Starting phenix.real_space_refine (version: dev) on Mon Dec 12 10:58:08 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nq0_0477/12_2022/6nq0_0477_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nq0_0477/12_2022/6nq0_0477.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nq0_0477/12_2022/6nq0_0477_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nq0_0477/12_2022/6nq0_0477_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nq0_0477/12_2022/6nq0_0477_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nq0_0477/12_2022/6nq0_0477.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nq0_0477/12_2022/6nq0_0477.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nq0_0477/12_2022/6nq0_0477_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nq0_0477/12_2022/6nq0_0477_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.007 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 112": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 663": "NH1" <-> "NH2" Residue "A ARG 664": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 112": "NH1" <-> "NH2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B ARG 524": "NH1" <-> "NH2" Residue "B ARG 663": "NH1" <-> "NH2" Residue "B ARG 664": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 10140 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5023 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 21, 'TRANS': 599} Chain breaks: 4 Chain: "B" Number of atoms: 5023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5023 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 21, 'TRANS': 599} Chain breaks: 4 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'EUJ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'EUJ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.96, per 1000 atoms: 0.59 Number of scatterers: 10140 At special positions: 0 Unit cell: (116.63, 125.19, 103.79, 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) S 60 16.00 P 6 15.00 O 1728 8.00 N 1622 7.00 C 6724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 623 " - pdb=" SG CYS B 623 " distance=2.05 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 180 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.07 Conformation dependent library (CDL) restraints added in 1.3 seconds 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2380 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 0 sheets defined 69.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 41 through 58 removed outlier: 3.666A pdb=" N VAL A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 removed outlier: 3.721A pdb=" N ARG A 75 " --> pdb=" O MET A 71 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 76 " --> pdb=" O TRP A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 98 removed outlier: 3.623A pdb=" N PHE A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N PHE A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N PHE A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.833A pdb=" N VAL A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 removed outlier: 3.790A pdb=" N SER A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 154 removed outlier: 3.565A pdb=" N LYS A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 177 removed outlier: 3.586A pdb=" N LEU A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 176 " --> pdb=" O TRP A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 198 removed outlier: 3.569A pdb=" N LEU A 190 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 191 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Proline residue: A 192 - end of helix removed outlier: 3.814A pdb=" N GLN A 197 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN A 198 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 210 removed outlier: 3.644A pdb=" N ARG A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 217 through 237 removed outlier: 3.882A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET A 232 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 270 removed outlier: 3.673A pdb=" N VAL A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 282 No H-bonds generated for 'chain 'A' and resid 279 through 282' Processing helix chain 'A' and resid 286 through 298 removed outlier: 3.560A pdb=" N ALA A 289 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE A 293 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 294 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE A 295 " --> pdb=" O PHE A 292 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 296 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 297 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 298 " --> pdb=" O PHE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 342 removed outlier: 3.520A pdb=" N LEU A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR A 308 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 334 " --> pdb=" O ARG A 330 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 368 removed outlier: 3.510A pdb=" N LEU A 363 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 384 removed outlier: 3.848A pdb=" N MET A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 404 removed outlier: 3.722A pdb=" N PHE A 400 " --> pdb=" O PHE A 396 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASN A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLU A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASP A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 429 removed outlier: 3.779A pdb=" N SER A 424 " --> pdb=" O PRO A 420 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 453 removed outlier: 3.847A pdb=" N ASN A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 491 removed outlier: 4.356A pdb=" N VAL A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 496 No H-bonds generated for 'chain 'A' and resid 493 through 496' Processing helix chain 'A' and resid 500 through 522 removed outlier: 3.840A pdb=" N LEU A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 510 " --> pdb=" O GLY A 506 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 561 removed outlier: 3.578A pdb=" N LEU A 547 " --> pdb=" O MET A 543 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 548 " --> pdb=" O THR A 544 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU A 556 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ARG A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILE A 558 " --> pdb=" O ARG A 554 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ILE A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Proline residue: A 560 - end of helix Processing helix chain 'A' and resid 563 through 582 removed outlier: 4.270A pdb=" N VAL A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A 568 " --> pdb=" O PRO A 564 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASN A 578 " --> pdb=" O GLY A 574 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ALA A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE A 582 " --> pdb=" O ASN A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 598 removed outlier: 3.552A pdb=" N VAL A 588 " --> pdb=" O GLY A 584 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 595 " --> pdb=" O TYR A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 639 through 645 removed outlier: 3.618A pdb=" N LEU A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 650 No H-bonds generated for 'chain 'A' and resid 647 through 650' Processing helix chain 'A' and resid 655 through 664 removed outlier: 3.701A pdb=" N LEU A 659 " --> pdb=" O TRP A 655 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 680 removed outlier: 3.806A pdb=" N LYS A 671 " --> pdb=" O PRO A 668 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 672 " --> pdb=" O TRP A 669 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A 674 " --> pdb=" O LYS A 671 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 675 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 676 " --> pdb=" O TYR A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 699 removed outlier: 3.525A pdb=" N LEU A 692 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 58 removed outlier: 3.665A pdb=" N VAL B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 77 removed outlier: 3.721A pdb=" N ARG B 75 " --> pdb=" O MET B 71 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B 76 " --> pdb=" O TRP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 98 removed outlier: 3.623A pdb=" N PHE B 88 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N PHE B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 94 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA B 97 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N PHE B 98 " --> pdb=" O LEU B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 removed outlier: 3.832A pdb=" N VAL B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 145 removed outlier: 3.789A pdb=" N SER B 141 " --> pdb=" O ALA B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 removed outlier: 3.566A pdb=" N LYS B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 177 removed outlier: 3.588A pdb=" N LEU B 165 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 176 " --> pdb=" O TRP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 198 removed outlier: 3.569A pdb=" N LEU B 190 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG B 191 " --> pdb=" O ARG B 188 " (cutoff:3.500A) Proline residue: B 192 - end of helix removed outlier: 3.815A pdb=" N GLN B 197 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN B 198 " --> pdb=" O LEU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 210 removed outlier: 3.644A pdb=" N ARG B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 217 through 237 removed outlier: 3.883A pdb=" N LEU B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET B 232 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 270 removed outlier: 3.673A pdb=" N VAL B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 282 No H-bonds generated for 'chain 'B' and resid 279 through 282' Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.559A pdb=" N ALA B 289 " --> pdb=" O ARG B 286 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 293 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL B 294 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE B 295 " --> pdb=" O PHE B 292 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B 296 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 297 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 298 " --> pdb=" O PHE B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 342 removed outlier: 3.520A pdb=" N LEU B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 308 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 334 " --> pdb=" O ARG B 330 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 368 removed outlier: 3.510A pdb=" N LEU B 363 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 366 " --> pdb=" O LEU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 384 removed outlier: 3.847A pdb=" N MET B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG B 384 " --> pdb=" O MET B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 404 removed outlier: 3.721A pdb=" N PHE B 400 " --> pdb=" O PHE B 396 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASN B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N GLU B 402 " --> pdb=" O LYS B 398 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LEU B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASP B 404 " --> pdb=" O PHE B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 429 removed outlier: 3.779A pdb=" N SER B 424 " --> pdb=" O PRO B 420 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA B 425 " --> pdb=" O PHE B 421 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 453 removed outlier: 3.847A pdb=" N ASN B 439 " --> pdb=" O ASP B 435 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 449 " --> pdb=" O ASN B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 491 removed outlier: 4.355A pdb=" N VAL B 475 " --> pdb=" O ILE B 471 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET B 484 " --> pdb=" O TYR B 480 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 496 No H-bonds generated for 'chain 'B' and resid 493 through 496' Processing helix chain 'B' and resid 500 through 522 removed outlier: 3.840A pdb=" N LEU B 508 " --> pdb=" O PHE B 504 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 510 " --> pdb=" O GLY B 506 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 561 removed outlier: 3.578A pdb=" N LEU B 547 " --> pdb=" O MET B 543 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN B 548 " --> pdb=" O THR B 544 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ARG B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE B 558 " --> pdb=" O ARG B 554 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ILE B 559 " --> pdb=" O PHE B 555 " (cutoff:3.500A) Proline residue: B 560 - end of helix Processing helix chain 'B' and resid 563 through 582 removed outlier: 4.270A pdb=" N VAL B 567 " --> pdb=" O LYS B 563 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL B 568 " --> pdb=" O PRO B 564 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL B 572 " --> pdb=" O VAL B 568 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 576 " --> pdb=" O VAL B 572 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLN B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASN B 578 " --> pdb=" O GLY B 574 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ALA B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE B 582 " --> pdb=" O ASN B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 598 removed outlier: 3.552A pdb=" N VAL B 588 " --> pdb=" O GLY B 584 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 595 " --> pdb=" O TYR B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 639 through 645 removed outlier: 3.618A pdb=" N LEU B 643 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 650 No H-bonds generated for 'chain 'B' and resid 647 through 650' Processing helix chain 'B' and resid 655 through 664 removed outlier: 3.702A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 680 removed outlier: 3.805A pdb=" N LYS B 671 " --> pdb=" O PRO B 668 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B 672 " --> pdb=" O TRP B 669 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 674 " --> pdb=" O LYS B 671 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 675 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 676 " --> pdb=" O TYR B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 699 removed outlier: 3.525A pdb=" N LEU B 692 " --> pdb=" O LEU B 688 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN B 696 " --> pdb=" O LEU B 692 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1134 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: 2.65 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1500 1.31 - 1.44: 2994 1.44 - 1.56: 5793 1.56 - 1.69: 9 1.69 - 1.81: 100 Bond restraints: 10396 Sorted by residual: bond pdb=" C SER B 419 " pdb=" N PRO B 420 " ideal model delta sigma weight residual 1.334 1.379 -0.046 2.34e-02 1.83e+03 3.79e+00 bond pdb=" C SER A 419 " pdb=" N PRO A 420 " ideal model delta sigma weight residual 1.334 1.379 -0.046 2.34e-02 1.83e+03 3.79e+00 bond pdb=" CA VAL A 459 " pdb=" CB VAL A 459 " ideal model delta sigma weight residual 1.540 1.562 -0.022 1.36e-02 5.41e+03 2.57e+00 bond pdb=" N VAL B 459 " pdb=" CA VAL B 459 " ideal model delta sigma weight residual 1.459 1.440 0.019 1.25e-02 6.40e+03 2.41e+00 bond pdb=" CA VAL B 459 " pdb=" CB VAL B 459 " ideal model delta sigma weight residual 1.540 1.561 -0.021 1.36e-02 5.41e+03 2.35e+00 ... (remaining 10391 not shown) Histogram of bond angle deviations from ideal: 92.02 - 100.45: 6 100.45 - 108.88: 573 108.88 - 117.31: 6563 117.31 - 125.74: 6804 125.74 - 134.17: 198 Bond angle restraints: 14144 Sorted by residual: angle pdb=" N SER B 177 " pdb=" CA SER B 177 " pdb=" C SER B 177 " ideal model delta sigma weight residual 111.28 119.33 -8.05 1.09e+00 8.42e-01 5.45e+01 angle pdb=" N SER A 177 " pdb=" CA SER A 177 " pdb=" C SER A 177 " ideal model delta sigma weight residual 111.28 119.29 -8.01 1.09e+00 8.42e-01 5.40e+01 angle pdb=" C1 EUJ B1000 " pdb=" C2 EUJ B1000 " pdb=" O2 EUJ B1000 " ideal model delta sigma weight residual 108.86 130.65 -21.79 3.00e+00 1.11e-01 5.27e+01 angle pdb=" C1 EUJ A1000 " pdb=" C2 EUJ A1000 " pdb=" O2 EUJ A1000 " ideal model delta sigma weight residual 108.86 130.61 -21.75 3.00e+00 1.11e-01 5.26e+01 angle pdb=" C3 EUJ A1000 " pdb=" C2 EUJ A1000 " pdb=" O2 EUJ A1000 " ideal model delta sigma weight residual 108.86 92.02 16.84 3.00e+00 1.11e-01 3.15e+01 ... (remaining 14139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 5335 17.00 - 33.99: 569 33.99 - 50.99: 116 50.99 - 67.98: 27 67.98 - 84.98: 10 Dihedral angle restraints: 6057 sinusoidal: 2389 harmonic: 3668 Sorted by residual: dihedral pdb=" CB CYS A 623 " pdb=" SG CYS A 623 " pdb=" SG CYS B 623 " pdb=" CB CYS B 623 " ideal model delta sinusoidal sigma weight residual -86.00 -26.95 -59.05 1 1.00e+01 1.00e-02 4.66e+01 dihedral pdb=" CA SER B 419 " pdb=" C SER B 419 " pdb=" N PRO B 420 " pdb=" CA PRO B 420 " ideal model delta harmonic sigma weight residual -180.00 -157.55 -22.45 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA SER A 419 " pdb=" C SER A 419 " pdb=" N PRO A 420 " pdb=" CA PRO A 420 " ideal model delta harmonic sigma weight residual -180.00 -157.57 -22.43 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 6054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.018: 1640 1.018 - 2.036: 0 2.036 - 3.053: 0 3.053 - 4.071: 0 4.071 - 5.089: 8 Chirality restraints: 1648 Sorted by residual: chirality pdb=" C5 EUJ B1000 " pdb=" C4 EUJ B1000 " pdb=" C6 EUJ B1000 " pdb=" O5 EUJ B1000 " both_signs ideal model delta sigma weight residual False 2.50 -2.58 5.09 2.00e-01 2.50e+01 6.47e+02 chirality pdb=" C5 EUJ A1000 " pdb=" C4 EUJ A1000 " pdb=" C6 EUJ A1000 " pdb=" O5 EUJ A1000 " both_signs ideal model delta sigma weight residual False 2.50 -2.58 5.09 2.00e-01 2.50e+01 6.47e+02 chirality pdb=" C6 EUJ B1000 " pdb=" C1 EUJ B1000 " pdb=" C5 EUJ B1000 " pdb=" O6 EUJ B1000 " both_signs ideal model delta sigma weight residual False 2.51 -2.48 4.99 2.00e-01 2.50e+01 6.23e+02 ... (remaining 1645 not shown) Planarity restraints: 1706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 191 " 0.049 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO B 192 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 192 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 192 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 191 " -0.049 5.00e-02 4.00e+02 7.35e-02 8.65e+00 pdb=" N PRO A 192 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 655 " 0.020 2.00e-02 2.50e+03 1.41e-02 4.94e+00 pdb=" CG TRP B 655 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 655 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 655 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 655 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 655 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 655 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 655 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 655 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 655 " 0.003 2.00e-02 2.50e+03 ... (remaining 1703 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1078 2.74 - 3.28: 9840 3.28 - 3.82: 15940 3.82 - 4.36: 18820 4.36 - 4.90: 31328 Nonbonded interactions: 77006 Sorted by model distance: nonbonded pdb=" O2 EUJ B1000 " pdb=" O3 EUJ B1000 " model vdw 2.200 2.432 nonbonded pdb=" O2 EUJ A1000 " pdb=" O3 EUJ A1000 " model vdw 2.200 2.432 nonbonded pdb=" O11 EUJ A1000 " pdb=" O2 EUJ A1000 " model vdw 2.200 2.440 nonbonded pdb=" O11 EUJ B1000 " pdb=" O2 EUJ B1000 " model vdw 2.200 2.440 nonbonded pdb=" O SER B 666 " pdb=" OG SER B 666 " model vdw 2.309 2.440 ... (remaining 77001 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 60 5.16 5 C 6724 2.51 5 N 1622 2.21 5 O 1728 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.450 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: 3.780 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 27.590 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 : 0.005 0.067 10396 Z= 0.349 Angle : 0.894 21.786 14144 Z= 0.466 Chirality : 0.347 5.089 1648 Planarity : 0.006 0.074 1706 Dihedral : 14.906 84.977 3668 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 0.54 % 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: -6.31 (0.14), residues: 1222 helix: -4.38 (0.07), residues: 860 sheet: None (None), residues: 0 loop : -2.95 (0.28), residues: 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 186 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 192 average time/residue: 0.1672 time to fit residues: 48.9405 Evaluate side-chains 118 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 1.273 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0948 time to fit residues: 2.0502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 40.0000 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN A 431 HIS A 502 ASN A 687 ASN ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN B 401 ASN B 431 HIS B 502 ASN B 687 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 10396 Z= 0.199 Angle : 0.638 8.106 14144 Z= 0.318 Chirality : 0.041 0.161 1648 Planarity : 0.004 0.037 1706 Dihedral : 7.350 88.954 1386 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 1.00 % 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: -3.64 (0.20), residues: 1222 helix: -2.26 (0.14), residues: 840 sheet: None (None), residues: 0 loop : -2.33 (0.30), residues: 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 1.201 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 150 average time/residue: 0.1525 time to fit residues: 36.3622 Evaluate side-chains 123 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0972 time to fit residues: 3.0079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN A 401 ASN ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 10396 Z= 0.216 Angle : 0.587 8.138 14144 Z= 0.291 Chirality : 0.041 0.198 1648 Planarity : 0.003 0.031 1706 Dihedral : 6.857 87.271 1386 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 1.72 % 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: -2.29 (0.22), residues: 1222 helix: -1.08 (0.16), residues: 842 sheet: None (None), residues: 0 loop : -2.26 (0.30), residues: 380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 1.281 Fit side-chains outliers start: 19 outliers final: 15 residues processed: 145 average time/residue: 0.1596 time to fit residues: 36.8140 Evaluate side-chains 132 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 1.164 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0903 time to fit residues: 4.1074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 107 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 10396 Z= 0.237 Angle : 0.614 10.754 14144 Z= 0.296 Chirality : 0.041 0.215 1648 Planarity : 0.003 0.029 1706 Dihedral : 6.728 86.736 1386 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 1.09 % 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: -1.53 (0.23), residues: 1222 helix: -0.50 (0.17), residues: 850 sheet: None (None), residues: 0 loop : -2.01 (0.33), residues: 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.222 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 135 average time/residue: 0.1472 time to fit residues: 32.2027 Evaluate side-chains 134 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0961 time to fit residues: 3.5515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 0.1980 chunk 102 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS B 151 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 10396 Z= 0.226 Angle : 0.592 10.167 14144 Z= 0.288 Chirality : 0.041 0.212 1648 Planarity : 0.003 0.029 1706 Dihedral : 6.623 86.391 1386 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 0.36 % 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: -1.12 (0.24), residues: 1222 helix: -0.11 (0.18), residues: 836 sheet: None (None), residues: 0 loop : -2.00 (0.31), residues: 386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 1.231 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 133 average time/residue: 0.1597 time to fit residues: 34.1034 Evaluate side-chains 122 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 1.250 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0888 time to fit residues: 1.9274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 687 ASN B 687 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.029 10396 Z= 0.294 Angle : 0.630 10.518 14144 Z= 0.309 Chirality : 0.043 0.213 1648 Planarity : 0.003 0.029 1706 Dihedral : 6.695 86.803 1386 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer Outliers : 1.00 % 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: -0.95 (0.24), residues: 1222 helix: 0.07 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -2.11 (0.31), residues: 380 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 1.163 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 125 average time/residue: 0.1565 time to fit residues: 31.4052 Evaluate side-chains 121 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0988 time to fit residues: 2.3501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 687 ASN B 548 ASN B 687 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 10396 Z= 0.159 Angle : 0.563 10.227 14144 Z= 0.273 Chirality : 0.040 0.209 1648 Planarity : 0.003 0.030 1706 Dihedral : 6.441 85.210 1386 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 0.54 % 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: -0.69 (0.24), residues: 1222 helix: 0.28 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -1.99 (0.31), residues: 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 1.134 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 143 average time/residue: 0.1879 time to fit residues: 40.2092 Evaluate side-chains 127 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 1.278 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0928 time to fit residues: 2.1981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 0.1980 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 0.0170 chunk 75 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 0.0970 chunk 108 optimal weight: 10.0000 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 10396 Z= 0.144 Angle : 0.571 10.057 14144 Z= 0.277 Chirality : 0.039 0.205 1648 Planarity : 0.003 0.028 1706 Dihedral : 6.277 85.268 1386 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.45 % 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: -0.57 (0.24), residues: 1222 helix: 0.33 (0.18), residues: 848 sheet: None (None), residues: 0 loop : -1.91 (0.32), residues: 374 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 134 time to evaluate : 1.218 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 137 average time/residue: 0.1558 time to fit residues: 33.5415 Evaluate side-chains 124 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0855 time to fit residues: 1.9056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 10396 Z= 0.231 Angle : 0.614 9.935 14144 Z= 0.297 Chirality : 0.041 0.202 1648 Planarity : 0.003 0.028 1706 Dihedral : 6.426 87.168 1386 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 0.36 % 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: -0.45 (0.24), residues: 1222 helix: 0.41 (0.18), residues: 848 sheet: None (None), residues: 0 loop : -1.84 (0.32), residues: 374 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 1.352 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 131 average time/residue: 0.1595 time to fit residues: 33.1019 Evaluate side-chains 127 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 55 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 10396 Z= 0.186 Angle : 0.621 10.078 14144 Z= 0.297 Chirality : 0.041 0.199 1648 Planarity : 0.003 0.028 1706 Dihedral : 6.377 86.853 1386 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 0.09 % 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: -0.45 (0.24), residues: 1222 helix: 0.40 (0.18), residues: 850 sheet: None (None), residues: 0 loop : -1.83 (0.32), residues: 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.279 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.1613 time to fit residues: 33.6118 Evaluate side-chains 124 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 98 optimal weight: 7.9990 chunk 41 optimal weight: 0.1980 chunk 101 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.114677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.086431 restraints weight = 22546.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.087810 restraints weight = 13077.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.088189 restraints weight = 9855.904| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 10396 Z= 0.152 Angle : 0.606 9.847 14144 Z= 0.288 Chirality : 0.040 0.194 1648 Planarity : 0.003 0.028 1706 Dihedral : 6.268 86.619 1386 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 0.09 % 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: 1222 helix: 0.42 (0.18), residues: 858 sheet: None (None), residues: 0 loop : -1.86 (0.31), residues: 364 =============================================================================== Job complete usr+sys time: 1629.86 seconds wall clock time: 30 minutes 44.88 seconds (1844.88 seconds total)