.152 15616 Z= 0.269 Chirality : 0.041 0.220 1792 Planarity : 0.003 0.047 1884 Dihedral : 7.350 62.844 2287 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.70 % Allowed : 15.45 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.23), residues: 1338 helix: 1.73 (0.19), residues: 724 sheet: -0.67 (0.35), residues: 207 loop : -0.90 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 676 HIS 0.003 0.001 HIS A 305 PHE 0.018 0.001 PHE A 222 TYR 0.015 0.001 TYR B 220 ARG 0.004 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7683 (mt-10) REVERT: A 615 ASP cc_start: 0.8079 (t0) cc_final: 0.7794 (t0) REVERT: B 206 GLN cc_start: 0.7816 (tp-100) cc_final: 0.7501 (tp-100) REVERT: B 272 MET cc_start: 0.7455 (mtp) cc_final: 0.7155 (mtp) outliers start: 20 outliers final: 18 residues processed: 105 average time/residue: 0.2201 time to fit residues: 34.6909 Evaluate side-chains 107 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 730 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11487 Z= 0.223 Angle : 0.549 8.862 15616 Z= 0.274 Chirality : 0.042 0.221 1792 Planarity : 0.003 0.047 1884 Dihedral : 7.388 59.817 2287 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.95 % Allowed : 15.70 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.23), residues: 1338 helix: 1.72 (0.19), residues: 725 sheet: -0.65 (0.35), residues: 204 loop : -0.87 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP B 676 HIS 0.002 0.001 HIS A 305 PHE 0.016 0.001 PHE A 258 TYR 0.014 0.001 TYR B 628 ARG 0.004 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 1.355 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7700 (mt-10) REVERT: A 142 MET cc_start: 0.8064 (ptm) cc_final: 0.7861 (ptm) REVERT: A 615 ASP cc_start: 0.8078 (t0) cc_final: 0.7821 (t0) REVERT: B 110 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8149 (m-40) REVERT: B 206 GLN cc_start: 0.7827 (tp-100) cc_final: 0.7514 (tp-100) REVERT: B 272 MET cc_start: 0.7484 (mtp) cc_final: 0.7170 (mtp) REVERT: B 393 HIS cc_start: 0.7186 (t-170) cc_final: 0.6984 (t70) outliers start: 23 outliers final: 19 residues processed: 110 average time/residue: 0.2313 time to fit residues: 38.5408 Evaluate side-chains 110 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 535 PHE Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 730 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11487 Z= 0.171 Angle : 0.527 8.743 15616 Z= 0.265 Chirality : 0.040 0.222 1792 Planarity : 0.003 0.047 1884 Dihedral : 7.224 59.800 2287 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.70 % Allowed : 16.21 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.23), residues: 1338 helix: 1.85 (0.19), residues: 723 sheet: -0.53 (0.35), residues: 204 loop : -0.81 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP B 676 HIS 0.003 0.001 HIS A 305 PHE 0.019 0.001 PHE A 222 TYR 0.016 0.001 TYR B 220 ARG 0.004 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7666 (mt-10) REVERT: A 530 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8636 (tt) REVERT: A 615 ASP cc_start: 0.8052 (t0) cc_final: 0.7797 (t0) REVERT: B 110 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.8100 (m-40) REVERT: B 206 GLN cc_start: 0.7770 (tp-100) cc_final: 0.7482 (tp-100) REVERT: B 272 MET cc_start: 0.7460 (mtp) cc_final: 0.7140 (mtp) outliers start: 20 outliers final: 17 residues processed: 108 average time/residue: 0.2101 time to fit residues: 33.9691 Evaluate side-chains 110 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 535 PHE Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 730 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.3980 chunk 78 optimal weight: 0.0870 chunk 60 optimal weight: 0.8980 chunk 89 optimal weight: 0.4980 chunk 134 optimal weight: 0.0370 chunk 123 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11487 Z= 0.131 Angle : 0.503 8.649 15616 Z= 0.254 Chirality : 0.039 0.226 1792 Planarity : 0.003 0.048 1884 Dihedral : 6.836 57.427 2287 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.27 % Allowed : 17.06 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.24 (0.23), residues: 1338 helix: 1.99 (0.19), residues: 722 sheet: -0.33 (0.35), residues: 207 loop : -0.62 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 676 HIS 0.003 0.001 HIS A 305 PHE 0.015 0.001 PHE A 258 TYR 0.010 0.001 TYR A 672 ARG 0.004 0.000 ARG A 539 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 1.247 Fit side-chains REVERT: A 76 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7539 (mt-10) REVERT: A 312 MET cc_start: 0.7466 (mtm) cc_final: 0.7093 (mtt) REVERT: A 530 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8625 (tt) REVERT: A 615 ASP cc_start: 0.8038 (t0) cc_final: 0.7811 (t0) REVERT: B 78 LEU cc_start: 0.8101 (mt) cc_final: 0.7817 (mt) REVERT: B 110 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.8100 (m-40) REVERT: B 206 GLN cc_start: 0.7684 (tp-100) cc_final: 0.7407 (tp-100) REVERT: B 272 MET cc_start: 0.7390 (mtp) cc_final: 0.7076 (mtp) outliers start: 15 outliers final: 12 residues processed: 107 average time/residue: 0.2184 time to fit residues: 35.3766 Evaluate side-chains 107 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 535 PHE Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 654 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 GLN ** B 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.082362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.074179 restraints weight = 31578.456| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.06 r_work: 0.3240 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11487 Z= 0.162 Angle : 0.517 9.109 15616 Z= 0.259 Chirality : 0.040 0.224 1792 Planarity : 0.003 0.046 1884 Dihedral : 6.883 58.072 2287 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.61 % Allowed : 16.72 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.24 (0.23), residues: 1338 helix: 1.97 (0.19), residues: 721 sheet: -0.23 (0.36), residues: 204 loop : -0.62 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 676 HIS 0.003 0.001 HIS A 305 PHE 0.016 0.001 PHE A 258 TYR 0.016 0.001 TYR B 220 ARG 0.004 0.000 ARG A 539 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2224.95 seconds wall clock time: 41 minutes 46.91 seconds (2506.91 seconds total)