Starting phenix.real_space_refine on Wed Feb 14 16:03:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mn6_23917/02_2024/7mn6_23917.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mn6_23917/02_2024/7mn6_23917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mn6_23917/02_2024/7mn6_23917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mn6_23917/02_2024/7mn6_23917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mn6_23917/02_2024/7mn6_23917.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mn6_23917/02_2024/7mn6_23917.pdb" } resolution = 3.09 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= 0.045 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: 4 Type Number sf(0) Gaussians S 118 5.16 5 C 5981 2.51 5 N 1713 2.21 5 O 1837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9649 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4614 Classifications: {'peptide': 599} Link IDs: {'PTRANS': 39, 'TRANS': 559} Chain breaks: 1 Chain: "B" Number of atoms: 4476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4476 Classifications: {'peptide': 579} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 540} Chain breaks: 3 Chain: "H" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.56, per 1000 atoms: 0.58 Number of scatterers: 9649 At special positions: 0 Unit cell: (78.49, 142.785, 131.095, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 118 16.00 O 1837 8.00 N 1713 7.00 C 5981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 56 " distance=2.03 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 218 " distance=2.02 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 226 " distance=2.02 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 235 " distance=2.03 Simple disulfide: pdb=" SG CYS A 231 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS A 246 " - pdb=" SG CYS A 255 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 286 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 354 " distance=2.04 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 493 " distance=2.03 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 509 " distance=2.02 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 517 " distance=2.02 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 529 " distance=2.04 Simple disulfide: pdb=" SG CYS A 533 " - pdb=" SG CYS A 549 " distance=2.02 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.04 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 573 " distance=2.02 Simple disulfide: pdb=" SG CYS A 576 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS A 610 " distance=2.05 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 621 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 629 " distance=2.05 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 53 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 192 " distance=2.02 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 204 " distance=2.02 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 212 " distance=2.08 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 227 " distance=2.02 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 235 " distance=2.05 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 244 " distance=2.04 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 252 " distance=2.02 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS B 295 " distance=2.05 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 311 " distance=2.14 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 331 " distance=2.04 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 338 " distance=2.05 Simple disulfide: pdb=" SG CYS B 342 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 504 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 528 " distance=2.08 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 544 " - pdb=" SG CYS B 560 " distance=2.02 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 576 " distance=2.06 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 584 " distance=2.02 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 596 " distance=2.03 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 623 " distance=2.03 Simple disulfide: pdb=" SG CYS H 182 " - pdb=" SG CYS H 196 " distance=2.09 Simple disulfide: pdb=" SG CYS H 190 " - pdb=" SG CYS H 210 " distance=2.02 Simple disulfide: pdb=" SG CYS H 212 " - pdb=" SG CYS H 221 " distance=2.01 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 ALPHA1-3 " BMA E 3 " - " MAN E 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG A1101 " - " ASN A 408 " " NAG A1102 " - " ASN A 353 " " NAG A1103 " - " ASN A 414 " " NAG B1501 " - " ASN B 530 " " NAG B1502 " - " ASN B 187 " " NAG C 1 " - " ASN A 469 " " NAG D 1 " - " ASN A 250 " " NAG E 1 " - " ASN B 259 " Time building additional restraints: 3.78 Conformation dependent library (CDL) restraints added in 2.3 seconds 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 29 sheets defined 15.1% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.214A pdb=" N TRP A 79 " --> pdb=" O PHE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.796A pdb=" N LYS A 191 " --> pdb=" O GLU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 4.010A pdb=" N CYS A 202 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 removed outlier: 3.514A pdb=" N VAL A 352 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.680A pdb=" N LEU A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 380 through 390 removed outlier: 4.234A pdb=" N THR A 389 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 463 through 468 removed outlier: 3.557A pdb=" N HIS A 466 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 467 " --> pdb=" O TYR A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 41 through 51 Processing helix chain 'B' and resid 71 through 77 removed outlier: 4.411A pdb=" N ASP B 76 " --> pdb=" O PHE B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.963A pdb=" N ILE B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.834A pdb=" N CYS B 212 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 4.328A pdb=" N CYS B 235 " --> pdb=" O PRO B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.762A pdb=" N ARG B 351 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 365 removed outlier: 3.620A pdb=" N PHE B 364 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.600A pdb=" N PHE B 381 " --> pdb=" O PRO B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 436 through 439 Processing helix chain 'B' and resid 481 through 485 Processing helix chain 'B' and resid 500 through 508 Processing helix chain 'H' and resid 185 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 7.391A pdb=" N CYS A 29 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 7.077A pdb=" N VAL A 38 " --> pdb=" O CYS H 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 removed outlier: 5.409A pdb=" N GLY A 146 " --> pdb=" O PHE A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 235 removed outlier: 3.806A pdb=" N ALA A 245 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLY A 234 " --> pdb=" O CYS A 243 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N CYS A 243 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 249 through 251 Processing sheet with id=AA7, first strand: chain 'A' and resid 263 through 265 Processing sheet with id=AA8, first strand: chain 'A' and resid 280 through 282 Processing sheet with id=AA9, first strand: chain 'A' and resid 300 through 302 Processing sheet with id=AB1, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 363 removed outlier: 6.515A pdb=" N LEU A 397 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N MET A 433 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE A 399 " --> pdb=" O MET A 433 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ARG A 453 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE A 454 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 523 through 525 removed outlier: 3.828A pdb=" N TYR A 523 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 528 " --> pdb=" O ARG A 525 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 542 through 545 Processing sheet with id=AB5, first strand: chain 'A' and resid 579 through 581 Processing sheet with id=AB6, first strand: chain 'A' and resid 593 through 595 Processing sheet with id=AB7, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AB8, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB9, first strand: chain 'B' and resid 60 through 63 removed outlier: 5.330A pdb=" N GLY B 152 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B 153 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 240 through 244 removed outlier: 7.202A pdb=" N GLY B 243 " --> pdb=" O CYS B 252 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N CYS B 252 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 258 through 260 Processing sheet with id=AC3, first strand: chain 'B' and resid 272 through 275 removed outlier: 3.627A pdb=" N GLU B 280 " --> pdb=" O ASN B 275 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 289 through 291 Processing sheet with id=AC5, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AC6, first strand: chain 'B' and resid 342 through 343 removed outlier: 6.786A pdb=" N CYS B 342 " --> pdb=" O PHE B 371 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 374 through 376 removed outlier: 6.553A pdb=" N LEU B 374 " --> pdb=" O TYR B 411 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LEU B 465 " --> pdb=" O TYR B 441 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 443 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA B 466 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N THR B 496 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE B 468 " --> pdb=" O THR B 496 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 553 through 556 Processing sheet with id=AC9, first strand: chain 'B' and resid 590 through 592 Processing sheet with id=AD1, first strand: chain 'B' and resid 615 through 617 Processing sheet with id=AD2, first strand: chain 'H' and resid 216 through 217 195 hydrogen bonds defined for protein. 375 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: 2.96 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1612 1.28 - 1.42: 2482 1.42 - 1.55: 5630 1.55 - 1.69: 14 1.69 - 1.82: 134 Bond restraints: 9872 Sorted by residual: bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.536 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" CA HIS B 589 " pdb=" C HIS B 589 " ideal model delta sigma weight residual 1.520 1.544 -0.024 4.80e-03 4.34e+04 2.52e+01 bond pdb=" CA MET B 347 " pdb=" C MET B 347 " ideal model delta sigma weight residual 1.522 1.580 -0.058 1.20e-02 6.94e+03 2.30e+01 bond pdb=" N GLU B 348 " pdb=" CA GLU B 348 " ideal model delta sigma weight residual 1.457 1.517 -0.059 1.29e-02 6.01e+03 2.11e+01 bond pdb=" N ARG B 351 " pdb=" CA ARG B 351 " ideal model delta sigma weight residual 1.459 1.509 -0.050 1.21e-02 6.83e+03 1.67e+01 ... (remaining 9867 not shown) Histogram of bond angle deviations from ideal: 100.86 - 107.87: 560 107.87 - 114.87: 5559 114.87 - 121.88: 5013 121.88 - 128.88: 2188 128.88 - 135.89: 80 Bond angle restraints: 13400 Sorted by residual: angle pdb=" C GLU B 109 " pdb=" N ASP B 110 " pdb=" CA ASP B 110 " ideal model delta sigma weight residual 122.45 135.89 -13.44 1.78e+00 3.16e-01 5.70e+01 angle pdb=" C SER H 177 " pdb=" N HIS H 178 " pdb=" CA HIS H 178 " ideal model delta sigma weight residual 122.54 133.19 -10.65 1.65e+00 3.67e-01 4.16e+01 angle pdb=" N CYS A 214 " pdb=" CA CYS A 214 " pdb=" C CYS A 214 " ideal model delta sigma weight residual 113.23 121.19 -7.96 1.24e+00 6.50e-01 4.13e+01 angle pdb=" C HIS A 486 " pdb=" CA HIS A 486 " pdb=" CB HIS A 486 " ideal model delta sigma weight residual 116.63 109.72 6.91 1.16e+00 7.43e-01 3.55e+01 angle pdb=" N GLU A 54 " pdb=" CA GLU A 54 " pdb=" C GLU A 54 " ideal model delta sigma weight residual 111.33 118.09 -6.76 1.21e+00 6.83e-01 3.12e+01 ... (remaining 13395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.34: 5951 19.34 - 38.68: 194 38.68 - 58.01: 59 58.01 - 77.35: 26 77.35 - 96.69: 11 Dihedral angle restraints: 6241 sinusoidal: 2738 harmonic: 3503 Sorted by residual: dihedral pdb=" CB CYS A 290 " pdb=" SG CYS A 290 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 178.45 -85.45 1 1.00e+01 1.00e-02 8.84e+01 dihedral pdb=" CB CYS B 299 " pdb=" SG CYS B 299 " pdb=" SG CYS B 311 " pdb=" CB CYS B 311 " ideal model delta sinusoidal sigma weight residual 93.00 173.79 -80.79 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS B 268 " pdb=" SG CYS B 268 " pdb=" SG CYS B 295 " pdb=" CB CYS B 295 " ideal model delta sinusoidal sigma weight residual 93.00 166.92 -73.92 1 1.00e+01 1.00e-02 6.94e+01 ... (remaining 6238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1317 0.120 - 0.240: 159 0.240 - 0.359: 11 0.359 - 0.479: 3 0.479 - 0.599: 2 Chirality restraints: 1492 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.76 0.36 2.00e-02 2.50e+03 3.28e+02 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.55e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.03e+02 ... (remaining 1489 not shown) Planarity restraints: 1772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 353 " -0.080 2.00e-02 2.50e+03 8.94e-02 9.98e+01 pdb=" CG ASN A 353 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 353 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 353 " 0.145 2.00e-02 2.50e+03 pdb=" C1 NAG A1102 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 50 " -0.119 2.00e-02 2.50e+03 6.76e-02 9.14e+01 pdb=" CG TYR A 50 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 50 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR A 50 " 0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR A 50 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR A 50 " 0.046 2.00e-02 2.50e+03 pdb=" CZ TYR A 50 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 50 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 530 " -0.070 2.00e-02 2.50e+03 7.26e-02 6.59e+01 pdb=" CG ASN B 530 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN B 530 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 530 " 0.111 2.00e-02 2.50e+03 pdb=" C1 NAG B1501 " -0.086 2.00e-02 2.50e+03 ... (remaining 1769 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 3473 2.89 - 3.40: 8353 3.40 - 3.90: 16368 3.90 - 4.40: 18467 4.40 - 4.90: 30392 Nonbonded interactions: 77053 Sorted by model distance: nonbonded pdb=" OD1 ASP A 313 " pdb=" NZ LYS A 318 " model vdw 2.392 2.520 nonbonded pdb=" OD1 ASP B 30 " pdb=" NZ LYS B 32 " model vdw 2.414 2.520 nonbonded pdb=" OH TYR B 411 " pdb=" OE1 GLN B 446 " model vdw 2.456 2.440 nonbonded pdb=" N ASP B 110 " pdb=" O ASP B 110 " model vdw 2.457 2.496 nonbonded pdb=" O5 NAG A1101 " pdb=" O6 NAG A1101 " model vdw 2.487 2.432 ... (remaining 77048 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 'C' selection = chain 'D' } 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: 5.840 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: 14.390 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.180 Find NCS groups from input model: 0.310 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 0.013 0.130 9872 Z= 0.828 Angle : 1.511 13.437 13400 Z= 1.029 Chirality : 0.079 0.599 1492 Planarity : 0.008 0.076 1764 Dihedral : 11.930 96.688 3841 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 0.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.47 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -0.15 (0.23), residues: 1211 helix: -2.18 (0.51), residues: 68 sheet: -1.16 (0.41), residues: 154 loop : 0.33 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.004 TRP B 415 HIS 0.001 0.000 HIS B 349 PHE 0.045 0.003 PHE B 400 TYR 0.119 0.005 TYR A 50 ARG 0.007 0.001 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: A 550 PHE cc_start: 0.8080 (m-80) cc_final: 0.7843 (m-80) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.3323 time to fit residues: 49.8694 Evaluate side-chains 39 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN A 545 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9872 Z= 0.338 Angle : 0.679 8.571 13400 Z= 0.355 Chirality : 0.049 0.237 1492 Planarity : 0.005 0.045 1764 Dihedral : 7.870 64.468 1587 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.03 % Allowed : 4.61 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -0.15 (0.24), residues: 1211 helix: -1.35 (0.55), residues: 74 sheet: -0.52 (0.39), residues: 172 loop : 0.16 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 482 HIS 0.011 0.001 HIS B 318 PHE 0.018 0.002 PHE A 219 TYR 0.016 0.002 TYR A 265 ARG 0.004 0.000 ARG A 475 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 550 PHE cc_start: 0.7804 (m-80) cc_final: 0.7580 (m-80) REVERT: H 208 TYR cc_start: 0.7953 (m-80) cc_final: 0.7691 (m-80) outliers start: 11 outliers final: 6 residues processed: 52 average time/residue: 0.1903 time to fit residues: 15.5310 Evaluate side-chains 38 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 502 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 87 optimal weight: 0.0050 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 HIS A 400 GLN B 302 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9872 Z= 0.236 Angle : 0.572 11.327 13400 Z= 0.295 Chirality : 0.047 0.234 1492 Planarity : 0.004 0.049 1764 Dihedral : 6.435 59.894 1587 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.32 % Allowed : 5.26 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -0.17 (0.24), residues: 1211 helix: -1.19 (0.58), residues: 75 sheet: -0.44 (0.38), residues: 182 loop : 0.11 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 510 HIS 0.008 0.001 HIS B 318 PHE 0.015 0.001 PHE A 443 TYR 0.011 0.001 TYR A 265 ARG 0.003 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 1.553 Fit side-chains REVERT: A 313 ASP cc_start: 0.8277 (t0) cc_final: 0.7947 (t0) outliers start: 14 outliers final: 9 residues processed: 49 average time/residue: 0.1862 time to fit residues: 15.4604 Evaluate side-chains 40 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 282 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 115 optimal weight: 0.0270 chunk 57 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 overall best weight: 1.2440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN A 400 GLN A 435 ASN B 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9872 Z= 0.267 Angle : 0.567 8.396 13400 Z= 0.291 Chirality : 0.046 0.233 1492 Planarity : 0.004 0.049 1764 Dihedral : 5.995 54.757 1587 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.32 % Allowed : 5.92 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -0.16 (0.24), residues: 1211 helix: -1.25 (0.58), residues: 75 sheet: -0.37 (0.41), residues: 166 loop : 0.10 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 510 HIS 0.008 0.001 HIS B 318 PHE 0.017 0.001 PHE B 534 TYR 0.014 0.001 TYR H 224 ARG 0.002 0.000 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 32 time to evaluate : 1.157 Fit side-chains REVERT: H 208 TYR cc_start: 0.8067 (m-80) cc_final: 0.7566 (m-80) outliers start: 14 outliers final: 9 residues processed: 42 average time/residue: 0.1590 time to fit residues: 11.7813 Evaluate side-chains 38 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 29 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 282 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 80 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN B 90 GLN B 302 ASN ** H 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9872 Z= 0.180 Angle : 0.515 6.678 13400 Z= 0.262 Chirality : 0.045 0.238 1492 Planarity : 0.004 0.047 1764 Dihedral : 5.615 53.864 1587 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 1.41 % Allowed : 6.58 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -0.05 (0.25), residues: 1211 helix: -0.58 (0.63), residues: 68 sheet: -0.43 (0.42), residues: 161 loop : 0.14 (0.21), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 510 HIS 0.007 0.001 HIS B 318 PHE 0.017 0.001 PHE B 534 TYR 0.008 0.001 TYR B 590 ARG 0.002 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 32 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 313 ASP cc_start: 0.8330 (t0) cc_final: 0.8036 (t0) REVERT: H 208 TYR cc_start: 0.7951 (m-80) cc_final: 0.7482 (m-80) outliers start: 15 outliers final: 11 residues processed: 44 average time/residue: 0.1745 time to fit residues: 13.0125 Evaluate side-chains 38 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 27 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain H residue 195 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.0040 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 0.3980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9872 Z= 0.180 Angle : 0.509 7.008 13400 Z= 0.258 Chirality : 0.045 0.236 1492 Planarity : 0.004 0.046 1764 Dihedral : 5.519 53.873 1587 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.63 % Favored : 96.28 % Rotamer: Outliers : 1.22 % Allowed : 6.95 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -0.02 (0.25), residues: 1211 helix: -0.47 (0.64), residues: 68 sheet: -0.42 (0.43), residues: 161 loop : 0.16 (0.21), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 205 HIS 0.007 0.001 HIS B 318 PHE 0.017 0.001 PHE B 534 TYR 0.008 0.001 TYR B 590 ARG 0.002 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 28 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: A 313 ASP cc_start: 0.8335 (t0) cc_final: 0.8053 (t0) REVERT: H 208 TYR cc_start: 0.7847 (m-80) cc_final: 0.7633 (m-80) outliers start: 13 outliers final: 9 residues processed: 38 average time/residue: 0.1547 time to fit residues: 10.5349 Evaluate side-chains 36 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 27 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain H residue 195 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9872 Z= 0.358 Angle : 0.597 8.804 13400 Z= 0.304 Chirality : 0.048 0.219 1492 Planarity : 0.004 0.048 1764 Dihedral : 5.976 55.598 1587 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.54 % Favored : 95.38 % Rotamer: Outliers : 1.41 % Allowed : 6.95 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -0.30 (0.25), residues: 1211 helix: -1.04 (0.60), residues: 75 sheet: -0.35 (0.44), residues: 158 loop : -0.06 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 482 HIS 0.007 0.001 HIS B 249 PHE 0.018 0.002 PHE A 443 TYR 0.012 0.002 TYR A 265 ARG 0.002 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 30 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ASP cc_start: 0.8433 (t0) cc_final: 0.8170 (t0) REVERT: B 198 MET cc_start: 0.8099 (mmm) cc_final: 0.7699 (tpp) REVERT: H 208 TYR cc_start: 0.8040 (m-80) cc_final: 0.7763 (m-80) outliers start: 15 outliers final: 11 residues processed: 42 average time/residue: 0.1730 time to fit residues: 12.2634 Evaluate side-chains 40 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 29 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 502 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 0.0570 chunk 57 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9872 Z= 0.160 Angle : 0.516 7.553 13400 Z= 0.261 Chirality : 0.045 0.228 1492 Planarity : 0.004 0.046 1764 Dihedral : 5.607 53.575 1587 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.39 % Favored : 96.53 % Rotamer: Outliers : 0.85 % Allowed : 7.52 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -0.14 (0.25), residues: 1211 helix: -0.48 (0.64), residues: 68 sheet: -0.39 (0.46), residues: 146 loop : 0.03 (0.21), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 510 HIS 0.007 0.001 HIS B 318 PHE 0.027 0.001 PHE B 534 TYR 0.008 0.001 TYR B 554 ARG 0.002 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 29 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: A 313 ASP cc_start: 0.8403 (t0) cc_final: 0.8104 (t0) REVERT: B 198 MET cc_start: 0.8044 (mmm) cc_final: 0.7693 (tpp) REVERT: H 208 TYR cc_start: 0.7955 (m-80) cc_final: 0.7690 (m-80) outliers start: 9 outliers final: 9 residues processed: 35 average time/residue: 0.1579 time to fit residues: 9.9791 Evaluate side-chains 36 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 27 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 502 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 69 optimal weight: 0.3980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9872 Z= 0.213 Angle : 0.522 7.410 13400 Z= 0.264 Chirality : 0.045 0.220 1492 Planarity : 0.004 0.044 1764 Dihedral : 5.592 53.987 1587 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.21 % Favored : 95.71 % Rotamer: Outliers : 1.03 % Allowed : 7.61 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -0.14 (0.25), residues: 1211 helix: -0.41 (0.66), residues: 68 sheet: -0.41 (0.47), residues: 143 loop : 0.03 (0.21), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.007 0.001 HIS B 318 PHE 0.026 0.001 PHE B 534 TYR 0.008 0.001 TYR A 265 ARG 0.002 0.000 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 31 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 313 ASP cc_start: 0.8428 (t0) cc_final: 0.8160 (t0) REVERT: B 198 MET cc_start: 0.7999 (mmm) cc_final: 0.7707 (tpp) REVERT: H 208 TYR cc_start: 0.7967 (m-80) cc_final: 0.7692 (m-80) outliers start: 11 outliers final: 9 residues processed: 39 average time/residue: 0.1621 time to fit residues: 11.3506 Evaluate side-chains 39 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 30 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 502 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.0970 chunk 79 optimal weight: 5.9990 chunk 119 optimal weight: 0.0170 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 75 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 overall best weight: 0.9218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9872 Z= 0.201 Angle : 0.519 7.959 13400 Z= 0.262 Chirality : 0.045 0.216 1492 Planarity : 0.004 0.044 1764 Dihedral : 5.529 53.790 1587 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.96 % Favored : 95.95 % Rotamer: Outliers : 0.75 % Allowed : 8.08 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: -0.14 (0.25), residues: 1211 helix: -0.41 (0.66), residues: 68 sheet: -0.45 (0.46), residues: 143 loop : 0.04 (0.21), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 510 HIS 0.007 0.001 HIS B 318 PHE 0.036 0.001 PHE B 534 TYR 0.007 0.001 TYR A 265 ARG 0.002 0.000 ARG A 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 30 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 313 ASP cc_start: 0.8439 (t0) cc_final: 0.8174 (t0) REVERT: B 198 MET cc_start: 0.8003 (mmm) cc_final: 0.7759 (tpp) REVERT: H 208 TYR cc_start: 0.7910 (m-80) cc_final: 0.7637 (m-80) outliers start: 8 outliers final: 8 residues processed: 35 average time/residue: 0.1491 time to fit residues: 9.5403 Evaluate side-chains 37 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 29 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 502 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 3.9990 chunk 14 optimal weight: 0.0040 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.107133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.074082 restraints weight = 20076.725| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.19 r_work: 0.3163 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9872 Z= 0.148 Angle : 0.495 7.872 13400 Z= 0.250 Chirality : 0.045 0.217 1492 Planarity : 0.004 0.043 1764 Dihedral : 5.366 53.199 1587 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.88 % Favored : 96.04 % Rotamer: Outliers : 1.03 % Allowed : 7.71 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % 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: 0.04 (0.25), residues: 1211 helix: 0.27 (0.72), residues: 61 sheet: -0.26 (0.45), residues: 148 loop : 0.11 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 482 HIS 0.006 0.001 HIS B 318 PHE 0.031 0.001 PHE B 534 TYR 0.008 0.001 TYR B 554 ARG 0.002 0.000 ARG A 453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2349.37 seconds wall clock time: 43 minutes 43.04 seconds (2623.04 seconds total)