Starting phenix.real_space_refine on Wed Feb 14 15:08:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mn5_23916/02_2024/7mn5_23916.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mn5_23916/02_2024/7mn5_23916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mn5_23916/02_2024/7mn5_23916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mn5_23916/02_2024/7mn5_23916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mn5_23916/02_2024/7mn5_23916.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mn5_23916/02_2024/7mn5_23916.pdb" } resolution = 2.93 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= 0.001 sd= 0.054 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 5896 2.51 5 N 1695 2.21 5 O 1817 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 PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 363": "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 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 224": "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 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 616": "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: 9526 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4496 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 37, 'TRANS': 547} Chain breaks: 2 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: "B" Number of atoms: 4471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4471 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 38, 'TRANS': 540} Chain breaks: 3 Chain: "C" 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: "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: 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: "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: 5.52, per 1000 atoms: 0.58 Number of scatterers: 9526 At special positions: 0 Unit cell: (80.995, 141.115, 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 1817 8.00 N 1695 7.00 C 5896 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=2.02 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=2.04 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=1.71 Simple disulfide: pdb=" SG CYS A 246 " - pdb=" SG CYS A 255 " distance=2.04 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=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 529 " distance=2.02 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=2.03 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=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 629 " distance=2.05 Simple disulfide: pdb=" SG CYS H 182 " - pdb=" SG CYS H 196 " distance=2.11 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=2.02 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 53 " distance=2.05 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 204 " distance=2.07 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 212 " distance=2.04 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 235 " distance=2.04 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 244 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 252 " distance=2.03 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=2.04 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=2.12 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=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 540 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 596 " distance=2.06 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 623 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM 9524 O5 NAG B1502 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " 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 B 259 " " NAG D 1 " - " ASN A 469 " " NAG E 1 " - " ASN A 250 " Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.9 seconds 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2222 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 26 sheets defined 15.7% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.181A 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 167 removed outlier: 3.920A pdb=" N ILE A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 380 through 390 removed outlier: 4.123A 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: 3.591A pdb=" N HIS A 466 " --> pdb=" O CYS A 463 " (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 'H' and resid 186 through 190 removed outlier: 3.802A pdb=" N CYS H 190 " --> pdb=" O LYS H 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 51 Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 199 through 203 removed outlier: 4.197A pdb=" N ARG B 203 " --> pdb=" O LYS B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.888A pdb=" N CYS B 212 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 360 through 365 Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.575A pdb=" N PHE B 381 " --> pdb=" O PRO B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 removed outlier: 3.995A pdb=" N GLN B 398 " --> pdb=" O PRO B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 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 507 Processing helix chain 'B' and resid 515 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 7.288A 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: 6.965A 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: 5.372A pdb=" N GLY A 146 " --> pdb=" O PHE A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 235 removed outlier: 7.732A pdb=" N GLY A 234 " --> pdb=" O CYS A 243 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N CYS A 243 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 249 through 251 Processing sheet with id=AA6, first strand: chain 'A' and resid 280 through 282 Processing sheet with id=AA7, first strand: chain 'A' and resid 300 through 302 removed outlier: 7.190A pdb=" N VAL A 296 " --> pdb=" O CYS A 320 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 363 removed outlier: 6.376A pdb=" N LEU A 397 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N MET A 433 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE A 399 " --> pdb=" O MET A 433 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE A 428 " --> pdb=" O ARG A 453 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N TYR A 455 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU A 430 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N SER A 457 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE A 432 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LYS A 485 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE A 456 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 523 through 525 removed outlier: 3.535A pdb=" N TYR A 523 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 528 " --> pdb=" O ARG A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 542 through 545 Processing sheet with id=AB3, first strand: chain 'A' and resid 579 through 581 Processing sheet with id=AB4, first strand: chain 'A' and resid 593 through 595 Processing sheet with id=AB5, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AB6, first strand: chain 'H' and resid 216 through 217 Processing sheet with id=AB7, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB8, first strand: chain 'B' and resid 60 through 63 removed outlier: 7.319A pdb=" N LEU B 154 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA B 115 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLN B 156 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU B 117 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B 153 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 258 through 260 Processing sheet with id=AC1, first strand: chain 'B' and resid 272 through 275 removed outlier: 3.622A pdb=" N GLU B 280 " --> pdb=" O ASN B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 289 through 291 Processing sheet with id=AC3, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AC4, first strand: chain 'B' and resid 342 through 343 removed outlier: 6.889A pdb=" N CYS B 342 " --> pdb=" O PHE B 371 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 374 through 376 removed outlier: 6.621A pdb=" N LEU B 374 " --> pdb=" O TYR B 411 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU B 465 " --> pdb=" O TYR B 441 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 443 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA B 466 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N THR B 496 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE B 468 " --> pdb=" O THR B 496 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 553 through 556 Processing sheet with id=AC7, first strand: chain 'B' and resid 590 through 592 Processing sheet with id=AC8, first strand: chain 'B' and resid 615 through 617 187 hydrogen bonds defined for protein. 333 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: 2.88 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2062 1.33 - 1.45: 2147 1.45 - 1.57: 5398 1.57 - 1.69: 2 1.69 - 1.81: 134 Bond restraints: 9743 Sorted by residual: bond pdb=" CA HIS A 578 " pdb=" C HIS A 578 " ideal model delta sigma weight residual 1.520 1.549 -0.029 4.80e-03 4.34e+04 3.77e+01 bond pdb=" N PRO A 512 " pdb=" CD PRO A 512 " ideal model delta sigma weight residual 1.473 1.399 0.074 1.40e-02 5.10e+03 2.79e+01 bond pdb=" CA PRO A 403 " pdb=" C PRO A 403 " ideal model delta sigma weight residual 1.514 1.542 -0.028 5.50e-03 3.31e+04 2.62e+01 bond pdb=" N PRO B 316 " pdb=" CD PRO B 316 " ideal model delta sigma weight residual 1.473 1.410 0.063 1.40e-02 5.10e+03 2.02e+01 bond pdb=" CA SER A 401 " pdb=" C SER A 401 " ideal model delta sigma weight residual 1.521 1.576 -0.055 1.26e-02 6.30e+03 1.89e+01 ... (remaining 9738 not shown) Histogram of bond angle deviations from ideal: 99.86 - 106.84: 421 106.84 - 113.82: 5120 113.82 - 120.80: 4392 120.80 - 127.78: 3201 127.78 - 134.76: 87 Bond angle restraints: 13221 Sorted by residual: angle pdb=" C GLU B 348 " pdb=" CA GLU B 348 " pdb=" CB GLU B 348 " ideal model delta sigma weight residual 116.54 109.39 7.15 1.15e+00 7.56e-01 3.87e+01 angle pdb=" CA LYS B 336 " pdb=" C LYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 117.68 121.52 -3.84 7.10e-01 1.98e+00 2.93e+01 angle pdb=" N ALA B 87 " pdb=" CA ALA B 87 " pdb=" C ALA B 87 " ideal model delta sigma weight residual 108.99 117.42 -8.43 1.57e+00 4.06e-01 2.88e+01 angle pdb=" C SER B 335 " pdb=" N LYS B 336 " pdb=" CA LYS B 336 " ideal model delta sigma weight residual 122.07 128.95 -6.88 1.44e+00 4.82e-01 2.28e+01 angle pdb=" CA ASP B 421 " pdb=" CB ASP B 421 " pdb=" CG ASP B 421 " ideal model delta sigma weight residual 112.60 117.36 -4.76 1.00e+00 1.00e+00 2.27e+01 ... (remaining 13216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.86: 5921 21.86 - 43.72: 170 43.72 - 65.59: 49 65.59 - 87.45: 19 87.45 - 109.31: 5 Dihedral angle restraints: 6164 sinusoidal: 2705 harmonic: 3459 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 -177.93 -89.07 1 1.00e+01 1.00e-02 9.44e+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 93.00 166.55 -73.55 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CB CYS B 199 " pdb=" SG CYS B 199 " pdb=" SG CYS B 212 " pdb=" CB CYS B 212 " ideal model delta sinusoidal sigma weight residual -86.00 -157.79 71.79 1 1.00e+01 1.00e-02 6.60e+01 ... (remaining 6161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1266 0.101 - 0.203: 174 0.203 - 0.304: 20 0.304 - 0.405: 12 0.405 - 0.507: 1 Chirality restraints: 1473 Sorted by residual: chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.47 -0.07 2.00e-02 2.50e+03 1.26e+01 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 -2.47 0.07 2.00e-02 2.50e+03 1.13e+01 chirality pdb=" C1 NAG B1502 " pdb=" ND2 ASN B 187 " pdb=" C2 NAG B1502 " pdb=" O5 NAG B1502 " both_signs ideal model delta sigma weight residual False -2.40 -2.91 0.51 2.00e-01 2.50e+01 6.42e+00 ... (remaining 1470 not shown) Planarity restraints: 1748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 187 " 0.058 2.00e-02 2.50e+03 1.19e-01 1.77e+02 pdb=" CG ASN B 187 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN B 187 " 0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN B 187 " -0.215 2.00e-02 2.50e+03 pdb=" C1 NAG B1502 " 0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 469 " -0.101 2.00e-02 2.50e+03 1.16e-01 1.70e+02 pdb=" CG ASN A 469 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 469 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 469 " 0.192 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 408 " 0.064 2.00e-02 2.50e+03 8.78e-02 9.64e+01 pdb=" CG ASN A 408 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 408 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 408 " -0.155 2.00e-02 2.50e+03 pdb=" C1 NAG A1101 " 0.100 2.00e-02 2.50e+03 ... (remaining 1745 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2314 2.83 - 3.35: 8451 3.35 - 3.86: 15566 3.86 - 4.38: 18729 4.38 - 4.90: 30639 Nonbonded interactions: 75699 Sorted by model distance: nonbonded pdb=" OG1 THR A 334 " pdb=" O PHE A 340 " model vdw 2.311 2.440 nonbonded pdb=" OD1 ASP A 581 " pdb=" NZ LYS A 602 " model vdw 2.389 2.520 nonbonded pdb=" O GLN A 298 " pdb=" OG1 THR A 299 " model vdw 2.434 2.440 nonbonded pdb=" CG ASN B 187 " pdb=" O5 NAG B1502 " model vdw 2.443 2.616 nonbonded pdb=" O4 BMA C 3 " pdb=" O6 BMA C 3 " model vdw 2.456 2.440 ... (remaining 75694 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 'D' selection = chain 'E' } 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: 2.600 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: 10.060 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.700 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 0.084 9743 Z= 0.817 Angle : 1.465 8.723 13221 Z= 1.007 Chirality : 0.080 0.507 1473 Planarity : 0.008 0.115 1740 Dihedral : 11.949 109.309 3792 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1195 helix: -2.59 (0.50), residues: 69 sheet: -1.10 (0.39), residues: 153 loop : 0.45 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.006 TRP B 415 HIS 0.001 0.000 HIS A 545 PHE 0.041 0.002 PHE A 535 TYR 0.051 0.003 TYR B 163 ARG 0.010 0.001 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 PHE cc_start: 0.4206 (p90) cc_final: 0.3542 (p90) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 1.3587 time to fit residues: 211.1497 Evaluate side-chains 55 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN B 57 GLN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN B 111 ASN B 141 GLN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 HIS B 470 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9743 Z= 0.290 Angle : 0.669 15.679 13221 Z= 0.349 Chirality : 0.049 0.183 1473 Planarity : 0.005 0.037 1740 Dihedral : 7.706 62.996 1571 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.48 % Allowed : 6.95 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.24), residues: 1195 helix: -2.45 (0.47), residues: 95 sheet: -0.80 (0.42), residues: 138 loop : 0.15 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 205 HIS 0.011 0.001 HIS B 564 PHE 0.016 0.002 PHE A 94 TYR 0.015 0.002 TYR B 274 ARG 0.005 0.001 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 49 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 484 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8315 (mt0) REVERT: B 538 GLN cc_start: 0.7787 (pt0) cc_final: 0.6802 (pp30) outliers start: 26 outliers final: 9 residues processed: 68 average time/residue: 1.1824 time to fit residues: 87.5426 Evaluate side-chains 54 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 484 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 0.0470 chunk 73 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 0.0980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9743 Z= 0.149 Angle : 0.539 14.689 13221 Z= 0.277 Chirality : 0.045 0.184 1473 Planarity : 0.004 0.039 1740 Dihedral : 6.682 59.564 1571 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.00 % Allowed : 7.33 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.24), residues: 1195 helix: -1.95 (0.53), residues: 88 sheet: -0.70 (0.44), residues: 136 loop : 0.10 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 521 HIS 0.005 0.001 HIS B 249 PHE 0.015 0.001 PHE A 543 TYR 0.007 0.001 TYR B 274 ARG 0.005 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 49 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 490 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7862 (tpp-160) REVERT: B 538 GLN cc_start: 0.7752 (pt0) cc_final: 0.6865 (pp30) outliers start: 21 outliers final: 8 residues processed: 64 average time/residue: 1.3650 time to fit residues: 94.0611 Evaluate side-chains 50 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 531 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 72 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 95 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 HIS B 319 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9743 Z= 0.157 Angle : 0.517 14.706 13221 Z= 0.262 Chirality : 0.045 0.179 1473 Planarity : 0.004 0.038 1740 Dihedral : 6.004 54.796 1571 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.19 % Allowed : 8.00 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.24), residues: 1195 helix: -1.68 (0.56), residues: 82 sheet: -0.75 (0.44), residues: 136 loop : 0.04 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 521 HIS 0.004 0.001 HIS B 249 PHE 0.010 0.001 PHE A 543 TYR 0.009 0.001 TYR B 274 ARG 0.010 0.000 ARG A 521 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 45 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 490 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7848 (tpp-160) REVERT: B 538 GLN cc_start: 0.7773 (pt0) cc_final: 0.6919 (pp30) outliers start: 23 outliers final: 11 residues processed: 62 average time/residue: 1.2948 time to fit residues: 87.8311 Evaluate side-chains 52 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 531 CYS Chi-restraints excluded: chain B residue 563 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 103 optimal weight: 0.0270 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN A 222 ASN A 224 ASN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 318 HIS B 319 ASN ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9743 Z= 0.244 Angle : 0.553 16.042 13221 Z= 0.279 Chirality : 0.046 0.166 1473 Planarity : 0.005 0.036 1740 Dihedral : 5.809 56.003 1571 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.48 % Allowed : 7.81 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.24), residues: 1195 helix: -1.60 (0.58), residues: 76 sheet: -0.84 (0.44), residues: 138 loop : -0.04 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 452 HIS 0.004 0.001 HIS B 174 PHE 0.013 0.002 PHE A 94 TYR 0.018 0.001 TYR A 523 ARG 0.007 0.001 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 45 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7865 (tpp-160) REVERT: B 538 GLN cc_start: 0.7761 (pt0) cc_final: 0.6888 (pp30) outliers start: 26 outliers final: 14 residues processed: 66 average time/residue: 1.0417 time to fit residues: 75.6351 Evaluate side-chains 54 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 39 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 198 MET Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 531 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 53 optimal weight: 30.0000 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 111 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 318 HIS B 393 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9743 Z= 0.183 Angle : 0.511 15.128 13221 Z= 0.259 Chirality : 0.045 0.170 1473 Planarity : 0.004 0.038 1740 Dihedral : 5.466 54.453 1571 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.10 % Allowed : 8.38 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.24), residues: 1195 helix: -1.67 (0.55), residues: 82 sheet: -0.79 (0.45), residues: 136 loop : -0.07 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 521 HIS 0.002 0.001 HIS B 249 PHE 0.011 0.001 PHE A 535 TYR 0.014 0.001 TYR A 523 ARG 0.006 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 43 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 490 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7811 (tpp-160) REVERT: B 538 GLN cc_start: 0.7757 (pt0) cc_final: 0.6874 (pp30) outliers start: 22 outliers final: 14 residues processed: 60 average time/residue: 1.0316 time to fit residues: 68.2296 Evaluate side-chains 56 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 41 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 531 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 96 optimal weight: 0.0060 chunk 64 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 0.0070 chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 0.4214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 318 HIS ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9743 Z= 0.134 Angle : 0.491 14.364 13221 Z= 0.249 Chirality : 0.044 0.177 1473 Planarity : 0.004 0.039 1740 Dihedral : 5.227 54.063 1571 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.81 % Allowed : 8.95 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.24), residues: 1195 helix: -1.20 (0.59), residues: 75 sheet: -0.88 (0.45), residues: 138 loop : 0.02 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 205 HIS 0.003 0.000 HIS B 249 PHE 0.010 0.001 PHE B 577 TYR 0.013 0.001 TYR A 523 ARG 0.005 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 42 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 538 GLN cc_start: 0.7697 (pt0) cc_final: 0.6901 (pp30) outliers start: 19 outliers final: 13 residues processed: 57 average time/residue: 0.9865 time to fit residues: 62.3422 Evaluate side-chains 52 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 531 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 72 optimal weight: 0.0770 chunk 78 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 318 HIS ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9743 Z= 0.241 Angle : 0.543 16.571 13221 Z= 0.273 Chirality : 0.046 0.161 1473 Planarity : 0.004 0.037 1740 Dihedral : 5.391 56.082 1571 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.90 % Allowed : 9.24 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1195 helix: -1.60 (0.56), residues: 81 sheet: -0.82 (0.44), residues: 143 loop : -0.08 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 452 HIS 0.004 0.001 HIS B 174 PHE 0.013 0.002 PHE A 543 TYR 0.013 0.001 TYR B 274 ARG 0.004 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 47 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 538 GLN cc_start: 0.7780 (pt0) cc_final: 0.6875 (pp30) outliers start: 20 outliers final: 12 residues processed: 64 average time/residue: 1.1328 time to fit residues: 79.4919 Evaluate side-chains 54 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 531 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 64 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 HIS B 318 HIS ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9743 Z= 0.285 Angle : 0.574 17.302 13221 Z= 0.289 Chirality : 0.047 0.158 1473 Planarity : 0.004 0.037 1740 Dihedral : 5.632 55.918 1571 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.71 % Allowed : 10.19 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.24), residues: 1195 helix: -1.65 (0.55), residues: 81 sheet: -0.93 (0.43), residues: 153 loop : -0.17 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 452 HIS 0.005 0.001 HIS B 174 PHE 0.013 0.002 PHE A 94 TYR 0.015 0.001 TYR B 274 ARG 0.006 0.001 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 43 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 538 GLN cc_start: 0.7826 (pt0) cc_final: 0.6895 (pp30) outliers start: 18 outliers final: 11 residues processed: 59 average time/residue: 1.0512 time to fit residues: 67.9705 Evaluate side-chains 53 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 531 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 118 optimal weight: 0.0020 chunk 109 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 318 HIS ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9743 Z= 0.153 Angle : 0.526 15.161 13221 Z= 0.263 Chirality : 0.044 0.172 1473 Planarity : 0.004 0.039 1740 Dihedral : 5.431 59.063 1571 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.05 % Allowed : 10.86 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.25), residues: 1195 helix: -1.13 (0.60), residues: 74 sheet: -0.74 (0.44), residues: 148 loop : -0.09 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 205 HIS 0.004 0.000 HIS B 249 PHE 0.014 0.001 PHE A 543 TYR 0.011 0.001 TYR A 523 ARG 0.005 0.000 ARG B 354 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 186 GLU cc_start: 0.7363 (pm20) cc_final: 0.7155 (pm20) REVERT: B 538 GLN cc_start: 0.7799 (pt0) cc_final: 0.6892 (pp30) outliers start: 11 outliers final: 8 residues processed: 54 average time/residue: 1.0317 time to fit residues: 61.4744 Evaluate side-chains 52 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 549 CYS Chi-restraints excluded: chain B residue 193 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 HIS B 318 HIS ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.121197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.080979 restraints weight = 16670.892| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.20 r_work: 0.3171 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9743 Z= 0.343 Angle : 0.602 18.732 13221 Z= 0.302 Chirality : 0.048 0.152 1473 Planarity : 0.005 0.035 1740 Dihedral : 5.688 57.160 1571 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.33 % Allowed : 10.29 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.25), residues: 1195 helix: -1.58 (0.58), residues: 75 sheet: -0.93 (0.43), residues: 153 loop : -0.20 (0.21), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 452 HIS 0.006 0.001 HIS B 174 PHE 0.014 0.002 PHE A 219 TYR 0.017 0.001 TYR B 274 ARG 0.005 0.001 ARG B 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3026.43 seconds wall clock time: 55 minutes 13.20 seconds (3313.20 seconds total)