Starting phenix.real_space_refine on Sat Dec 9 02:27:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1o_8959/12_2023/6e1o_8959_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1o_8959/12_2023/6e1o_8959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1o_8959/12_2023/6e1o_8959.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1o_8959/12_2023/6e1o_8959.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1o_8959/12_2023/6e1o_8959_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e1o_8959/12_2023/6e1o_8959_updated.pdb" } resolution = 3.59 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= 0.007 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 38 5.16 5 C 6482 2.51 5 N 1592 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B ARG 276": "NH1" <-> "NH2" Residue "B TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B ARG 425": "NH1" <-> "NH2" Residue "B ARG 427": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B ARG 647": "NH1" <-> "NH2" Residue "B ARG 651": "NH1" <-> "NH2" Residue "B ARG 708": "NH1" <-> "NH2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 427": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A ARG 647": "NH1" <-> "NH2" Residue "A ARG 651": "NH1" <-> "NH2" Residue "A ARG 708": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9784 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4808 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 27, 'TRANS': 563} Chain breaks: 8 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 57 Chain: "A" Number of atoms: 4808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4808 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 27, 'TRANS': 563} Chain breaks: 8 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 84 Unusual residues: {' CA': 2, '8K6': 1, 'D10': 1, 'D12': 4, 'HEX': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 84 Unusual residues: {' CA': 2, '8K6': 1, 'D10': 1, 'D12': 4, 'HEX': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Time building chain proxies: 5.51, per 1000 atoms: 0.56 Number of scatterers: 9784 At special positions: 0 Unit cell: (132.628, 75.6309, 103.033, 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 38 16.00 O 1668 8.00 N 1592 7.00 C 6482 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: 3.46 Conformation dependent library (CDL) restraints added in 1.6 seconds 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2284 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 2 sheets defined 61.5% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 removed outlier: 4.252A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 85 removed outlier: 3.571A pdb=" N ARG B 82 " --> pdb=" O GLN B 78 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.529A pdb=" N ILE B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 152 removed outlier: 3.557A pdb=" N GLN B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 171 removed outlier: 3.573A pdb=" N ARG B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 203 removed outlier: 4.082A pdb=" N MET B 192 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N PHE B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Proline residue: B 194 - end of helix Processing helix chain 'B' and resid 212 through 237 removed outlier: 3.712A pdb=" N CYS B 217 " --> pdb=" O THR B 213 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 221 " --> pdb=" O CYS B 217 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE B 224 " --> pdb=" O CYS B 220 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N CYS B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 274 through 309 removed outlier: 3.774A pdb=" N TYR B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU B 282 " --> pdb=" O TYR B 278 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLN B 283 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL B 284 " --> pdb=" O GLN B 280 " (cutoff:3.500A) Proline residue: B 285 - end of helix removed outlier: 3.710A pdb=" N ALA B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU B 305 " --> pdb=" O CYS B 301 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 347 removed outlier: 3.524A pdb=" N ILE B 323 " --> pdb=" O LEU B 320 " (cutoff:3.500A) Proline residue: B 324 - end of helix removed outlier: 3.665A pdb=" N VAL B 328 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 330 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU B 331 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE B 332 " --> pdb=" O SER B 329 " (cutoff:3.500A) Proline residue: B 333 - end of helix removed outlier: 4.318A pdb=" N SER B 336 " --> pdb=" O PRO B 333 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 340 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 342 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 344 " --> pdb=" O THR B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 372 removed outlier: 3.709A pdb=" N LYS B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 372 " --> pdb=" O VAL B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 382 removed outlier: 4.645A pdb=" N THR B 381 " --> pdb=" O PRO B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 393 No H-bonds generated for 'chain 'B' and resid 390 through 393' Processing helix chain 'B' and resid 425 through 434 removed outlier: 3.671A pdb=" N PHE B 433 " --> pdb=" O GLN B 429 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 445 removed outlier: 3.635A pdb=" N PHE B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 458 removed outlier: 3.684A pdb=" N ARG B 457 " --> pdb=" O GLN B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 501 Processing helix chain 'B' and resid 508 through 524 removed outlier: 4.390A pdb=" N GLU B 514 " --> pdb=" O ASP B 510 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN B 518 " --> pdb=" O GLU B 514 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY B 520 " --> pdb=" O CYS B 516 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 522 " --> pdb=" O GLN B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 553 Proline residue: B 533 - end of helix removed outlier: 4.213A pdb=" N ILE B 538 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN B 540 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP B 541 " --> pdb=" O ILE B 538 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU B 543 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 544 " --> pdb=" O TRP B 541 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER B 546 " --> pdb=" O GLU B 543 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASP B 547 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B 550 " --> pdb=" O ASP B 547 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B 551 " --> pdb=" O PHE B 548 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL B 553 " --> pdb=" O LYS B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 590 removed outlier: 3.661A pdb=" N GLY B 574 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 575 " --> pdb=" O ASP B 571 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR B 589 " --> pdb=" O SER B 585 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 634 removed outlier: 3.581A pdb=" N ILE B 623 " --> pdb=" O HIS B 619 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 627 " --> pdb=" O ILE B 623 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 655 removed outlier: 3.845A pdb=" N GLU B 643 " --> pdb=" O ASN B 639 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 644 " --> pdb=" O THR B 640 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU B 646 " --> pdb=" O ARG B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 721 removed outlier: 3.941A pdb=" N GLY B 719 " --> pdb=" O SER B 715 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 721 " --> pdb=" O GLU B 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 43 removed outlier: 4.253A pdb=" N ILE A 33 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 85 removed outlier: 3.572A pdb=" N ARG A 82 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.529A pdb=" N ILE A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 152 removed outlier: 3.558A pdb=" N GLN A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 171 removed outlier: 3.573A pdb=" N ARG A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 203 removed outlier: 4.082A pdb=" N MET A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N PHE A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 212 through 237 removed outlier: 3.711A pdb=" N CYS A 217 " --> pdb=" O THR A 213 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 221 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 224 " --> pdb=" O CYS A 220 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N CYS A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 274 through 309 removed outlier: 3.775A pdb=" N TYR A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLN A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix removed outlier: 3.708A pdb=" N ALA A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 305 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 347 removed outlier: 3.524A pdb=" N ILE A 323 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Proline residue: A 324 - end of helix removed outlier: 3.665A pdb=" N VAL A 328 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 330 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A 331 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE A 332 " --> pdb=" O SER A 329 " (cutoff:3.500A) Proline residue: A 333 - end of helix removed outlier: 4.318A pdb=" N SER A 336 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 340 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 342 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 344 " --> pdb=" O THR A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 372 removed outlier: 3.709A pdb=" N LYS A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 372 " --> pdb=" O VAL A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 382 removed outlier: 4.645A pdb=" N THR A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 393 No H-bonds generated for 'chain 'A' and resid 390 through 393' Processing helix chain 'A' and resid 425 through 434 removed outlier: 3.670A pdb=" N PHE A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 445 removed outlier: 3.634A pdb=" N PHE A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 458 removed outlier: 3.684A pdb=" N ARG A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 501 Processing helix chain 'A' and resid 508 through 524 removed outlier: 4.390A pdb=" N GLU A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 520 " --> pdb=" O CYS A 516 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 521 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 522 " --> pdb=" O GLN A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 553 Proline residue: A 533 - end of helix removed outlier: 4.212A pdb=" N ILE A 538 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 540 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP A 541 " --> pdb=" O ILE A 538 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU A 543 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 544 " --> pdb=" O TRP A 541 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A 546 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASP A 547 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 550 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 551 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL A 553 " --> pdb=" O LYS A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 591 removed outlier: 3.660A pdb=" N GLY A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 575 " --> pdb=" O ASP A 571 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 634 removed outlier: 3.581A pdb=" N ILE A 623 " --> pdb=" O HIS A 619 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 627 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 655 removed outlier: 3.845A pdb=" N GLU A 643 " --> pdb=" O ASN A 639 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 644 " --> pdb=" O THR A 640 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU A 646 " --> pdb=" O ARG A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 721 removed outlier: 3.941A pdb=" N GLY A 719 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 721 " --> pdb=" O GLU A 717 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 18 through 21 removed outlier: 3.681A pdb=" N TYR B 18 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 18 through 21 removed outlier: 3.682A pdb=" N TYR A 18 " --> pdb=" O VAL A 64 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 993 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: 2.26 Time building geometry restraints manager: 3.78 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: 2936 1.34 - 1.46: 2238 1.46 - 1.57: 4786 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10016 Sorted by residual: bond pdb=" N VAL B 588 " pdb=" CA VAL B 588 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.21e-02 6.83e+03 7.42e+00 bond pdb=" N LEU B 524 " pdb=" CA LEU B 524 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.16e+00 bond pdb=" N LEU A 524 " pdb=" CA LEU A 524 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.05e+00 bond pdb=" N VAL A 588 " pdb=" CA VAL A 588 " ideal model delta sigma weight residual 1.460 1.491 -0.032 1.21e-02 6.83e+03 6.95e+00 bond pdb=" N MET B 590 " pdb=" CA MET B 590 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.48e+00 ... (remaining 10011 not shown) Histogram of bond angle deviations from ideal: 98.00 - 105.39: 210 105.39 - 112.77: 5154 112.77 - 120.16: 4292 120.16 - 127.54: 3768 127.54 - 134.93: 114 Bond angle restraints: 13538 Sorted by residual: angle pdb=" C ILE B 447 " pdb=" N VAL B 448 " pdb=" CA VAL B 448 " ideal model delta sigma weight residual 120.24 123.31 -3.07 6.30e-01 2.52e+00 2.37e+01 angle pdb=" C ILE A 447 " pdb=" N VAL A 448 " pdb=" CA VAL A 448 " ideal model delta sigma weight residual 120.24 123.27 -3.03 6.30e-01 2.52e+00 2.32e+01 angle pdb=" N VAL B 52 " pdb=" CA VAL B 52 " pdb=" C VAL B 52 " ideal model delta sigma weight residual 109.34 101.04 8.30 2.08e+00 2.31e-01 1.59e+01 angle pdb=" N VAL A 52 " pdb=" CA VAL A 52 " pdb=" C VAL A 52 " ideal model delta sigma weight residual 109.34 101.08 8.26 2.08e+00 2.31e-01 1.58e+01 angle pdb=" CA VAL A 393 " pdb=" C VAL A 393 " pdb=" N PRO A 394 " ideal model delta sigma weight residual 118.88 124.94 -6.06 1.54e+00 4.22e-01 1.55e+01 ... (remaining 13533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 5367 14.33 - 28.66: 411 28.66 - 42.99: 129 42.99 - 57.32: 13 57.32 - 71.65: 6 Dihedral angle restraints: 5926 sinusoidal: 2426 harmonic: 3500 Sorted by residual: dihedral pdb=" CA THR A 127 " pdb=" C THR A 127 " pdb=" N PRO A 128 " pdb=" CA PRO A 128 " ideal model delta harmonic sigma weight residual 180.00 151.24 28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA THR B 127 " pdb=" C THR B 127 " pdb=" N PRO B 128 " pdb=" CA PRO B 128 " ideal model delta harmonic sigma weight residual 180.00 151.26 28.74 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ARG B 129 " pdb=" C ARG B 129 " pdb=" N HIS B 130 " pdb=" CA HIS B 130 " ideal model delta harmonic sigma weight residual -180.00 -153.58 -26.42 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 5923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 963 0.053 - 0.107: 423 0.107 - 0.160: 97 0.160 - 0.213: 21 0.213 - 0.266: 8 Chirality restraints: 1512 Sorted by residual: chirality pdb=" CB VAL B 117 " pdb=" CA VAL B 117 " pdb=" CG1 VAL B 117 " pdb=" CG2 VAL B 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB VAL A 117 " pdb=" CA VAL A 117 " pdb=" CG1 VAL A 117 " pdb=" CG2 VAL A 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA THR B 29 " pdb=" N THR B 29 " pdb=" C THR B 29 " pdb=" CB THR B 29 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1509 not shown) Planarity restraints: 1662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 578 " -0.019 2.00e-02 2.50e+03 1.96e-02 9.56e+00 pdb=" CG TRP A 578 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 578 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 578 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 578 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 578 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 578 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 578 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 578 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 578 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 578 " 0.019 2.00e-02 2.50e+03 1.93e-02 9.36e+00 pdb=" CG TRP B 578 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 578 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 578 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 578 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 578 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 578 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 578 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 578 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 578 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 127 " 0.050 5.00e-02 4.00e+02 7.46e-02 8.92e+00 pdb=" N PRO A 128 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 128 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 128 " 0.041 5.00e-02 4.00e+02 ... (remaining 1659 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1674 2.75 - 3.29: 9291 3.29 - 3.83: 15284 3.83 - 4.36: 18262 4.36 - 4.90: 29991 Nonbonded interactions: 74502 Sorted by model distance: nonbonded pdb=" OH TYR B 589 " pdb=" O ILE B 605 " model vdw 2.219 2.440 nonbonded pdb=" OH TYR A 589 " pdb=" O ILE A 605 " model vdw 2.238 2.440 nonbonded pdb=" OH TYR A 506 " pdb=" OD2 ASP A 511 " model vdw 2.302 2.440 nonbonded pdb=" OH TYR B 506 " pdb=" OD2 ASP B 511 " model vdw 2.302 2.440 nonbonded pdb=" O SER B 374 " pdb=" OH TYR B 521 " model vdw 2.314 2.440 ... (remaining 74497 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.100 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 27.360 Find NCS groups from input model: 0.500 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 : 0.008 0.079 10016 Z= 0.529 Angle : 1.210 9.928 13538 Z= 0.609 Chirality : 0.063 0.266 1512 Planarity : 0.008 0.075 1662 Dihedral : 11.661 71.647 3642 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.78 % Allowed : 5.38 % Favored : 93.84 % 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: -5.85 (0.17), residues: 1146 helix: -4.19 (0.09), residues: 712 sheet: -3.24 (1.00), residues: 22 loop : -2.92 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP A 578 HIS 0.007 0.003 HIS A 15 PHE 0.030 0.003 PHE B 208 TYR 0.036 0.003 TYR A 385 ARG 0.006 0.001 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 202 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 210 average time/residue: 0.2736 time to fit residues: 76.3473 Evaluate side-chains 73 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1078 time to fit residues: 1.6600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN B 150 GLN B 230 GLN B 280 GLN A 148 ASN A 150 GLN A 230 GLN A 280 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10016 Z= 0.177 Angle : 0.673 10.235 13538 Z= 0.342 Chirality : 0.041 0.152 1512 Planarity : 0.006 0.057 1662 Dihedral : 8.100 59.307 1418 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.03 % Allowed : 11.55 % Favored : 85.42 % 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: -4.31 (0.20), residues: 1146 helix: -2.56 (0.14), residues: 746 sheet: -3.14 (0.90), residues: 22 loop : -3.14 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 578 HIS 0.003 0.001 HIS A 619 PHE 0.016 0.002 PHE A 433 TYR 0.014 0.001 TYR A 187 ARG 0.005 0.001 ARG B 492 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 113 time to evaluate : 1.230 Fit side-chains outliers start: 31 outliers final: 11 residues processed: 141 average time/residue: 0.1675 time to fit residues: 36.5927 Evaluate side-chains 93 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1025 time to fit residues: 3.4345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 89 optimal weight: 0.0970 chunk 72 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 HIS ** B 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN A 247 HIS ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10016 Z= 0.218 Angle : 0.618 8.996 13538 Z= 0.314 Chirality : 0.041 0.141 1512 Planarity : 0.005 0.043 1662 Dihedral : 7.250 54.323 1418 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.33 % Allowed : 14.19 % Favored : 82.49 % 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: -3.21 (0.22), residues: 1146 helix: -1.55 (0.17), residues: 748 sheet: -2.95 (0.95), residues: 22 loop : -3.05 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 155 HIS 0.003 0.001 HIS B 15 PHE 0.013 0.001 PHE B 615 TYR 0.020 0.001 TYR A 187 ARG 0.003 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 85 time to evaluate : 1.087 Fit side-chains outliers start: 34 outliers final: 20 residues processed: 109 average time/residue: 0.1690 time to fit residues: 28.9675 Evaluate side-chains 96 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 1.085 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1006 time to fit residues: 5.0499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS ** B 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS A 185 GLN ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10016 Z= 0.211 Angle : 0.601 9.414 13538 Z= 0.301 Chirality : 0.041 0.141 1512 Planarity : 0.004 0.045 1662 Dihedral : 6.902 55.759 1418 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.33 % Allowed : 14.19 % Favored : 82.49 % 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: -2.39 (0.23), residues: 1146 helix: -0.86 (0.18), residues: 746 sheet: -2.97 (1.08), residues: 22 loop : -2.84 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 578 HIS 0.003 0.001 HIS A 15 PHE 0.014 0.001 PHE B 615 TYR 0.022 0.001 TYR B 187 ARG 0.003 0.000 ARG B 492 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 84 time to evaluate : 1.039 Fit side-chains outliers start: 34 outliers final: 12 residues processed: 112 average time/residue: 0.1713 time to fit residues: 30.1204 Evaluate side-chains 87 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 1.162 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1055 time to fit residues: 3.7783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 6.9990 chunk 64 optimal weight: 0.0770 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 10016 Z= 0.354 Angle : 0.663 9.416 13538 Z= 0.337 Chirality : 0.044 0.145 1512 Planarity : 0.005 0.051 1662 Dihedral : 7.317 55.150 1418 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.05 % Allowed : 16.44 % Favored : 81.51 % 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: -2.11 (0.24), residues: 1146 helix: -0.61 (0.19), residues: 744 sheet: -3.38 (1.09), residues: 22 loop : -2.76 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 578 HIS 0.005 0.001 HIS A 15 PHE 0.016 0.002 PHE B 615 TYR 0.024 0.002 TYR B 187 ARG 0.003 0.001 ARG B 625 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 1.153 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 87 average time/residue: 0.1748 time to fit residues: 23.6918 Evaluate side-chains 76 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1115 time to fit residues: 3.4780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10016 Z= 0.301 Angle : 0.634 10.062 13538 Z= 0.322 Chirality : 0.043 0.143 1512 Planarity : 0.005 0.052 1662 Dihedral : 7.272 56.808 1418 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.76 % Allowed : 16.83 % Favored : 81.41 % 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: -1.84 (0.25), residues: 1146 helix: -0.36 (0.19), residues: 748 sheet: -3.50 (1.09), residues: 22 loop : -2.75 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 155 HIS 0.004 0.001 HIS B 15 PHE 0.015 0.002 PHE B 615 TYR 0.021 0.001 TYR B 187 ARG 0.003 0.000 ARG B 625 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 1.134 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 83 average time/residue: 0.1788 time to fit residues: 23.2161 Evaluate side-chains 74 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0953 time to fit residues: 3.1511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 10016 Z= 0.422 Angle : 0.705 9.870 13538 Z= 0.360 Chirality : 0.046 0.207 1512 Planarity : 0.005 0.061 1662 Dihedral : 7.887 59.473 1418 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.37 % Allowed : 17.32 % 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: -1.89 (0.24), residues: 1146 helix: -0.46 (0.19), residues: 756 sheet: -3.69 (1.08), residues: 22 loop : -2.66 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 155 HIS 0.006 0.002 HIS A 15 PHE 0.017 0.002 PHE B 615 TYR 0.025 0.002 TYR B 187 ARG 0.004 0.001 ARG B 625 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 1.147 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 74 average time/residue: 0.1941 time to fit residues: 22.6137 Evaluate side-chains 71 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 1.179 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1108 time to fit residues: 3.5172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 67 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 72 optimal weight: 0.0050 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 518 GLN ** B 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN A 518 GLN ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10016 Z= 0.142 Angle : 0.575 10.634 13538 Z= 0.286 Chirality : 0.039 0.140 1512 Planarity : 0.004 0.057 1662 Dihedral : 6.880 58.893 1418 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.88 % Allowed : 17.32 % Favored : 81.80 % 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: -1.37 (0.25), residues: 1146 helix: -0.05 (0.19), residues: 760 sheet: -3.48 (1.08), residues: 22 loop : -2.49 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 155 HIS 0.003 0.001 HIS B 14 PHE 0.016 0.001 PHE A 615 TYR 0.011 0.001 TYR A 187 ARG 0.004 0.000 ARG B 492 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 1.178 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 92 average time/residue: 0.1754 time to fit residues: 25.4435 Evaluate side-chains 74 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1134 time to fit residues: 2.6121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN A 518 GLN ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10016 Z= 0.277 Angle : 0.623 8.029 13538 Z= 0.315 Chirality : 0.042 0.140 1512 Planarity : 0.004 0.055 1662 Dihedral : 7.028 58.755 1418 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.78 % Allowed : 18.40 % Favored : 80.82 % 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: -1.28 (0.25), residues: 1146 helix: -0.01 (0.19), residues: 758 sheet: -3.41 (1.12), residues: 22 loop : -2.38 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 155 HIS 0.004 0.001 HIS A 15 PHE 0.016 0.002 PHE A 615 TYR 0.017 0.001 TYR B 187 ARG 0.002 0.000 ARG B 625 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 1.148 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 74 average time/residue: 0.1846 time to fit residues: 21.5835 Evaluate side-chains 73 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 1.142 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1130 time to fit residues: 2.5855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10016 Z= 0.194 Angle : 0.596 7.762 13538 Z= 0.299 Chirality : 0.040 0.138 1512 Planarity : 0.004 0.056 1662 Dihedral : 6.777 58.756 1418 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.78 % Allowed : 18.00 % Favored : 81.21 % 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: -1.14 (0.25), residues: 1146 helix: 0.14 (0.20), residues: 760 sheet: -3.37 (1.12), residues: 22 loop : -2.45 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 155 HIS 0.003 0.001 HIS B 15 PHE 0.015 0.001 PHE A 615 TYR 0.015 0.001 TYR B 187 ARG 0.003 0.000 ARG B 492 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 1.092 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 78 average time/residue: 0.1835 time to fit residues: 22.5743 Evaluate side-chains 74 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0943 time to fit residues: 2.0538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.094547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.079869 restraints weight = 22919.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.081930 restraints weight = 12127.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.083256 restraints weight = 8008.001| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10016 Z= 0.198 Angle : 0.591 7.767 13538 Z= 0.295 Chirality : 0.040 0.137 1512 Planarity : 0.004 0.056 1662 Dihedral : 6.608 58.326 1418 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.29 % Allowed : 18.59 % Favored : 81.12 % 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: -0.94 (0.26), residues: 1146 helix: 0.29 (0.20), residues: 766 sheet: -3.38 (1.11), residues: 22 loop : -2.40 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 155 HIS 0.002 0.001 HIS B 15 PHE 0.015 0.001 PHE A 615 TYR 0.012 0.001 TYR A 187 ARG 0.003 0.000 ARG B 492 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1727.92 seconds wall clock time: 32 minutes 26.97 seconds (1946.97 seconds total)