Starting phenix.real_space_refine on Fri Mar 15 06:31:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm5_4588/03_2024/6qm5_4588.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm5_4588/03_2024/6qm5_4588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm5_4588/03_2024/6qm5_4588.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm5_4588/03_2024/6qm5_4588.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm5_4588/03_2024/6qm5_4588.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm5_4588/03_2024/6qm5_4588.pdb" } resolution = 3.6 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 40 5.16 5 C 7066 2.51 5 N 1818 2.21 5 O 1946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 15": "OE1" <-> "OE2" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A ASP 173": "OD1" <-> "OD2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 367": "OD1" <-> "OD2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A GLU 425": "OE1" <-> "OE2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A GLU 481": "OE1" <-> "OE2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A GLU 676": "OE1" <-> "OE2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "A ARG 699": "NH1" <-> "NH2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B ASP 173": "OD1" <-> "OD2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B GLU 268": "OE1" <-> "OE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 367": "OD1" <-> "OD2" Residue "B GLU 420": "OE1" <-> "OE2" Residue "B GLU 425": "OE1" <-> "OE2" Residue "B GLU 477": "OE1" <-> "OE2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B ASP 499": "OD1" <-> "OD2" Residue "B GLU 665": "OE1" <-> "OE2" Residue "B GLU 668": "OE1" <-> "OE2" Residue "B ARG 672": "NH1" <-> "NH2" Residue "B GLU 676": "OE1" <-> "OE2" Residue "B GLU 691": "OE1" <-> "OE2" Residue "B ARG 699": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10874 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5435 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 29, 'TRANS': 643} Chain breaks: 5 Chain: "B" Number of atoms: 5435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5435 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 29, 'TRANS': 643} Chain breaks: 5 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.26, per 1000 atoms: 0.58 Number of scatterers: 10874 At special positions: 0 Unit cell: (87.032, 142.692, 108.284, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 40 16.00 O 1946 8.00 N 1818 7.00 C 7066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.15 Conformation dependent library (CDL) restraints added in 2.0 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2548 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 4 sheets defined 69.1% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 33 through 49 removed outlier: 3.882A pdb=" N ALA A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 89 removed outlier: 4.132A pdb=" N LYS A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 111 through 124 removed outlier: 3.520A pdb=" N LEU A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.700A pdb=" N ALA A 139 " --> pdb=" O PRO A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 165 removed outlier: 3.711A pdb=" N LYS A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 187 removed outlier: 3.515A pdb=" N ASN A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLU A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N SER A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL A 185 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 removed outlier: 3.516A pdb=" N SER A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 removed outlier: 3.683A pdb=" N PHE A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 246 removed outlier: 3.771A pdb=" N GLY A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER A 228 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP A 241 " --> pdb=" O LYS A 237 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.534A pdb=" N ARG A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 319 removed outlier: 3.639A pdb=" N PHE A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 330 through 356 removed outlier: 3.542A pdb=" N GLY A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Proline residue: A 341 - end of helix removed outlier: 3.505A pdb=" N SER A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 392 removed outlier: 3.636A pdb=" N THR A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 399 removed outlier: 4.008A pdb=" N ILE A 399 " --> pdb=" O PHE A 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 399' Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.732A pdb=" N ARG A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 Processing helix chain 'A' and resid 442 through 453 removed outlier: 3.772A pdb=" N ASN A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 460 removed outlier: 3.521A pdb=" N GLN A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 Processing helix chain 'A' and resid 482 through 493 Processing helix chain 'A' and resid 499 through 516 removed outlier: 3.838A pdb=" N ASP A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 511 " --> pdb=" O MET A 507 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 524 Proline residue: A 522 - end of helix Processing helix chain 'A' and resid 525 through 545 removed outlier: 3.873A pdb=" N VAL A 530 " --> pdb=" O CYS A 526 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN A 531 " --> pdb=" O CYS A 527 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG A 537 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 572 removed outlier: 3.724A pdb=" N PHE A 567 " --> pdb=" O THR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 removed outlier: 4.249A pdb=" N VAL A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A 581 " --> pdb=" O SER A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 587 Processing helix chain 'A' and resid 598 through 627 removed outlier: 4.033A pdb=" N TYR A 613 " --> pdb=" O ALA A 609 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 625 " --> pdb=" O ARG A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 651 removed outlier: 3.649A pdb=" N GLU A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 640 " --> pdb=" O ARG A 636 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 682 Processing helix chain 'A' and resid 691 through 696 removed outlier: 4.052A pdb=" N TRP A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 717 removed outlier: 3.516A pdb=" N GLU A 706 " --> pdb=" O GLN A 702 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 712 " --> pdb=" O GLY A 708 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN A 715 " --> pdb=" O MET A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 49 removed outlier: 3.883A pdb=" N ALA B 38 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR B 48 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 89 removed outlier: 4.132A pdb=" N LYS B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 111 through 124 removed outlier: 3.520A pdb=" N LEU B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.700A pdb=" N ALA B 139 " --> pdb=" O PRO B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 165 removed outlier: 3.711A pdb=" N LYS B 157 " --> pdb=" O HIS B 153 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 187 removed outlier: 3.516A pdb=" N ASN B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP B 179 " --> pdb=" O ASP B 175 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS B 180 " --> pdb=" O ASN B 176 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLU B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N SER B 184 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL B 185 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 197 removed outlier: 3.515A pdb=" N SER B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 3.683A pdb=" N PHE B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 246 removed outlier: 3.772A pdb=" N GLY B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER B 228 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.534A pdb=" N ARG B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 319 removed outlier: 3.639A pdb=" N PHE B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 329 No H-bonds generated for 'chain 'B' and resid 327 through 329' Processing helix chain 'B' and resid 330 through 356 removed outlier: 3.542A pdb=" N GLY B 339 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.504A pdb=" N SER B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 392 removed outlier: 3.636A pdb=" N THR B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER B 382 " --> pdb=" O ASN B 378 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA B 385 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 391 " --> pdb=" O PHE B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 399 removed outlier: 4.007A pdb=" N ILE B 399 " --> pdb=" O PHE B 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 399' Processing helix chain 'B' and resid 400 through 413 removed outlier: 3.732A pdb=" N ARG B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 442 Processing helix chain 'B' and resid 442 through 453 removed outlier: 3.771A pdb=" N ASN B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 460 removed outlier: 3.521A pdb=" N GLN B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 Processing helix chain 'B' and resid 482 through 493 Processing helix chain 'B' and resid 499 through 516 removed outlier: 3.839A pdb=" N ASP B 503 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 504 " --> pdb=" O VAL B 500 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE B 511 " --> pdb=" O MET B 507 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 514 " --> pdb=" O GLN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 524 Proline residue: B 522 - end of helix Processing helix chain 'B' and resid 525 through 545 removed outlier: 3.874A pdb=" N VAL B 530 " --> pdb=" O CYS B 526 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN B 531 " --> pdb=" O CYS B 527 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 572 removed outlier: 3.724A pdb=" N PHE B 567 " --> pdb=" O THR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 583 removed outlier: 4.249A pdb=" N VAL B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 587 Processing helix chain 'B' and resid 598 through 627 removed outlier: 4.033A pdb=" N TYR B 613 " --> pdb=" O ALA B 609 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 625 " --> pdb=" O ARG B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 651 removed outlier: 3.649A pdb=" N GLU B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 640 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 643 " --> pdb=" O ARG B 639 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 682 Processing helix chain 'B' and resid 691 through 696 removed outlier: 4.052A pdb=" N TRP B 695 " --> pdb=" O GLU B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 717 removed outlier: 3.515A pdb=" N GLU B 706 " --> pdb=" O GLN B 702 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 712 " --> pdb=" O GLY B 708 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 713 " --> pdb=" O ARG B 709 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN B 715 " --> pdb=" O MET B 711 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 268 removed outlier: 3.639A pdb=" N HIS A 265 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 267 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 268 removed outlier: 3.639A pdb=" N HIS B 265 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 267 " --> pdb=" O VAL B 276 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1572 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: 2.83 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3446 1.34 - 1.46: 2110 1.46 - 1.57: 5528 1.57 - 1.69: 0 1.69 - 1.80: 66 Bond restraints: 11150 Sorted by residual: bond pdb=" C ILE B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.21e+00 bond pdb=" CA PHE A 396 " pdb=" CB PHE A 396 " ideal model delta sigma weight residual 1.524 1.564 -0.040 1.62e-02 3.81e+03 6.20e+00 bond pdb=" C ILE A 394 " pdb=" N PRO A 395 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.20e+00 bond pdb=" CA PHE B 396 " pdb=" CB PHE B 396 " ideal model delta sigma weight residual 1.524 1.564 -0.040 1.62e-02 3.81e+03 6.18e+00 bond pdb=" CB PRO B 202 " pdb=" CG PRO B 202 " ideal model delta sigma weight residual 1.492 1.405 0.087 5.00e-02 4.00e+02 3.00e+00 ... (remaining 11145 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.16: 253 106.16 - 113.16: 5887 113.16 - 120.16: 4617 120.16 - 127.17: 4205 127.17 - 134.17: 158 Bond angle restraints: 15120 Sorted by residual: angle pdb=" N VAL B 319 " pdb=" CA VAL B 319 " pdb=" C VAL B 319 " ideal model delta sigma weight residual 106.53 112.19 -5.66 1.41e+00 5.03e-01 1.61e+01 angle pdb=" N VAL A 319 " pdb=" CA VAL A 319 " pdb=" C VAL A 319 " ideal model delta sigma weight residual 106.53 112.17 -5.64 1.41e+00 5.03e-01 1.60e+01 angle pdb=" CA ILE B 394 " pdb=" C ILE B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 118.88 124.70 -5.82 1.54e+00 4.22e-01 1.43e+01 angle pdb=" CA ILE A 394 " pdb=" C ILE A 394 " pdb=" N PRO A 395 " ideal model delta sigma weight residual 118.88 124.69 -5.81 1.54e+00 4.22e-01 1.43e+01 angle pdb=" N VAL A 134 " pdb=" CA VAL A 134 " pdb=" C VAL A 134 " ideal model delta sigma weight residual 109.34 102.14 7.20 2.08e+00 2.31e-01 1.20e+01 ... (remaining 15115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 5784 17.89 - 35.77: 630 35.77 - 53.66: 112 53.66 - 71.55: 22 71.55 - 89.43: 20 Dihedral angle restraints: 6568 sinusoidal: 2642 harmonic: 3926 Sorted by residual: dihedral pdb=" CA HIS A 401 " pdb=" C HIS A 401 " pdb=" N PRO A 402 " pdb=" CA PRO A 402 " ideal model delta harmonic sigma weight residual 180.00 161.10 18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA HIS B 401 " pdb=" C HIS B 401 " pdb=" N PRO B 402 " pdb=" CA PRO B 402 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ALA B 139 " pdb=" C ALA B 139 " pdb=" N LYS B 140 " pdb=" CA LYS B 140 " ideal model delta harmonic sigma weight residual 180.00 162.86 17.14 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 6565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1211 0.051 - 0.101: 355 0.101 - 0.152: 75 0.152 - 0.202: 13 0.202 - 0.253: 4 Chirality restraints: 1658 Sorted by residual: chirality pdb=" CA THR B 340 " pdb=" N THR B 340 " pdb=" C THR B 340 " pdb=" CB THR B 340 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA THR A 340 " pdb=" N THR A 340 " pdb=" C THR A 340 " pdb=" CB THR A 340 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL A 229 " pdb=" CA VAL A 229 " pdb=" CG1 VAL A 229 " pdb=" CG2 VAL A 229 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1655 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 401 " 0.050 5.00e-02 4.00e+02 7.46e-02 8.90e+00 pdb=" N PRO A 402 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 402 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 402 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 401 " 0.050 5.00e-02 4.00e+02 7.44e-02 8.87e+00 pdb=" N PRO B 402 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 402 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 402 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 125 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO B 126 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " 0.033 5.00e-02 4.00e+02 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3542 2.83 - 3.35: 9667 3.35 - 3.86: 17289 3.86 - 4.38: 20239 4.38 - 4.90: 34700 Nonbonded interactions: 85437 Sorted by model distance: nonbonded pdb=" OH TYR B 188 " pdb=" OD2 ASP B 539 " model vdw 2.311 2.440 nonbonded pdb=" OH TYR A 188 " pdb=" OD2 ASP A 539 " model vdw 2.311 2.440 nonbonded pdb=" OE1 GLU A 145 " pdb=" OG SER A 146 " model vdw 2.338 2.440 nonbonded pdb=" OE1 GLU B 145 " pdb=" OG SER B 146 " model vdw 2.339 2.440 nonbonded pdb=" OH TYR A 498 " pdb=" OD2 ASP A 503 " model vdw 2.340 2.440 ... (remaining 85432 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 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 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: 2.930 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 31.230 Find NCS groups from input model: 0.490 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 : 0.007 0.087 11150 Z= 0.412 Angle : 0.831 9.037 15120 Z= 0.461 Chirality : 0.052 0.253 1658 Planarity : 0.006 0.075 1920 Dihedral : 15.765 89.434 4020 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % 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: -6.65 (0.13), residues: 1322 helix: -4.69 (0.06), residues: 874 sheet: -4.21 (0.36), residues: 54 loop : -2.99 (0.24), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 235 HIS 0.007 0.001 HIS A 479 PHE 0.023 0.002 PHE A 396 TYR 0.012 0.002 TYR B 195 ARG 0.003 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.199 Fit side-chains REVERT: A 124 THR cc_start: 0.9217 (m) cc_final: 0.8934 (p) REVERT: A 145 GLU cc_start: 0.7604 (tm-30) cc_final: 0.6891 (tm-30) REVERT: A 312 LEU cc_start: 0.8876 (tt) cc_final: 0.8577 (tt) REVERT: A 408 ARG cc_start: 0.7766 (mtp85) cc_final: 0.7542 (ttp80) REVERT: A 457 TYR cc_start: 0.7277 (t80) cc_final: 0.6914 (t80) REVERT: A 542 LYS cc_start: 0.8781 (ttpt) cc_final: 0.8429 (ttpp) REVERT: A 692 GLU cc_start: 0.8100 (mp0) cc_final: 0.7619 (mp0) REVERT: B 692 GLU cc_start: 0.8238 (mp0) cc_final: 0.7689 (mp0) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2385 time to fit residues: 55.4219 Evaluate side-chains 107 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN A 510 GLN A 617 GLN A 650 ASN B 79 GLN B 256 GLN B 510 GLN B 650 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11150 Z= 0.171 Angle : 0.544 7.607 15120 Z= 0.290 Chirality : 0.040 0.167 1658 Planarity : 0.005 0.048 1920 Dihedral : 4.840 15.416 1446 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.12 % Allowed : 11.68 % Favored : 87.20 % 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: -4.39 (0.17), residues: 1322 helix: -2.72 (0.13), residues: 894 sheet: -3.22 (0.40), residues: 74 loop : -2.66 (0.27), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 521 HIS 0.003 0.001 HIS B 479 PHE 0.029 0.001 PHE A 205 TYR 0.012 0.001 TYR A 513 ARG 0.005 0.000 ARG B 710 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 1.308 Fit side-chains REVERT: A 124 THR cc_start: 0.9340 (m) cc_final: 0.8925 (p) REVERT: A 145 GLU cc_start: 0.7669 (tm-30) cc_final: 0.6972 (tm-30) REVERT: A 290 LEU cc_start: 0.9050 (tp) cc_final: 0.8789 (tt) REVERT: A 318 GLU cc_start: 0.8565 (mp0) cc_final: 0.8305 (mp0) REVERT: A 692 GLU cc_start: 0.8423 (mp0) cc_final: 0.8221 (mp0) REVERT: B 79 GLN cc_start: 0.8404 (tp40) cc_final: 0.8135 (tp-100) REVERT: B 82 ARG cc_start: 0.7818 (ttp-170) cc_final: 0.7490 (ttp80) REVERT: B 145 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7076 (tm-30) REVERT: B 290 LEU cc_start: 0.9094 (tp) cc_final: 0.8870 (tt) REVERT: B 312 LEU cc_start: 0.8839 (tt) cc_final: 0.8594 (tt) REVERT: B 318 GLU cc_start: 0.8591 (mp0) cc_final: 0.8349 (mp0) outliers start: 13 outliers final: 9 residues processed: 135 average time/residue: 0.2053 time to fit residues: 41.6358 Evaluate side-chains 116 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 569 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS B 378 ASN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11150 Z= 0.205 Angle : 0.516 7.157 15120 Z= 0.270 Chirality : 0.040 0.161 1658 Planarity : 0.004 0.042 1920 Dihedral : 4.487 14.962 1446 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.38 % Allowed : 13.75 % Favored : 84.86 % 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: -2.86 (0.21), residues: 1322 helix: -1.48 (0.16), residues: 898 sheet: -2.66 (0.43), residues: 74 loop : -2.33 (0.29), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 235 HIS 0.004 0.001 HIS B 479 PHE 0.028 0.001 PHE B 205 TYR 0.009 0.001 TYR B 513 ARG 0.004 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 1.185 Fit side-chains REVERT: A 145 GLU cc_start: 0.7727 (tm-30) cc_final: 0.6985 (tm-30) REVERT: A 318 GLU cc_start: 0.8531 (mp0) cc_final: 0.8256 (mp0) REVERT: B 82 ARG cc_start: 0.7769 (ttp-170) cc_final: 0.7480 (ttp80) REVERT: B 145 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7122 (tm-30) REVERT: B 312 LEU cc_start: 0.8820 (tt) cc_final: 0.8533 (tt) REVERT: B 318 GLU cc_start: 0.8562 (mp0) cc_final: 0.8294 (mp0) outliers start: 16 outliers final: 13 residues processed: 131 average time/residue: 0.1850 time to fit residues: 36.9358 Evaluate side-chains 113 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 569 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.0570 chunk 91 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 overall best weight: 1.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 ASN B 378 ASN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11150 Z= 0.240 Angle : 0.533 6.968 15120 Z= 0.275 Chirality : 0.041 0.165 1658 Planarity : 0.004 0.041 1920 Dihedral : 4.395 16.793 1446 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.38 % Allowed : 16.26 % Favored : 82.35 % 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: -2.10 (0.22), residues: 1322 helix: -0.86 (0.17), residues: 902 sheet: -2.11 (0.47), residues: 78 loop : -2.28 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 235 HIS 0.003 0.001 HIS B 479 PHE 0.024 0.001 PHE B 205 TYR 0.009 0.001 TYR A 26 ARG 0.005 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 1.366 Fit side-chains REVERT: A 145 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7071 (tm-30) REVERT: A 318 GLU cc_start: 0.8524 (mp0) cc_final: 0.8225 (mp0) REVERT: A 406 PHE cc_start: 0.8997 (t80) cc_final: 0.8636 (t80) REVERT: A 648 GLN cc_start: 0.7073 (pp30) cc_final: 0.6764 (pp30) REVERT: B 79 GLN cc_start: 0.8411 (tp-100) cc_final: 0.8171 (tp-100) REVERT: B 82 ARG cc_start: 0.7764 (ttp-170) cc_final: 0.7453 (ttp80) REVERT: B 145 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7153 (tm-30) REVERT: B 312 LEU cc_start: 0.8821 (tt) cc_final: 0.8566 (tt) REVERT: B 318 GLU cc_start: 0.8513 (mp0) cc_final: 0.8218 (mp0) outliers start: 16 outliers final: 15 residues processed: 124 average time/residue: 0.2031 time to fit residues: 37.9473 Evaluate side-chains 119 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 616 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 53 optimal weight: 0.1980 chunk 110 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11150 Z= 0.224 Angle : 0.529 11.304 15120 Z= 0.269 Chirality : 0.040 0.163 1658 Planarity : 0.004 0.040 1920 Dihedral : 4.292 17.085 1446 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.82 % Allowed : 16.87 % Favored : 81.31 % 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: -1.62 (0.23), residues: 1322 helix: -0.50 (0.18), residues: 904 sheet: -2.02 (0.57), residues: 58 loop : -2.09 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 235 HIS 0.003 0.001 HIS B 479 PHE 0.023 0.001 PHE B 205 TYR 0.008 0.001 TYR A 26 ARG 0.005 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.191 Fit side-chains REVERT: A 145 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7088 (tm-30) REVERT: A 318 GLU cc_start: 0.8503 (mp0) cc_final: 0.8208 (mp0) REVERT: A 384 MET cc_start: 0.8507 (tpt) cc_final: 0.8239 (tpp) REVERT: A 406 PHE cc_start: 0.9015 (t80) cc_final: 0.8665 (t80) REVERT: A 648 GLN cc_start: 0.7138 (pp30) cc_final: 0.6818 (pp30) REVERT: B 79 GLN cc_start: 0.8382 (tp-100) cc_final: 0.8116 (tp-100) REVERT: B 82 ARG cc_start: 0.7757 (ttp-170) cc_final: 0.7429 (ttp80) REVERT: B 145 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7123 (tm-30) REVERT: B 312 LEU cc_start: 0.8832 (tt) cc_final: 0.8553 (tt) REVERT: B 318 GLU cc_start: 0.8499 (mp0) cc_final: 0.8203 (mp0) REVERT: B 406 PHE cc_start: 0.9008 (t80) cc_final: 0.8677 (t80) outliers start: 21 outliers final: 15 residues processed: 132 average time/residue: 0.2011 time to fit residues: 39.6503 Evaluate side-chains 125 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 701 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 129 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11150 Z= 0.275 Angle : 0.552 10.134 15120 Z= 0.281 Chirality : 0.041 0.167 1658 Planarity : 0.004 0.041 1920 Dihedral : 4.348 15.308 1446 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.73 % Allowed : 17.56 % Favored : 80.71 % 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: -1.52 (0.23), residues: 1322 helix: -0.40 (0.18), residues: 914 sheet: -1.81 (0.59), residues: 58 loop : -2.22 (0.29), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 235 HIS 0.004 0.001 HIS B 479 PHE 0.023 0.001 PHE B 205 TYR 0.010 0.001 TYR A 195 ARG 0.007 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.248 Fit side-chains REVERT: A 145 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7098 (tm-30) REVERT: A 318 GLU cc_start: 0.8507 (mp0) cc_final: 0.8195 (mp0) REVERT: A 384 MET cc_start: 0.8553 (tpt) cc_final: 0.8294 (tpp) REVERT: A 406 PHE cc_start: 0.9024 (t80) cc_final: 0.8673 (t80) REVERT: A 648 GLN cc_start: 0.7048 (pp30) cc_final: 0.6755 (pp30) REVERT: B 79 GLN cc_start: 0.8424 (tp-100) cc_final: 0.8113 (tp-100) REVERT: B 145 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7160 (tm-30) REVERT: B 312 LEU cc_start: 0.8838 (tt) cc_final: 0.8568 (tt) REVERT: B 318 GLU cc_start: 0.8514 (mp0) cc_final: 0.8203 (mp0) REVERT: B 406 PHE cc_start: 0.9048 (t80) cc_final: 0.8668 (t80) outliers start: 20 outliers final: 16 residues processed: 130 average time/residue: 0.2228 time to fit residues: 43.3851 Evaluate side-chains 124 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 701 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 129 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11150 Z= 0.351 Angle : 0.587 9.748 15120 Z= 0.300 Chirality : 0.043 0.172 1658 Planarity : 0.004 0.042 1920 Dihedral : 4.515 16.324 1446 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.90 % Allowed : 19.20 % Favored : 78.89 % 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: -1.55 (0.23), residues: 1322 helix: -0.42 (0.18), residues: 914 sheet: -1.80 (0.60), residues: 58 loop : -2.23 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 235 HIS 0.005 0.001 HIS B 479 PHE 0.022 0.001 PHE B 205 TYR 0.012 0.001 TYR B 195 ARG 0.006 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 1.395 Fit side-chains REVERT: A 145 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7074 (tm-30) REVERT: A 318 GLU cc_start: 0.8514 (mp0) cc_final: 0.8182 (mp0) REVERT: A 648 GLN cc_start: 0.7068 (pp30) cc_final: 0.6753 (pp30) REVERT: B 79 GLN cc_start: 0.8483 (tp-100) cc_final: 0.8277 (tp-100) REVERT: B 145 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7159 (tm-30) REVERT: B 312 LEU cc_start: 0.8869 (tt) cc_final: 0.8608 (tt) REVERT: B 318 GLU cc_start: 0.8531 (mp0) cc_final: 0.8222 (mp0) REVERT: B 648 GLN cc_start: 0.7063 (pp30) cc_final: 0.6681 (pp30) outliers start: 22 outliers final: 19 residues processed: 134 average time/residue: 0.1959 time to fit residues: 39.7451 Evaluate side-chains 130 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 701 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11150 Z= 0.203 Angle : 0.531 9.765 15120 Z= 0.269 Chirality : 0.040 0.156 1658 Planarity : 0.004 0.044 1920 Dihedral : 4.239 15.381 1446 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.90 % Allowed : 19.20 % Favored : 78.89 % 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: -1.20 (0.23), residues: 1322 helix: -0.11 (0.18), residues: 914 sheet: -1.57 (0.52), residues: 78 loop : -2.25 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 235 HIS 0.003 0.001 HIS A 58 PHE 0.024 0.001 PHE B 205 TYR 0.010 0.001 TYR A 26 ARG 0.007 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: A 145 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7099 (tm-30) REVERT: A 318 GLU cc_start: 0.8501 (mp0) cc_final: 0.8177 (mp0) REVERT: A 384 MET cc_start: 0.8546 (tpt) cc_final: 0.8296 (tpp) REVERT: A 406 PHE cc_start: 0.8890 (t80) cc_final: 0.8534 (t80) REVERT: A 437 MET cc_start: 0.8991 (tpp) cc_final: 0.8735 (mmm) REVERT: A 648 GLN cc_start: 0.7070 (pp30) cc_final: 0.6737 (pp30) REVERT: B 79 GLN cc_start: 0.8437 (tp-100) cc_final: 0.8073 (tp-100) REVERT: B 145 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7172 (tm-30) REVERT: B 312 LEU cc_start: 0.8851 (tt) cc_final: 0.8575 (tt) REVERT: B 318 GLU cc_start: 0.8487 (mp0) cc_final: 0.8170 (mp0) REVERT: B 406 PHE cc_start: 0.8883 (t80) cc_final: 0.8509 (t80) REVERT: B 437 MET cc_start: 0.9009 (tpp) cc_final: 0.8738 (mmm) REVERT: B 648 GLN cc_start: 0.6971 (pp30) cc_final: 0.6732 (pp30) outliers start: 22 outliers final: 21 residues processed: 129 average time/residue: 0.1919 time to fit residues: 37.3483 Evaluate side-chains 131 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 701 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 GLN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11150 Z= 0.196 Angle : 0.527 9.569 15120 Z= 0.266 Chirality : 0.040 0.159 1658 Planarity : 0.004 0.043 1920 Dihedral : 4.165 15.819 1446 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.90 % Allowed : 19.64 % Favored : 78.46 % 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: -0.98 (0.23), residues: 1322 helix: 0.06 (0.18), residues: 914 sheet: -1.53 (0.52), residues: 78 loop : -2.18 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 235 HIS 0.003 0.001 HIS A 58 PHE 0.024 0.001 PHE B 205 TYR 0.010 0.001 TYR A 26 ARG 0.007 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 1.330 Fit side-chains revert: symmetry clash REVERT: A 145 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7115 (tm-30) REVERT: A 318 GLU cc_start: 0.8499 (mp0) cc_final: 0.8176 (mp0) REVERT: A 384 MET cc_start: 0.8544 (tpt) cc_final: 0.8278 (tpp) REVERT: A 406 PHE cc_start: 0.8873 (t80) cc_final: 0.8506 (t80) REVERT: A 437 MET cc_start: 0.8978 (tpp) cc_final: 0.8710 (mmm) REVERT: A 648 GLN cc_start: 0.6937 (pp30) cc_final: 0.6646 (pp30) REVERT: B 79 GLN cc_start: 0.8434 (tp-100) cc_final: 0.8068 (tp-100) REVERT: B 145 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7161 (tm-30) REVERT: B 312 LEU cc_start: 0.8851 (tt) cc_final: 0.8578 (tt) REVERT: B 318 GLU cc_start: 0.8481 (mp0) cc_final: 0.8172 (mp0) REVERT: B 406 PHE cc_start: 0.8886 (t80) cc_final: 0.8538 (t80) REVERT: B 437 MET cc_start: 0.9002 (tpp) cc_final: 0.8723 (mmm) REVERT: B 516 MET cc_start: 0.8504 (mtm) cc_final: 0.8294 (mtp) REVERT: B 526 CYS cc_start: 0.8390 (t) cc_final: 0.8095 (m) REVERT: B 648 GLN cc_start: 0.6950 (pp30) cc_final: 0.6725 (pp30) outliers start: 22 outliers final: 20 residues processed: 126 average time/residue: 0.1894 time to fit residues: 36.6964 Evaluate side-chains 128 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 701 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 133 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 11 optimal weight: 0.0470 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 overall best weight: 2.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11150 Z= 0.300 Angle : 0.572 9.613 15120 Z= 0.290 Chirality : 0.042 0.168 1658 Planarity : 0.004 0.042 1920 Dihedral : 4.324 14.776 1446 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.99 % Allowed : 19.29 % Favored : 78.72 % 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: -1.11 (0.23), residues: 1322 helix: -0.04 (0.18), residues: 914 sheet: -1.56 (0.53), residues: 78 loop : -2.24 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 235 HIS 0.004 0.001 HIS A 58 PHE 0.022 0.001 PHE B 205 TYR 0.011 0.001 TYR A 195 ARG 0.006 0.000 ARG A 710 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 1.319 Fit side-chains REVERT: A 145 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7039 (tm-30) REVERT: A 318 GLU cc_start: 0.8502 (mp0) cc_final: 0.8165 (mp0) REVERT: A 384 MET cc_start: 0.8608 (tpt) cc_final: 0.8360 (tpp) REVERT: A 406 PHE cc_start: 0.8935 (t80) cc_final: 0.8588 (t80) REVERT: A 648 GLN cc_start: 0.6981 (pp30) cc_final: 0.6699 (pp30) REVERT: B 79 GLN cc_start: 0.8470 (tp-100) cc_final: 0.8256 (tp-100) REVERT: B 145 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7132 (tm-30) REVERT: B 312 LEU cc_start: 0.8880 (tt) cc_final: 0.8592 (tt) REVERT: B 318 GLU cc_start: 0.8504 (mp0) cc_final: 0.8169 (mp0) REVERT: B 406 PHE cc_start: 0.8949 (t80) cc_final: 0.8578 (t80) REVERT: B 526 CYS cc_start: 0.8582 (t) cc_final: 0.8265 (m) REVERT: B 648 GLN cc_start: 0.7013 (pp30) cc_final: 0.6716 (pp30) outliers start: 23 outliers final: 22 residues processed: 126 average time/residue: 0.2018 time to fit residues: 38.5816 Evaluate side-chains 129 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 701 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.0030 chunk 98 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 13 optimal weight: 0.0570 chunk 19 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.5910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.139167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.107824 restraints weight = 15425.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110770 restraints weight = 9073.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112609 restraints weight = 6648.189| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11150 Z= 0.141 Angle : 0.519 9.823 15120 Z= 0.261 Chirality : 0.039 0.157 1658 Planarity : 0.004 0.044 1920 Dihedral : 4.099 15.812 1446 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.47 % Allowed : 20.07 % Favored : 78.46 % 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: -0.73 (0.24), residues: 1322 helix: 0.23 (0.18), residues: 918 sheet: -1.47 (0.53), residues: 78 loop : -2.07 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 235 HIS 0.004 0.001 HIS B 58 PHE 0.025 0.001 PHE B 205 TYR 0.010 0.001 TYR A 26 ARG 0.008 0.000 ARG A 710 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1950.94 seconds wall clock time: 36 minutes 4.82 seconds (2164.82 seconds total)